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SORTIE-ND User Manual Version 7.01 Beta

1. o Model menu o Tools menu o Help menu e Math in SORTIE ND e References e GPL License SORTIE ND License Software Copyright 2001 2005 Charles D Canham Software Author Lora E Murphy Institute of Ecosystem Studies Box AB Millbrook NY 12545 Software license This program is free software you can redistribute it and or modify it under the terms of the GNU General Public License as published by the Free Software Foundation either version 2 of the License or at your option any later version This program is distributed in the hope that it will be useful but WITHOUT ANY WARRANTY without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE See the GNU General Public License for more details Data license You may use the SORTIE ND software for any purpose including the creation of data for publication in a scientific book or journal One of the primary goals of scientific experiments is replicability of results Therefore if you have modified the SORTIE ND software you may not publish data from it using the names SORTIE or SORTIE ND unless you do one of the following 1 send a copy of the source code of your changes back to the SORTIE ND team at the Institute of Ecosystem Studies for inclusion in the standard version or 2 publish enough detail about your changes so that they could be replicated by a reasonably proficient programmer This product includes software developed by t
2. Output options Use this option to set up output for a run By default no output is saved This controls both short output files and detailed output files For more details on this option see the Output setup window topic Parameters window This window is reached using the menu option Edit gt Parameters from the main SORTIE window It allows you to edit the parameter values for your run Choose which parameters to display This is a small window that appears before the main window to allow you to choose what you want to see displayed There may not be parameters for all choices that you see on the list Choose any subset of parameters to display or choose All to see everything Editing values The main parameter display window shows you your chosen parameter groups Only those parameters that are applicable to the behaviors that are currently active in the run are shown To edit a value double click its cell You can copy and paste back and forth from Excel and within the parameter window itself You can use the menu commands on the parameter window Edit gt Copy and Edit gt Paste or the keyboard shortcuts Ctrl C for copy and Ctrl V for paste Saving the values to a file for review You can save the parameter window you are currently viewing as a tab delimited text file for your own reference Choose File gt Save window as file You can then open the file you have saved in any spreadsheet or text editor program The
3. How to apply it This behavior can be applied to seedlings saplings and adults of any species Any tree species type combination to which it is applied must also have a light behavior and a diameter growth behavior applied Relative growth behaviors Several behaviors apply a relative growth version of the Michaelis Menton function Parameters for these behaviors Parameter name Adult Constant Area Growth in sq cm yr Adult Constant Radial Growth in mm yr Asymptotic Diameter Growth A Asymptotic Height Growth A Slope of Growth Response S Relative Michaelis Menton Growth Diameter Exponent Description The constant amount of basal area by which to increase a tree s basal area Applies to basal area increment limited behaviors The constant value by which to increase a tree s radius at breast height Applies to radial increment limited growth behaviors Asymptote of the Michaelis Menton growth function at high light function term A below for diameter growth Asymptote of the Michaelis Menton growth function at high light function term A for height growth Slope of the Michaelis Menton growth function at zero light function term S below The exponent to be used with diameter when calculating relative growth Relative growth is calculated with the equation Axrvrrs AEGI AY rarr 4y a t OLL where e Yis the amount of annual relative growth e A is the Asymptotic Diameter Growth
4. This is the same as the first harvest type except the amount to harvest is different This harvest removes a set proportion of the plot s basal area Set this proportion between 0 and 1 in the Competition Harvest Amount to Harvest parameter e Fixed interval cutting plots back to a basal area threshold Harvests occur at a fixed interval set in the Competition Harvest Fixed Interval Harvest Interval yr parameter The first timestep will have a harvest Harvests remove trees until the plot reaches a specific amount of basal area set in the Competition Harvest Amount to Harvest parameter Competition Harvest uses these criteria to determine when and how much to cut Harvests occur over the the entire plot area During a harvest Competition Harvest calculates how much basal area it needs to cut It can select trees without regard to species or it can remove trees in a set ratio Species ratio is set in the Competition Harvest Amount of Harvest Per Species 0 1 parameter If all values are set to 1 this means that species identity is ignored when selecting individuals for harvesting Otherwise the species are cut in the proportions entered The values should add up to one For example if Species 1 is set to 0 25 and Species 2 is 0 75 then Competition Harvest will try to make 25 of the basal area removed come from Species individuals and 75 come from Species 2 Of course there are trade offs between removing the most competitiv
5. assuming the tree is below the maximum DBH at which to apply self thinning After evaluating this function for a tree it uses a random number to determine whether the tree dies How to apply it This behavior can be applied to seedlings saplings and adults of any species Senescence Senescence mortality provides for an uptick in mortality rates It is meant to slightly increase the death rate among large adult trees Trees killed by this behavior will have a mortality reason code of natural Parameters for this behavior Parameter name Description Senescence Ff i ls th 4 Morality Alpha Controls the senescence mortality rate Senescence 1s th te Mortality Bela Controls the senescence mortality rate DBH at Onset of j DBH at which senescence takes effect Senescence in cm DBH of Maximum Senescence The DBH at which maximum mortality occurs Trees with a DBH greater Mortality Rate as an than this value experience no further increase in the mortality rate integer in cm How it works All trees to which senescence is applied are evaluated for senescence mortality In practice trees below the onset of senescence DBH very rarely die The probability of death rises with DBH until the DBH of maximum senescence rate is reached at which point it levels off To assess whether a tree will die due to senescence the following function is evaluated a DBH DEH m a a DBH DBH l e where
6. Probability of a snag that did not fall remaining in decay class 5 This value is always 1 Maximum height at which snags break The actual height is a random draw between this value and the minimum Minimum height at which snags break The actual height is a random draw between this value and the maximum Trees that died in the current timestep have a certain probability of falling before the end of the current timestep Note that trees that die in a mortality episode do NOT count as trees that died in the current timestep but as existing snags The behavior represents the probability of falling before the end of the timestep as Sofa JX Pr falh __ f x Lee Sx a Psp DBH 6 BA 1H d DBH H where e Pr fall is the probability of the tree falling e ais the Snag Decay Class Dynamics Tree Fall Alpha parameter e spp is the Snag Decay Class Dynamics Tree Fall Beta parameter for the tree s species e DBH is the DBH in cm e ois the Snag Decay Class Dynamics Tree Fall Delta parameter e is the Snag Decay Class Dynamics Tree Fall Theta parameter e BA is the basal area m2 ha of live trees in the current tree s cell of the Snag Decay Class Dynamics Basal Area grid e 1is the Snag Decay Class Dynamics Tree Fall Iota parameter e His whether 1 or not 0 a harvest occurred this timestep e Ais the Snag Decay Class Dynamics Tree Fall Lambda parameter For snags that were created in a previous timestep
7. that you have full access to data members Open Edit gt Harvest Interface and complete the setup This adds the harvest interface behavior to your run To remove it use the Model flow window Insect Infestation This behavior simulates an insect outbreak It chooses and marks affected trees allowing other behaviors to make use of this information The number of affected trees is a function of time since infestation began The infestation has no spatial pattern This behavior only chooses trees for infestation It does not kill them or alter their dynamics in any way Other behaviors may take advantage of the infestation status information of trees Parameters for this behavior Parameter name Description Insect Infestation i i The timestep that an insect infestation begins First Timestep P gt Insect Infestation E The rate of infestation on the first timestep of the outbreak Initial Rate Insect Infestation The maximum rate of infestation Max Rate Insect Infestation Min DBH The minimum DBH of trees that can become infested Insect Infestation XO The time at which 0 5 of the maximum infestation rate occurs Insect Infestation Xb Parameter controlling the steepness of the rise of the infestation rate How it works The proportion of trees of a particular species infested as a function of time is as follows Max I 14 D P i where e P is the proportion of the eligible tree populati
8. 52 How it works The initial density of the predator population in numbers per m This will be used the first time this behavior is run Whether this density is used for subsequent behavior mini model runs depends on the value of the Keep Predator Densities Between Timesteps parameter During the period that germination occurs this is the fraction of the seed pool that is removed due to seed germination Expressed as a value between 0 and 1 The filename where the mini model will store its intermediate results for later analysis if desired This value is not required The week during the behavior mini model run that germination begins to occur If you do not want germination to occur set this value greater than or equal to the Weeks to run seed predation model 1 52 parameter This value must be between 0 and 52 The week that the second season begins if desired The number of weeks timesteps to run the behavior s mini model This number must be between 1 and 52 This behavior is used together with the Neighborhood seed predation behavior linked behavior The two behaviors work together to model seed predation This behavior performs the functional response model in almost exactly the same way as the Functional response seed predation behavior However instead of removing the eaten seeds it calculates a whole plot offtake rate for the group of species to which it has been applied This rate is always for the
9. Each timestep Detailed Substrate looks for harvest events and new tree inputs It finds harvest events by looking in the Harvest grid Harvest events add new scarified soil tip up and log substrate The behavior finds fallen and broken trees by looking for the flags set by mortality and snag dynamics behaviors Each fallen and broken tree or snag rolls the dice with a random number to determine the log decay class it will enter as substrate Fallen adult trees and snags also use a random number to determine whether they expose tip up mound substrate All the new substrate created by harvest and tree inputs is then totaled up When there is new substrate in a grid cell Detailed Substrate reduces the other substrate amounts in the cell to make way for the amount of new substrate All existing substrates are decayed each timestep as they age After they reach their maximum lifespan which is set by parameters they are deleted The final proportions of scarified soil tip up and logs are found by adding up the values representing each substrate age The final proportion of the moss litter pool is whatever grid cell area is left over The pool is further split into moss and litter by using fixed proportions of each in the pool as specified by the Proportion of Forest Floor Litter Moss Pool that is Moss parameter How to apply it Apply Detailed Substrate to all trees which can create substrate by becoming fallen logs This generally means that
10. If a simulation within a batch fails for some reason SORTIE ND will attempt to skip that simulation and complete the others specified in the file The parameter file What is a parameter file A parameter file is a document containing all the data that the model needs to perform a simulation It is in the XML data format and is written in plain text Parameter files have a xml extension Contents of a parameter file At the least the parameter file must specify the length of the run describe the plot define the tree species and their attributes list the behaviors in the order in which they will run and provide whatever parameters the behaviors need In addition parameter files can define initial conditions for trees and grids using parameters or maps from detailed output files Editing a parameter file The SORTIE ND model interface gives you all the tools you need to create and modify your parameter files Since they are in plain text you can look at them in other programs but modifying them directly is not recommended For detailed instructions on creating a new parameter file from scratch see the Creating a parameter file topic To edit existing parameter files you can use the different choices in the Edit menu Validating a parameter file In order to run a parameter file must be complete and all data in it valid As you edit a parameter file the part that you are editing will be validated as part of the edit proces
11. Mast NS Disperse Masting Group Mu parameter for the inverse Gaussian distribution for choosing seeds in masting conditions Values are only required for those species using this distribution when masting Mast NS Disperse Mast Inv Gauss Mu Mast NS Disperse Lambda parameter for the inverse Gaussian distribution for choosing Mast Inv Gauss seeds in masting conditions Values are only required for those species Lambda using this distribution when masting Mast NS Disperse Mu parameter for the inverse Gaussian distribution for choosing seeds in Non Mast Inv non masting conditions Values are only required for those species using Gauss Mu this distribution when not masting Mast NS Disperse Lambda parameter for the inverse Gaussian distribution for choosing Non Mast Inv Gauss Lambda Mast NS Disperse Mast Normal Mean Mast NS Disperse Mast Normal Standard Deviation Mast NS Disperse Non Mast Normal Mean Mast NS Disperse Non Mast Normal Standard Deviation Mast NS Disperse PDF Masting Conditions Mast NS Disperse PDF Non Masting Conditions Minimum DBH for Reproduction in cm Seed Distribution Seed Dist Clumping seeds in non masting conditions Values are only required for those species using this distribution when not masting Mean parameter for the normal distribution for choosing seeds in masting conditions Values are only required for those species using this distribution
12. Partitioned DBH Biomass Branch The slope in the linear biomass equation for branches Slope a Partitioned DBH Biomass Branch The intercept in the linear biomass equation for branches Intercept b Partitioned DBH Biomass Leaf The slope in the linear biomass equation for leaves Slope a Partitioned DBH Biomass Leaf The intercept in the linear biomass equation for leaves Intercept b How it works The mass of all components is calculated using the same equation but using different parameters The equation is Bio di DBH bi where e Bio biomass in kg dry weight of the component in question e a the a parameter for the component e b the b parameter for the component e DBH tree s DBH in cm The amount of each type of biomass in metric tons for each species is saved in a grid called Partitioned Biomass You can save these values in a detailed output file for analysis You of course can skip any of the components by entering 0 s for their parameter values How to apply it Apply this behavior to saplings adults or snags of any species This behavior does not automatically create output Once you have added this behavior to your run the Detailed output grid setup window will list the Partitioned Biomass grid You can then view the contents of this grid as a table using SORTIE s data visualization system Partitioned Height Biomass This behavior calculates biomass as a linear funct
13. Stochasticity parameter then supply a standard deviation in the Storm Light Standard Deviation parameter Using Deterministic as the stochasticity causes the GLA to be used as is How to apply it You do not need to apply this behavior to individual trees While it is recommended that you also include the Storm damage applier behavior in your run this is not required Growth behaviors Growth behaviors change the size of a tree A tree has two basic size dimensions diameter and height A growth behavior can change the tree size dimensions using one of two methods In the first method the behavior calculates an amount of diameter change and then adds this amount to the tree s diameter The tree s new height is calculated from the new diameter using the appropriate allometry equation This is the default method Behaviors using this method have the tag diam with auto height in their name In the second method diameter change and height change are calculated separately by two different behaviors Behaviors that operate on diameter and height independently must be paired together Behaviors using this method have the tag diam only or height only in their names When incrementing a tree s diameter with new growth seedlings and saplings have the amount of growth change applied to their diameter at 10 cm Adults have the amount applied to their DBH For more on tree types and their measurements see the tree life history stages topic
14. The plot also has a climate and a geographical location Some behaviors use this information but others do not This information is ignored if it is not needed Plot parameters Parameter name Number of timesteps Number of years per timestep Random seed Plot Length in the X E W Direction in meters Plot Length in the Y N S Direction in meters Plot Latitude in decimal degrees Mean Annual Description lt th The number of timesteps to run the model See more on timesteps The length of the timestep in years It is recommended that this value be a whole number An integer to use as the seed for SORTIE s random number generator Zero means that SORTIE chooses its own new seed every time and repeat runs with the same parameter file will come out different Any non zero value triggers one particular sequence of random numbers In that case repeat runs with the same parameter file will be the same The length of the plot in the east west direction in meters The length of the plot in the north south direction in meters The plot latitude expressed in decimal degrees i e 39 10 This information may not be needed in the run depending on the behaviors that you select if it is not needed this value will be ignored The mean annual precipitation of the plot in millimeters This Precipitation mm information may not be needed in the run depending on the behaviors that you select if it is not needed t
15. This behavior calculates light levels as a function of the basal area of trees in a neighborhood The light levels are randomized using a lognormal probability distribution Because of this random element to ensure some continuity through time light levels only change when the local neighborhood tree basal area has changed by a certain amount Parameters for this behavior Parameter name Description Basal Area Light Angiosperm b The b value used to calculate mean GLI from angiosperm basal area Parameter Basal Area Light Angiosperm c The c value used to calculate mean GLI from angiosperm basal area Parameter Basal Area Light The b value used to calculate mean GLI from conifer basal area Conifer b Parameter Basal Area Light Conifer c The c value used to calculate mean GLI from conifer basal area Parameter Basal Area Light Lognormal PDF Sigma value for the lognormal probability distribution Sigma Basal Area Light Mean GLI a The a value used to calculate mean GLI from basal area Parameter Basal Area Light Minimum BA Change for New GLI m2 The amount by which total basal area angiosperm plus conifer in square meters must change in order to trigger a new GLI calculation in a grid cell Basal Area Light Minimum DBH for The minimum DBH in cm of trees that count towards basal area Trees Basal Area Light Search Radius for The radius in meters of the circle that is sea
16. This grid is created by the Gap Light behavior Each grid cell holds the cell s gap status either TRUE or FALSE The grid cell resolution defaults to 8 m X 8 m You can set whatever new resolution you wish Data in the grid Data member name Description Is Gap Whether TRUE or not FALSE that grid cell has gap status GLI Map Grid This grid is created by the GLI Map Creator behavior The grid holds a GLI value in each cell The grid cell resolution defaults to 8 m X 8 m You can set whatever new resolution you wish Data in the grid Data member name Description GLI GLI value as a percentage of full sun between 0 and 100 Harvest Master Cuts Grid This grid is created by the Harvest behavior This is where directions to SORTIE for harvests for the run are stored The actual name of the grid is harvestmastercuts The only thing you may change in this grid is the grid cell resolution You may set it to anything you wish You can change it with either the Grid Setup window accessible only if harvest events have already been created or with the Edit Episodic Events Window Data in the grid There is no user accessible data in the grid Harvest Results Grid This grid is created by the Harvest behavior This is where data on harvest results is stored The data is stored raw no conversion to per hectare amounts The grid cell resolution is always set to match the Harvest Master Cuts grid Any changes you make to the grid ce
17. A or Asymptotic Height Growth A parameter e Sis the Slope of Growth Response S or Slope of Height Growth Response S parameter e GLIis the global light index calculated by a light behavior Diameter growth is compounded over multiple timesteps with the equation G Y 1 1 diam where e Gis the amount of diameter growth for the timestep in cm e diam is the diameter of the tree in cm at 10 cm height if seedling or sapling or DBH if adult e Tis the number of years per timestep e Xis the Relative Michaelis Menton Growth Diameter Exponent parameter Relative height growth is calculated slightly differently The details are discussed in the section for the Relative growth height only behavior below Relative growth is discussed in Pacala et al 1996 Relative growth limited to radial increment How it works This behavior calculates an amount of diameter growth according to the relative growth equation Growth is limited to a maximum of the constant radial growth increment for the species of tree to which it is being applied The increment is calculated as described in the Constant radial growth behavior Note that the increment parameter specifies radial growth the behavior makes all necessary conversions How to apply it This behavior can be applied to seedlings saplings and adults of any species Any tree species type combination to which it is applied must also have a light behavior applied You can use ei
18. A random number is compared to this probability to decide whether or not harvest will occur The frequency of harvest in previous time steps is not take into account If harvest is to occur the percentage of adult basal area to remove is calculated as follows BAR ge Bio where e BAR is the mean percent of total plot adult basal area to remove between 0 and 100 e Bio is the total plot adult biomass in Mg ha as calculated by the Dimension analysis behavior e ais the Gen Harvest Regime Remove Amount Alpha parameter e fis the Gen Harvest Regime Remove Amount Beta parameter e is the Gen Harvest Regime Remove Amount Mu parameter Note that the BAR is the mean removal rate This value is used along with the Gen Harvest Regime Gamma Scale Parameter in a draw on the gamma distribution in order to get the actual target removal rate The plot biomass in the equations above is the total adult biomass for all species All species must participate in harvest and only adults are counted and cut Once a basal area removal target has been established the individuals to cut must be selected A preference function determines the probability that an individual will be cut as follows P 1 ype PPAR y Jeo where e P is the probability that individual i will be cut e a is the Gen Harvest Regime Cut Preference Alpha parameter for the species of individual i e 1s the Gen Harvest Regime Cut Preference Beta paramete
19. Asymptotic Diam Growth Full Light in mm yr a parameter for diameter growth or the Logistic Asymptotic Height Growth Full Light in cm yr a parameter for height growth e b Logistic Diam Shape Param 1 b parameter for diameter growth or the Logistic Height Shape Param 1 b parameter for height growth e c Logistic Diam Shape Param 2 c parameter for diameter growth or the Logistic Height Shape Param 2 c parameter for height growth e GLI global light index as a percentage between 0 and 100 calculated by a light behavior e T number of years per timestep How to apply it This behavior can be applied to seedlings saplings and adults of any species Any tree species type combination to which it is applied must also have a light behavior applied You can choose either a diam with auto height diam only or height only version Logistic growth w size dependent asymptote This behavior does either diameter or height growth as a function of tree size and GLI Parameters for this behavior Parameter name Size Dep Logistic Diam Intercept a Size Dep Logistic Diam Shape Param 1 c Size Dep Logistic Diam Shape Param 2 d Size Dep Logistic Diam Slope b Size Dep Logistic Height Intercept a Size Dep Logistic Height Shape Param 1 c Size Dep Logistic Height Shape Param 2 d Size Dep Logistic Height Slope b How it works Description Intercept of
20. DBH Exponent b parameter e DBH is the tree s DBH in cm e sis the storm s severity set in the parameter for its return interval Below severity 0 1 the model becomes unreliable so in that case the severity is treated as a straight probability of mortality for all trees For example if a storm occurs of severity 0 05 all trees have the same 5 chance of dying If a storm return interval s severity is set to 0 then that storm never occurs It is possible for a storm to occur and kill no trees especially if it is a very mild storm or the forest has no large trees Unlike the other SORTIE storm behaviors there is no damaged but alive state After a windstorm a tree is either dead or in perfect health Storm events happen independently Every time a storm happens all eligible trees have a separate chance of mortality Of course the storms can never truly be independent A storm can only kill the trees that another storm hasn t already killed Trees killed in a windstorm are treated like trees killed in natural mortality They will form snags if the run uses snags and are available for processes such as substrate Seedlings and snags are never killed by storms For adults and saplings only those trees to which the Windstorms behavior has been applied will be considered for storm mortality and of those trees only those trees with a DBH larger than the value in the Windstorm Minimum DBH for Windstorm Mortality parameter can be kill
21. Growth is limited to a maximum of a constant basal area increment The amount of diameter increase is calculated by dividing the annual basal area increment of the tree s species by the diameter of the tree The increment is calculated as described in the Constant basal area growth behavior How to apply it This behavior can be applied to seedlings saplings and adults of any species Any tree species type combination to which it is applied must also have a light behavior applied You can use either the diam with auto height or diam only version Non limited relative growth How it works The amount of increase returned by the relative growth equation is applied to the tree How to apply it This behavior can be applied to seedlings saplings and adults of any species Any tree species type combination to which it is applied must also have a light behavior applied Relative growth height only This behavior uses the Michaelis Menton function to do height growth How it works After the Michaelis Menton function is used to calculate Y as described in the section above the amount of height growth is calculated as where G Y Height e Gis the amount of height growth for one year in cm e Height is the height of the tree in cm e Xis the Relative Michaelis Menton Growth Height Exponent parameter If the timestep is more than one year long growth is recalculated for each year of the timestep increasing the height each time
22. If your run does not work with snags you can ignore this Otherwise a value must be provided for all species Fraction of light transmitted through the snag tree crown for each species Applies to those snags whose age is greater than Upper Age Yrs of Snag Light Transmission Class 1 but is less than or equal to Upper Age Yrs of Snag Light Transmission Class 2 Expressed as a fraction between 0 and 1 If your run does not work with snags you can ignore this Otherwise a value must be provided for all species Fraction of light transmitted through the snag tree crown for each species Applies to those snags whose age is greater than Upper Age Yrs of Snag Light Transmission Class 2 Expressed as a fraction between 0 and 1 If your run does not work with snags you can ignore this Otherwise a value must be provided for all species The upper age limit in years defining the first age class of snag light transmission Snags with an age less than or equal to this age have a light transmission coefficient matching Snag Age Class 1 Light Transmission Coefficient If your run does not work with snags you can ignore this The upper age limit in years defining the second age class of snag light transmission Snags with an age greater than the upper limit for size class 1 but less than or equal to this age have a light transmission coefficient matching Snag Age Class 2 Light Transmission Coefficient Snags with an age greater th
23. Initial Conditions Proportion of Tip Up Mounds Initial Large Logs Mean Diameter cm Initial Small Logs Mean Diameter cm Maximum Number of Years that Decay Occurs Partial Cut Large Logs Mean Diameter cm Partial Cut Small Logs Mean Diameter cm Prop Live Trees The proportion of substrate that is tip up mounds substrate in areas that had a clear cut harvest event as a value between 0 and 1 This is not required if the Harvest behavior is not used After a gap cut harvest the mean diameter of logs in the small size class in cm This is not required if the Harvest behavior is not used After a gap cut harvest the mean diameter of logs in the large size class in cm This is not required if the Harvest behavior is not used The proportion of substrate that is scarified soil in areas that had a gap cut harvest event as a value between 0 and 1 This is not required if the Harvest behavior is not used The proportion of substrate that is tip up mounds substrate in areas that had a gap cut harvest event as a value between 0 and 1 This is not required if the Harvest behavior is not used The proportion of plot substrate that is scarified soil when the run starts as a value between 0 and 1 If a map of substrate values is included in the parameter file see Grid initial conditions for information on how to do this then the map values will be used for the initial conditions and this number will be ignor
24. Parameter name Beam Fraction of Global Radiation Clear Sky Transmission Coefficient First Day of Growing Season Last Day of Growing Season Amount Canopy Light Transmission 0 1 Snag Age Class 1 Amount Canopy Light Transmission 0 1 Description The fraction of total solar radiation that is direct beam radiation as opposed to diffuse Expressed as a value between 0 and 1 Used to determine the amount of solar radiation seen at the plot location The first day of the growing season as a Julian day number between 1 and 365 Trees only get light during the growing season The last day of the growing season as a Julian day number between 1 and 365 Trees only get light during the growing season Fraction of light transmitted through the tree crown for each species Expressed as a fraction between 0 and 1 A value must be provided for all species even if they don t all use light Fraction of light transmitted through the snag tree crown for each species Applies to those snags whose age is less than or equal to Upper Age Yrs of Snag Light Transmission Class 1 Expressed as a fraction between 0 and 1 If your run does not work with snags you can ignore this Otherwise a value must be provided for all species Fraction of light transmitted through the snag tree crown for each Snag Age Class 2 species Applies to those snags whose age is greater than Upper Age Amount Canopy Yrs of Snag Light Transmis
25. Weibull Climate Survival Precip Effect C Weibull Climate Survival Size Effect X0 Weibull Climate Survival Size Effect Xb Weibull Climate Survival Temp Effect A Weibull Climate Survival Temp Effect B Weibull Climate Survival Temp Effect C Weibull Climate The D parameter for the competition effect The gamma parameter for the competition effect This controls the response of a target tree to competition as a function of its size The maximum possible annual probability of survival for a target tree expressed as a probability between 0 and 1 The A parameter for the precipitation effect Units of precipitation are millimeters per year The B parameter for the precipitation effect Units of precipitation are millimeters per year The C parameter for the precipitation effect Units of precipitation are millimeters per year The mode of the size effect curve The variance of the size effect curve The A parameter for the temperature effect The effect is based on mean annual temperature in degrees Celsius The B parameter for the temperature effect The effect is based on mean annual temperature in degrees Celsius The C parameter for the temperature effect The effect is based on mean annual temperature in degrees Celsius The maximum distance in m at which a neighboring tree has Survival Max competitive effects on a target tree Neighbor Search Radius m Weibull Climate
26. density or as an absolute amount of tree density The Harvest behavior selects the trees to remove in the same way for all three harvest types When it is determining which trees to remove it starts by finding the largest tree in the area of the plot affected by the harvest It works its way through the trees from largest to smallest assessing whether to cut each one until it either runs out of trees or reaches its cut target This process preferentially removes the largest trees in each size range unless the harvest is a percentage of density cut in which case all trees in the target size ranges have an equal probability of being cut If Harvest is cutting a percentage of basal area or an absolute amount of basal area it will only cut a tree if its basal area will not cause the total to be more than the target This means that for basal area defined cuts the Harvest behavior may skip some bigger trees and cut smaller ones in order to more exactly cut its target Each species is cut separately So a request to remove 20 of three species will remove 20 of each of them no matter what their relative proportions to each other Trees can be prioritized for harvest You can choose a tree data member and a range of values for that data member For instance you could prioritize trees with growth values between 5 and 10 Trees meeting a priority are cut first You can set up to three priorities All trees meeting the first priority are cut first t
27. f Xe 1 X where Y is the amount of growth calculated by this behavior f X is the allometry equation relating diameter and height X is the other tree dimension either height or diameter before the primary growth is applied and X is the other tree dimension after primary growth is applied The allometric diameter growth behavior can be paired with any height only growth behavior and the allometric height growth behavior can be paired with any diam only growth behavior How to apply it These behaviors can be applied to seedlings saplings and adults of any species Any tree species type combination to which it is applied must also have a growth behavior applied that grows the opposite tree dimension Allometric diameter and height growth How it works These behaviors are designed to be secondary growth behaviors If you have a behavior that primarily updates one tree dimension diameter or height one of these behaviors can be used on the other dimension to ensure even growth These behaviors calculate a growth amount based on the allometry equations The amount of growth is Y f Xt 1 X where Y is the amount of growth calculated by this behavior f X is the allometry equation relating diameter and height X is the other tree dimension either height or diameter before the primary growth is applied and X is the other tree dimension after primary growth is applied The allometric diameter growth behavior can be
28. parameter a is the Non Spatial Exp Density Dep Crown Radius a parameter b is the Non Spatial Exp Density Dep Crown Radius b parameter c is the Non Spatial Exp Density Dep Crown Radius c parameter d is the Non Spatial Exp Density Dep Crown Radius d parameter e is the Non Spatial Exp Density Dep Crown Radius e parameter e fis the Non Spatial Exp Density Dep Crown Radius f parameter e DBH is the tree s DBH in cm e Height is the tree height in meters e ch is the instrumental crown depth of the target tree in meters calculated using the function below e STPH is number of stems per hectare of adult trees within the entire plot e BAPH is the basal area in m per hectare of adult trees within the entire plot e BAL is the sum of the basal area of all trees taller than the height of the target tree in m per hectare The instrumental equation for calculating ch is as follows ch a b DBH c Height d DBH e Height f DBH g STPH h BAPH i BAL j Height DBH where e ais the Non Spatial Density Dep Inst Crown Height a parameter e bis the Non Spatial Density Dep Inst Crown Height b parameter e cis the Non Spatial Density Dep Inst Crown Height c parameter e dis the Non Spatial Density Dep Inst Crown Height d parameter e eis the Non Spatial Density Dep Inst Crown Height e parameter e fis the Non Spatial Density Dep Inst Crown Height f parameter e g
29. put into an archive file using the TAR program The detailed output output for a single run is one file with a gz tar extension For example if the parameter file testpar xml was used to run 5 timesteps with a detailed output file to be saved named my detailed output at the end of the run there would be a file named my detailed output gz tar This TAR archive would contain the following files my detailed output gz a copy of the testpar xml parameter file e my detailed output_0 gz the data saved after setup occurred before the model started running These are the initial conditions e my detailed output_1 gz the data saved after the first timestep had run e my detailed output_2 gz the data saved after the second timestep had run e my detailed output_3 gz the data saved after the third timestep had run e my detailed output_4 gz the data saved after the fourth timestep had run e my detailed output_5 gz the data saved after the fifth timestep had run The gz extension indicates that these files are compressed If uncompressed the gz extension would be replaced with xml Detailed output files are very flexible and can contain any subset of the model s underlying tree and grid data You pick each individual piece of data that you wish to save and the frequency with which you wish to save it The data can be saved at any interval from every timestep to only at the first and last timesteps and ea
30. the effect depends on the relationship between the target species and the neighbor species Seedlings never compete You set whether or not snags compete in the Include Snags in NCI Calculations parameter The crowding effect is optional You can omit it by setting either the NCI Crowding Effect Slope C or NCI Max Radius of Crowding Neighbors in m parameters to 0 NCI is calculated as S N ie NCI gt A fe gee j 1k 1 ik where e the calculation sums over j 5 species and k N neighbors of each species of at least a DBH of NCI Minimum Neighbor DBH in cm out to a distance of NCI Max Radius of Crowding Neighbors in m e 7 1s the storm damage parameter of the kth neighbor depending on the damage status optional If the neighbor is undamaged the value is 1 If the neighbor has medium damage the value is the NCI Neighbor Storm Damage eta Medium 0 1 parameter for the target species If the neighbor has complete damage the value is the NCI Neighbor Storm Damage eta Complete 0 1 parameter for the target species To omit the storm damage term set all values for the above two parameters to 1 e ais the NCI Alpha parameter for the target tree s species e fis the NCI Beta parameter for the target tree s species e DBH is the DBH of the kth neighbor in cm e qis the NCI DBH Divisor q parameter Set this to a value greater than 1 to rescale the competitive effects of neighbors e Ax is the Species j NCI
31. 1 1 py Once the probability of mortality is calculated for a tree SORTIE generates a random number to which to compare it to determine whether the tree will live or die This model was originally described in Kobe et al 1995 How to apply it The GMF mortality function assumes a timestep length of five years so that must be your timestep length in order to use this behavior This behavior can be applied to seedlings saplings and adults of any species Any tree species type combination to which it is applied must also have a growth behavior applied Gompertz Density Self Thinning Mortality This behavior calculates the probability of mortality of an individual tree as a function of the density of conspecific neighborhood trees Trees killed by this behavior will have a mortality reason code of natural Parameters for this behavior Parameter name Description Gompertz Density 5 Oe S lf Thinning G G in the function for probability of mortality Gompertz Density mA Self Thinning H H in the function for probability of mortality Gompertz Density E Self Thinning I I in the function for probability of mortality Gompertz Density Seine Ma Minimum height for conspecific neighbors to be counted towards Neighbor Height m seus Gompertz Density ek dinag Radius for which to search for conspecific neighbors Neighbor Search Radius m How it works The density of conspecific neighbors is the n
32. 1 p Q 1 hi H pHi 3 H e zi hi H proportional height above the ground e Dis the outside bark diameter in cm at breast height 1 35 m equation below e His the total tree height m e hiis the height from the ground m at which to calculate the diameter inside the bark e diis the inside bark diameter at h height from ground cm e dois the Taper Equation Initial Multiplier a0 parameter e ais the Taper Equation DBH Exponent al parameter e dis the Taper Equation Height Exponent a2 parameter e bis the Taper Equation X Exponent 1 b1 parameter e bis the Taper Equation X Exponent 2 b2 parameter e b3is the Taper Equation X Exponent 3 b3 parameter e b4is the Taper Equation X Exponent 4 b4 parameter e bsis the Taper Equation X Exponent 5 b5 parameter e bois the Taper Equation X Exponent 6 b6 parameter SORTIE ND considers its DBH parameter to be diameter without bark To find the diameter outside the bark the equation is D a amp DBH a3DBH where e Dis the diameter outside the bark in cm e DBH is the diameter inside the bark in cm SORTIE s DBH e ais the Diameter Outside Bark Constant a1 parameter e isthe Diameter Outside Bark First Degree Parameter a2 parameter e azis the Diameter Outside Bark Second Degree Parameter a3 parameter Important note The math in this behavior is particularly susceptible to producing extreme numbers if the parameters are not chosen very caref
33. All plot locations are directly assigned the storm s severity index 4 Uniform Stochastic The storm damage index for each location is determined by performing a random draw on a probability distribution function with the overall storm severity providing the function mean How to apply it Add the behavior to the behavior list for your run A few rules e If you set the Plot Storm Susceptibility Pattern parameter equal to Mapped you must provide a map of plot susceptibility values You do this by using the Grid Value Edit Window to enter values 0 or greater for each cell of the grid called Storm Susceptibility e If you set the Storm Damage Application parameter equal to Stochastic you must choose a probability function in the Stochastic Pattern Damage Distribution If you choose Lognormal or Normal you must provide a function standard deviation in the Standard Deviation lognormal or normal parameter e If you do not also enable the Storm damage applier behavior storms may occur but nothing else will happen trees won t suffer any damage as a result You can also set all storm return intervals to 0 to turn off storms Storm damage applier The purpose of this behavior is to apply storm damage to individual trees This behavior decides which trees are damaged when a storm has occurred and how badly It also keeps track of the time since damage for damaged trees and after a healing period returns them to healthy undamag
34. Alpha parameter e fis the Michaelis Menton with Photoinhibition Beta parameter e D is the Michaelis Menton with Photoinhibition D parameter e gis the Michaelis Menton with Photoinhibition Phi parameter e His the tree s height in cm If the timestep is more than one year long growth is recalculated for each year of the timestep increasing the height each time How to apply it This behavior can be applied to seedlings saplings and adults of any species Any tree species type combination to which it is applied must also have a light behavior and a diameter growth behavior applied NCI growth This behavior uses the effects of neighbor competitiveness to influence growth rates NCI stands for neighborhood competition index A tree s maximum potential growth rate is reduced due to competitiveness and several other possible factors You can use certain parameter values to turn these influences on and off to reflect the conditions appropriate for your run Parameters for this behavior Parameter name Description NCI Alpha NCI function exponent NCI Beta NCI function exponent NCI Crowding Effect Slope C NCI Crowding Effect Steepness D NCI Damage Effect Complete Storm Damage 0 1 NCI Damage Effect Medium Storm Damage 0 1 Species i NCI lambda neighbors NCI Maximum Crowding Distance in meters NCI Maximum Potential Growth cm yr NCI Minimum Neighbor DBH in cm NCI DBH Divisor q NCI
35. Biomass for species Amount of storm killed palm leaf biomass for species X X in Mg Mg Bole Palm Biomass for species Amount of storm killed palm bole biomass for species X X in Mg Storm Light Grid This grid is created by the Storm Light behavior Each grid cell holds a light level value The grid cell resolution defaults to 8 m X 8 m You can set whatever new resolution you wish Data in the grid Data member name Description Light The light level as calculated by the Storm Light behavior Storm Susceptibility Grid This grid is created by the Storm disturbance behavior Each grid cell holds a storm susceptibility index between 0 and 1 The grid resolution default is 8 m X 8 m You can change this to whatever you wish but if you are also using the grid Storm Damage the resolutions must match Data in the grid Data member ee Description name IEOS A storm damage susceptibility for each cell from 0 not susceptible to damage to gt 1 very susceptible to damage Substrate Grid This grid is created by the Substrate behavior The grid holds the relative proportions of the various substrate types If the Harvest behavior is present for the run then this grid s resolution must match the Harvest Results grid Otherwise it defaults to a cell resolution of 8 m X 8 m which you can change This grid holds packages with a different data structure from the main grid to track Substrate cohorts Data in the grid Data membe
36. Class 2 How it works You provide as input a file that contains the list of points for which you would like GLI values The file is tab delimited text and has the following format The first row is assumed to be a header row and is ignored Each subsequent row is a single point for which to calculate GLI You can include as many as you wish The first column is the point s X coordinate the second is the Y coordinate and the third column is the height above the ground in meters Name the file whatever you wish Put the file name for the points file in the GLI Points Input File parameter It is best to use a fully qualified path name i e c sortie my_points txt SORTIE ND will load the points into the parameter file If you are working with a parameter file that already contains GLI points because they were saved into it previously you do not need to enter another file and can leave the GLI Points Input File parameter blank Each timestep this behavior calculates GLI at each of the points specified It then writes the results to another tab delimited text file You enter the filename of this file in the GLI Points Output File parameter It should be fully qualified i e c sortie points_output txt and should have a txt extension If the file already exists when the SORTIE ND run begins the contents will be overwritten This means that this behavior cannot successfully be used in batch runs where a parameter file will be run mult
37. For more on tree size relationships including how trees transition between life history stages see the allometry topic Note All behaviors convert growth to diameter growth in cm for internal consistency The equations below reflect this Some behaviors may take parameters in mm or for radial growth Take careful note of your behavior s parameters It is important to be careful when using different behaviors for height and diameter growth The values are not required to conform to the tree s allometry equation This may create trees whose dimensions are no longer linked with an allometric function This is not considered a problem although it may have unintended effects For instance if tree seedlings or saplings get separate diameter and height increments then their diameters and heights will be uncoupled This means that you cannot use one of the size dimensions to predict the other through an allometric equation Trees with the same diameter will have different heights and vice versa If you assign the adults to a behavior that increments diameter and then automatically updates height according to the allometry equations you are likely to notice strange results for new adult trees You will lose the variability in height diameter ratio that was developed Suddenly all trees with the same diameter will have the same height again and vice versa This means that individuals may suddenly jump in height or even shrink The Allomet
38. Germinating on conditions that survive to become seedlings Expressed as a value Canopy Decayed between 0 and 1 Logs Fraction Seeds Germinating on Canopy Fresh Logs Fraction Seeds Germinating on Canopy Forest Floor Litter Fraction Seeds Germinating on Canopy Forest Floor Moss Fraction Seeds Germinating on Canopy Scarified Soil Fraction Seeds Germinating on Canopy Tip Up Fraction Seeds Germinating on Gap Decayed Logs Fraction Seeds Germinating on Gap Fresh Logs Fraction Seeds Germinating on Gap Forest Floor Litter Fraction Seeds Germinating on Gap Forest Floor Moss Fraction Seeds Germinating on Gap Scarified Soil Fraction Seeds Germinating on Gap Tip Up The proportion of those seeds that land on fresh logs under canopy conditions that survive to become seedlings Expressed as a value between 0 and 1 The proportion of those seeds that land on forest floor litter under canopy conditions that survive to become seedlings Expressed as a value between 0 and 1 The proportion of those seeds that land on forest floor moss under canopy conditions that survive to become seedlings Expressed as a value between 0 and 1 The proportion of those seeds that land on scarified soil under canopy conditions that survive to become seedlings Expressed as a value between 0 and 1 The proportion of those seeds that land on tip up mounds substrate under canopy conditions that survive to become seedlings Expr
39. Lambda parameter for the target species relative to the kth neighbor s species e distance 1s distance from target to neighbor in m The value of Damage Effect is optional If you elect not to use storms in your run set all values in the NCI Damage Effect Medium Storm Damage 0 1 and NCI Damage Effect Complete Storm Damage 0 1 parameters to 1 If you are using storms then the value of Damage Effect depends on the tree s damage category If the tree is undamaged Damage Effect equals 1 If the tree has medium storm damage the value is the NCI Damage Effect Medium Storm Damage 0 1 parameter If the tree has complete storm damage the value is the NCI Damage Effect Complete Storm Damage 0 1 parameter The survival probability as calculated above is an annual probability For multi year timesteps the timestep probability is AP where AP is the annual probability and X is the number of years per timestep Once a tree s timestep survival probability has been calculated it is compared to a random number to determine whether the tree lives or dies How to apply it This behavior can be applied to saplings and adults of any species It cannot be applied to seedlings If the Shading Effect term is activated in the growth equation then the trees to which this behavior is applied must also have a light behavior applied the Sail light behavior is the one designed to work with the NCI behavior The use of any other light behavior is at
40. Light Transmission 0 1 Description The fraction of total solar radiation that is direct beam radiation as opposed to diffuse Expressed as a value between 0 and 1 Used to determine the amount of solar radiation seen at the plot location The first day of the growing season as a Julian day number between 1 and 365 Trees only get light during the growing season The last day of the growing season as a Julian day number between 1 and 365 Trees only get light during the growing season Fraction of light transmitted through the tree crown for each species Expressed as a fraction between 0 and 1 A value must be provided for all species even if they don t all use light Fraction of light transmitted through the snag tree crown for each species Applies to those snags whose age is less than or equal to Upper Age Yrs of Snag Light Transmission Class 1 Expressed as a fraction between 0 and 1 If your run does not work with snags you can ignore Snag Age Class 2 Amount Canopy Light Transmission 0 1 Snag Age Class 3 Amount Canopy Light Transmission 0 1 Upper Age Yrs of Snag Light Transmission Class 1 Upper Age Yrs of Snag Light Transmission Class 2 How it works this Otherwise a value must be provided for all species Fraction of light transmitted through the snag tree crown for each species Applies to those snags whose age is greater than Upper Age Yrs of Snag Light Transmission Class 1 b
41. Neighbor Storm Damage eta Complete 0 1 NCI Neighbor Storm Damage eta Medium 0 1 NCI Shading Effect Coefficient m NCI Shading Effect Exponent n NCI Size Effect Mode in cm X0 The slope of the curve for the crowding effect equation The steepness of the curve for the crowding effect equation The fraction by which a tree s growth rate is reduced when it has sustained complete storm damage Set this to 1 if you are not including storms in your run The fraction by which a tree s growth rate is reduced when it has sustained medium storm damage Set this to 1 if you are not including storms in your run The competitive effect of neighbors of species i on the target tree species s growth between 0 and 1 The maximum distance in m at which a neighboring tree has competitive effects on a target tree Maximum potential diameter growth for a tree in cm yr The minimum DBH for trees of that species to compete as neighbors Used for all species not just those using NCI growth The value by which neighbor DBHs are divided when calculating NCI This can be used to make units adjustments The fraction to which a neighbor s competitive effect is reduced when the neighbor has sustained complete storm damage Set this to 1 if you are not including storms in your run The fraction to which a neighbor s competitive effect is reduced when the neighbor has sustained medium storm damage Set this to 1 if you ar
42. Run from the main menu or the Run button with the single right facing arrow you can pause the run at any point to start viewing data 3 Once the run is paused click the View run output button SORTIE will load the output files from the current run and analyze them to determine what charts you can view SORTIE will not force you to first pause the run but it is highly recommended This ensures that the model is not trying to write new output to the files at the same time as it is trying to open them to be read 4 Open the charts you wish to view see Displaying the data from a file If a chart you want is not listed for any output file it means that the data it requires is not being saved You must stop the run change your output options and start a new run 5 Start the model running again As the model completes each timestep it will update any open charts while it does this you may see a message that the model is paused at the bottom of the screen this is normal You can open new charts or close existing ones at any point in the run again pausing is recommended before opening new charts ae Note While displaying a current run s output is a useful feature it is not the most efficient way to do arun If you do not actually need to keep tabs on a run s progress or if you are satisfied with the way a current run is going allow it to run without open charts The run will execute much faster If you currently have charts o
43. Shading Effect Coefficient m parameter e nis the NCI Shading Effect Exponent n parameter e Sis the amount of shade cast by neighbors from 0 no shade to 1 full shade This value should come from the Sail light behavior This effect is not required To omit the Shading Effect set the NCI Shading Effect Coefficient m parameter to 0 Crowding Effect is calculated as CE e O DBHY nc where e Cis the NCI Crowding Effect Slope C parameter e DBH 1s of the target tree in cm e yis the NCI Size Sensitivity to NCI gamma parameter for the target tree s species e Dis the NCI Crowding Effect Steepness D parameter e NCTis this tree s NCI value equation below The NCI value sums up the competitive effect of all neighbors with a DBH at least that of the NCI Minimum Neighbor DBH in cm parameter out to a maximum distance set in the NCI Max Radius of Crowding Neighbors in m parameter The competitiveness of a neighbor increases with the neighbor s size and decreases with distance and storm damage to the neighbor optional The neighbor s species also matters the effect depends on the relationship between the target species and the neighbor species Seedlings never compete You set whether or not snags compete in the Include Snags in NCI Calculations parameter The crowding effect is optional You can omit it by setting either the NCI Crowding Effect Slope C or NCI Max Radius of Crowding Neighbors in m parameters to 0 N
44. Species group X decay class Y large log volume in m3 per ha Description The age of the substrate cohort in timesteps Substrate cohort new scarified soil The proportion of cell area that is scarified soil added in substrate Substrate cohort new tip up mounds substrate this cohort The proportion of cell area that is tip up mounds substrate added in this cohort Detailed Substrate calcs Grid This grid is called detailedsubstratecalcs and is created by the Detailed Substrate behavior This grid is used for intermediate calculations when calculating the values in the Detailed Substrate grid The grid cell resolution must match Detailed Substrate s Data in the grid Data member name Amount of new tip up mounds New Log Area Sp Group X Small Decay Y New Log Area Sp Group X Large Decay Y Prop Sp Group X Small Decay Y Timestep Z Prop Sp Group X Large Decay Y Timestep Z Description New tip up mounds area by grid cell in square meters Area of new small logs added this timestep for species group X decay class Y in square meters Area of new large logs added this timestep for species group X decay class Y in square meters Fresh small logs added Z timesteps ago for species group X decay class Y as a proportion of grid cell area Fresh large logs added Z timesteps ago for species group X decay class Y as a proportion of grid cell area Dispersed Seeds Grid This grid is created by the Disperse behavio
45. a non masting timestep as a value between 0 and 1 The dispersal value for the weibull function under masting conditions This is only required for a species if the canopy probability distribution function for that species is weibull The 8 for the weibull function under masting conditions This is only required for a species if the canopy probability distribution function for that species is weibull If the STR value is stochastic this determines whether a new value is generated once per species per timestep or once per tree per timestep If the Masting Disperse STR Draw PDF is Deterministic then this value is not used Whether the STR value should be deterministic or generated each timestep using a normal or lognormal distribution The minimum DBH at which a tree can reproduce This value does not have to match the Minimum adult DBH The distribution method to be applied to seeds randomization The forms for these functions can be found here Choices are e Deterministic no randomization e Poisson use the number of seeds as the mean in a Poisson probability distribution function e Normal use the number of seeds as the mean in a normal probability distribution function You must then supply a standard deviation for the function e Lognormal use the number of seeds as the mean in a lognormal probability distribution function You must then supply a standard deviation for the function e Negative binomial use
46. a percentage between 0 and 100 calculated by a light behavior e diam diameter diameter at 10 cm for seedlings and saplings DBH for adults For diameter growth Assume that the number of years per timestep is X In order to find the total amount of diameter increase for a timestep the logistic growth equation is calculated X times with the diameter incremented by the amount of diameter increase for the previous year The total diameter increment is the sum of the X individual diameter increments For height growth In order to find the total amount of height increase for a timestep the behavior takes as an input the amount of diameter growth increase Assume that the number of years per timestep is X The amount of diameter increase is divided by X Then the logistic growth equation is calculated X times with the diameter incremented by the amount of diameter increase per timestep each time The total height increment is the sum of the X individual height increments How to apply it This behavior can be applied to seedlings saplings and adults of any species Any tree species type combination to which it is applied must also have a light behavior applied You can choose either a diam with auto height diam only or height only version Lognormal bi level growth height only This behavior increments growth according to a lognormal equation with the possibility of two sets of parameters for each species one for high light conditions
47. and one for low light conditions This can also be used alone without the light levels Parameters for this behavior Parameter name Description Lognormal Bi Level Max Growth in The maximum height growth in meters under high light conditions High Light m Lognormal Bi Level Max Growth in The maximum height growth in meters under low light conditions Low Light m Lognormal Bi Level X0 for High Light The Xo parameter to use under high light growth conditions Growth Lognormal Bi Level X0 for Low Light The Xo parameter to use under low light growth conditions Growth Lognormal Bi Level Xb for High Light The X parameter to use under high light growth conditions Growth Lognormal Bi Level Xb for Low Light The X parameter to use under low light growth conditions Growth Lognormal Bi Level Threshold for High Light Growth 0 100 The light threshold value between high light and low light conditions How it works The equation used by this behavior to increment growth is where e Y amount of height growth in m e MG maximum growth in meters in high light conditions this is the Lognormal Bi Level Max Growth in High Light m parameter in low light conditions this is the Lognormal Bi Level Max Growth in Low Light m parameter e Xo in high light conditions this is the Lognormal Bi Level X0 for High Light Growth parameter in low light conditions this is the Lognormal Bi Level X
48. applies to be promoted directly to adult tree status even if it is a seedling This tree represents the winner All other trees in the cell do not grow In cells that are not in gap no trees grow How to apply it This behavior can be applied to seedlings saplings and adults of any species Any tree species type combination to which it is applied must also have the Gap Light behavior applied Weibull climate growth This behavior calculates tree growth as a function of climate and larger neighbor trees A tree has a maximum potential growth rate that is reduced due to several possible factors Parameters for this behavior Parameter name Description Weibull Climate Growth Competition Effect The C parameter for the competition effect Weibull Climate Growth Competition Effect D The D parameter for the competition effect Weibull Climate Growth Competition Gamma The gamma parameter for the competition effect This controls the response of a target tree to competition as a function of its size Weibull Climate The A parameter for the precipitation effect Units of precipitation are Growth Precip millimeters per year Pu eters per year Weibull Climate The B parameter for the precipitation effect Units of precipitation are Growth Precip millimeters per year Effect B U Weibull Climate The C parameter for the precipitation effect Units of precipitation are Growth Precip millimeters pe
49. assessed to see how much light each blocks their crowns can either conform to each neighbor s true crown height or they can be approximated at the full height of the tree When a fish eye photo is simulated for a tree this positions the photo at either the top of the crown or at mid crown Seedlings always get fisheye photos at top of crown no matter what this value is The fraction of total solar radiation that is direct beam radiation as Global Radiation Clear Sky Transmission Coefficient First Day of Growing Season Last Day of Growing Season Amount Canopy Light Transmission 0 1 Snag Age Class 1 Amount Canopy Light Transmission 0 1 Snag Age Class 2 Amount Canopy Light Transmission 0 1 Snag Age Class 3 Amount Canopy Light Transmission 0 1 Upper Age Yrs of Snag Light Transmission Class 1 Upper Age Yrs of Snag Light Transmission Class 2 How it works opposed to diffuse Expressed as a value between 0 and 1 Used to determine the amount of solar radiation seen at the plot location The first day of the growing season as a Julian day number between 1 and 365 Trees only get light during the growing season The last day of the growing season as a Julian day number between 1 and 365 Trees only get light during the growing season Fraction of light transmitted through the tree crown for each species Expressed as a fraction between 0 and 1 A value must be provided for all
50. at the top of the first 16 foot log is established by the form classes A species s form class is the percentage of DBH to which the bole has tapered at the top of the first 16 foot log This value is entered as the Bole Volume Form Class 60 100 parameter Then the behavior determines how many more logs the tree contains The amount of taper at the top of the first 16 foot log is subtracted from the DBH to see how much taper is left before the 60 merchantable height diameter is reached There is no formula that establishes clearly how many logs will fit the behavior uses a trial and error approach taken from Messavage and Girard 1956 This paper includes the table below for upper log taper for trees of various DBH and bole heights The behavior uses this table to determine the maximum number of logs it can fit into the taper available Trees below 10 inches of DBH have no volume Trees greater than 40 inches of DBH are treated like 40 inch trees 2 log 3 log DBH tree tree 4 log tree 5 log tree 6 log tree in 2d 2d 3d 2d 3d 4th 2d 3d 4th 5th 2d 3d 4th 5th 6th log log log log log log log log log log log log log log log erin fo fa a ff a aw Fe Fe fet bee Jee fe jis f2 i4 f2 2s ii i7 23 209 a fs fis J2 fis fez fes fox fos fea an E p pa fas s fis fes er fia fis fas a2 ps es as as foe fea fas x2 x9 ae os foo fra faa a2 ow o fe
51. auto height or diam only version Absolute growth behaviors Several behaviors apply an absolute growth version of the Michaelis Menton function Parameters for these behaviors Parameter name Description Adult Constant Area The constant amount of basal area by which to increase a tree s basal Growth in sq cm yr area Applies to basal area increment limited behaviors Akl SUS Ne The constant value by which to increase a tree s radius at breast height Radial Growth in e ee Applies to radial increment limited growth behaviors mm yr Asymptotic ee Damen Goch Asymptote of the Michaelis Menton growth function at high light function term A below A Slope of Growth Slope of the Michaelis Menton growth function at zero light function Response S term S below Length of Current Controls the magnitude of the effects of release Release Factor Length of Last e Saar Controls the magnitude of the effects of suppression Defines the growth rate for suppressed status in terms of tree mortality The value is expressed as the proportion of trees which die at the growth rate which defines suppressed status expressed as a fraction between 0 and 1 For instance if this value is 0 1 the growth rate for suppressed status is one at which 10 of trees die with that growth Mortality Threshold for Suppression Years Exceeding Threshold Before a Tree is Suppressed The number of years for which a tree s growth must be bel
52. basal area threshold harvest with proportion of total to cut Fixed BA this is the proportion of the total plot s basal area to cut between 0 and 1 The slope of the curve C of the competitive effect of a target on a neighbor of each species The steepness of the curve D of the competitive effect of a target on a neighbor of each species Exponent controlling the effect of a target s DBH on neighbors Exponent controlling the effect of distance between target and neighbors Optional If there is a value in this field the Competition Harvest behavior will write a tab delimited text file of this name with all the trees cut during the run In batch runs this will get overwritten and only contain the last run s list Competition Harvest Fixed BA Harvest Threshold m2 ha Competition Harvest Fixed Interval Harvest Interval yr Competition Harvest Harvest Type Competition Harvest Minimum DBH to Harvest Competition Harvest Min Years Between Fixed BA Harvests Competition Harvest Maximum DBH to Harvest Competition Harvest Max Radius of Competitive Effects m Competition Harvest Species 1 Target Lambda Competition Harvest Size Sensitivity gamma Competition Harvest Target DBH For fixed basal area threshold harvests the value in Competition Harvest Harvest Type is set to either Fixed BA or Fixed BA Amt this is the amount of basal area that the plot must have before a har
53. behavior applies a constant rate of mortality to trees with different rates for high light and low light conditions There are two versions designed to work with different behaviors that calculate light levels Stochastic Bi Level Mortality Storm Light and Stochastic bi level mortality GLI Trees killed by this behavior will have a mortality reason code of natural Parameters for this behavior Parameter name Description Stochastic Bi Level High Light Mortality Probability 0 1 The annual probability of mortality under high light conditions as a proportion between 0 and 1 Stochastic Bi Level High Light Mortality Threshold The threshold between low light and high light mortality rates as a value between 0 and 100 Stochastic Bi Level Low Light Mortality Probability 0 1 The annual probability of mortality under low light conditions as a proportion between 0 and 1 How it works In the version of the behavior called Stochastic Bi Level Mortality Storm Light light levels come from the Storm Light grid produced by the Storm Light behavior In the version called Stochastic Bi Level Mortality GLI light levels come from any light behavior that can be applied directly to trees The threshold between the use of high light and low light parameters is set in the Stochastic Bi Level High Light Mortality Threshold parameter The units depend on which index of light is being used Check the documentation on your
54. behavior calculates an amount of diameter growth according to the absolute growth equation Growth is limited to a maximum of a constant basal area increment The amount of diameter increase is calculated by dividing the annual basal area increment of the tree s species by the diameter of the tree The increment is calculated as described in the Constant basal area growth behavior How to apply it This behavior can be applied to seedlings saplings and adults of any species Any tree species type combination to which it is applied must also have a light behavior applied You can use either the diam with auto height or diam only version Non limited absolute growth diam with auto height How it works The amount of diameter increase returned by the absolute growth equation is applied to the tree How to apply it This behavior can be applied to seedlings saplings and adults of any species Any tree species type combination to which it is applied must also have a light behavior applied You can use either the diam with auto height or diam only version Allometric diameter and height growth How it works These behaviors are designed to be secondary growth behaviors If you have a behavior that primarily updates one tree dimension diameter or height one of these behaviors can be used on the other dimension to ensure even growth These behaviors calculate a growth amount based on the allometry equations The amount of growth is Y
55. cell by examining the trees within the distance given in the Storm Light Max Radius m for Damaged Neighbors parameter The first term in the equation T M 100 corrects the light level if the point is not under full canopy All adults and snags no matter what storm damage are counted up and assigned to T If T gt M then the first term is set to 0 and only the second part a b N is evaluated If T lt M then the first term adds to the linear portion the proportion of full sun equal to the proportion of trees missing from the full canopy For the second linear term the behavior counts the number of dead and heavily damaged trees as a proportion of all adults and snags Trees count as heavily damaged if they are either snags that were created as a result of a storm killing an adult tree or live adults with heavy storm damage All storm damaged trees have a time since damage counter only those eligible trees with a counter value less than or equal to the value in the Storm Light Max Years Damaged Trees Affect Light parameter are counted Saplings and seedlings never count All snags count whether they were created by a tree or another mortality process Their age as a snag must also be less than the Storm Light Max Years Snags Affect Light parameter The GLA value can be used as is or it can be used as the mean in a PDF to introduce a stochastic element You can choose either Normal or Lognormal in the Storm Light
56. chosen light behavior carefully For each tree a random number is compared to that species s probability of mortality to determine if it dies If light levels qualify as high light the probability of mortality is the value in the Stochastic Bi Level High Light Mortality Probability 0 1 parameter if the light levels are low the probability of mortality is the value in the Stochastic Bi Level Low Light Mortality Probability 0 1 parameter If the timestep length is not one year the probability of mortality is adjusted from an annual mortality probability to a timestep probability How to apply it This behavior can be applied to seedlings saplings and adults of any species If you have chosen the version marked Storm Light you must also use the Storm Light behavior If you have chosen the version marked GLI you must assign a light behavior to all trees to which you assign this mortality Stochastic mortality This behavior produces a background mortality rate Individuals within the pool of trees to which this behavior applies are randomly selected to die Trees killed by this behavior will have a mortality reason code of natural Parameters for this behavior Parameter name Description Backeround The proportion of trees that die each year as a value between 0 and 1 Mortality Rate i l How it works For each tree a random number is compared to that species s Background Mortality Rate parameter to determine if it f
57. compounded over multiple timesteps with the equation G Y 1 1 diam where e Gis the amount of diameter growth for the timestep in cm e diam is the diameter of the tree in cm at 10 cm height if seedling or sapling or DBH if adult e Tis the number of years per timestep e Xis the Relative Michaelis Menton Growth Diameter Exponent parameter Relative height growth is calculated slightly differently The details are discussed in the section for the Relative growth height only behavior below Relative growth is discussed in Pacala et al 1996 Relative growth limited to radial increment How it works This behavior calculates an amount of diameter growth according to the relative growth equation Growth is limited to a maximum of the constant radial growth increment for the species of tree to which it is being applied The increment is calculated as described in the Constant radial growth behavior Note that the increment parameter specifies radial growth the behavior makes all necessary conversions How to apply it This behavior can be applied to seedlings saplings and adults of any species Any tree species type combination to which it is applied must also have a light behavior applied You can use either the diam with auto height or diam only version Relative growth limited to basal area increment How it works This behavior calculates an amount of diameter growth according to the relative growth equation
58. cycles along with sea surface temperature This behavior can thus change the storm frequency over time using either a sinusoidal pattern a constant linear change or both together In the figure below curve 1 is a basic sine wave Curve 2 has a sinusoidal pattern plus an upwards trend 4 _ e Curve 1 a Curve 2 dh he A a gt kk 9 a a a Cae f E ai K N a N x a FN a F a Se tk a a A si 2 a S T T a T M i 2 4 4 5 The actual probability of an individual storm that takes place in a storm regime with a cyclical frequency is P F P F d sin x x g 2f mx if Note that the new probability is a baseline probability P Fi multiplied by a value that adjusts the probability according to where the model is at the given time in the frequency cycle The frequency cycle multiplier is itself made up of two terms added together The first term is the sine curve cycling and the second term is the overall trend upwards or downwards Terms in the equation e P F is this timestep s annual probability of a storm of the ith return interval adjusted according to the frequency cyclicity e P F is the baseline probability of a storm of the ith return interval that is the inverse of the values specified in the Windstorm Severity for X Year Return Interval Storm parameters e x 4 t Sr where tis the number of yea
59. e Bis the Slope of Asymptotic Height parameter e DBH is tree DBH in cm In some articles B Slope of Asymptotic Height is a published parameter Other articles instead use H and another parameter H2 which was called the DBH to height relationship In this case B can be calculated from published values as B H2 H The standard seedling diamjo height function is height 0 1 30 1 4 4 io where e height is tree height in meters e ais the Slope of Height Diameter at 10 cm Relationship parameter e diamyjo is tree diameter at 10 cm height in cm The linear diameter height relationship The linear diameter height relationship is the same for all life history stages but each stage can use a different set of parameter values Parameters Parameter name Description The maximum tree height for a species in meters No tree no matter what allometric function it uses is allowed to get taller than this Used by all species Maximum Tree Height in meters Adult Linear The intercept of the adult linear function for DBH and height Function Intercept Adult Linear The slope of the adult linear function for DBH and height Function Slope Sapling Linear Bunction Intercept The intercept of the sapling linear function for DBH and height Sapling Linear a The intercept of the sapling linear function for DBH and height Seedling Linear e The intercept of the seedling linear function for DBH and height See
60. each cell of the Dispersed Seeds grid this multiples the number of seeds present by the Proportion Germinating Between 0 and 1 parameter reducing the total number available The new number of seeds is placed back in the Dispersed Seeds grid How to apply it Apply this behavior to seeds of any species Any species to which this is applied must have a Disperse behavior applied as well Seed Establishment This behavior converts seeds into seedlings How it works This behavior goes through each grid cell in the Dispersed Seeds grid and for each species to which this behavior applies converts each seed into a seedling The seedlings are randomly placed within the grid cell area and have a slightly randomized value of New seedling diameter at 10 cm How to apply it Apply this behavior to seeds of any species A species to which this is applied must also have a Disperse behavior applied Storm Light Dependent Seed Survival This behavior assesses seed survival as a function of the light level of the location in which a seed lands Light level calculations are performed by the Storm Light behavior This behavior is exactly like Light Dependent Seed Survival except for the method of light level calculation Parameters for this behavior Parameter name Description GLI of Optimum The GLI value of optimum survival for seeds as a value between 0 and Establishment 0 100 100 Slope of Dropoff Above the Optimum GLI The slo
61. each year as a value between 0 and 1 Mortality Rate l Browsed The proportion of browsed trees that die each year as a value between 0 Background Mortality Rate L How it works Whether or not a tree is browsed is determined by the Random browse behavior For each tree if it has not been browsed that species s Background Mortality Rate parameter is used if it has been browsed the species s Browsed Background Mortality Rate parameter is used A random number is compared to the appropriate rate to decide if the tree dies How to apply it This behavior can be applied to seedlings saplings and adults of any species Any tree species type combination to which it is applied must also have the Random browse behavior applied Competition Mortality Competition mortality is a growth based mortality behavior It uses the results of the NCI growth behavior Trees killed by this behavior will have a mortality reason code of natural Parameters for this behavior Parameter name Description Competition Mortality Shape Determines the shape of the mortality function Parameter Z Competition Mortality Maximum The maximum relative increment of growth subject to mortality Parameter max How it works NCI growth in SORTIE is calculated in the following way Growth Max Growth Size Effect Shading Effect Crowding Effect Damage Effect Max Growth is the maximum diameter growth the tree can attain in cm yr entered in the
62. file that you save cannot be used as input to SORTIE Error messages when you click OK When you click OK in the parameter window the data in the window is checked to make sure it is complete and valid If there is a problem you are given an error message and the opportunity to correct the problem You are not allowed to save invalid data changes For more on what an individual piece of data is and what limitations may be placed on it consult the individual behavior documentation Edit Harvest Interface Window This window is reached from the Edit menu by selecting Harvest Interface It allows you to set up the Harvest interface behavior Path and filename of the executable This is the full path and filename of the executable that SORTIE will call to perform harvests The filename and file extension must be something that the operating system can recognize and treat as an executable Be sure to provide the complete filename SORTIE makes no assumptions about the file Tree file that SORTIE will write This is the full path and filename of the file that SORTIE writes each harvest timestep with the list of trees eligible to be harvested Input the filename and extension as the executable expects to find it Tree harvest file that the executable will write This is the full path and filename of the file that the executable writes with the list of trees to be harvested Input the filename and extension as it will be written by the exe
63. find the timestep in the previous run where the interesting curve shape started then use that timestep as initial conditions to your new run For your new run you would save less data For more information on using detailed output output as initial conditions see the Using output as input to a new run topic Tree output You can save both high level plot wide tree information and data on individual trees Dead trees and live trees in output You can collect output information on both living trees and trees that died for both types of output files This allows you to view various charts and examine statistics for the trees that died each timestep Dead trees are only recorded in the timestep in which they died If a tree dies and creates a snag it will show up twice once when it creates the snag and once when the snag is removed from the model The snag itself is considered alive because it is still interacting with the model Dead trees are classed by mortality reason code When you choose what data to save for output if you save dead trees you select which mortality codes you would like data for If you do not save information for a particular mortality reason it will not show up in the output even though there may be trees that died for that reason All mortality reasons are always listed although a particular run may not kill trees for that reason Check the documentation for your chosen disturbance behaviors and mortality behav
64. for their species They are given disease as a mortality reason What happens to dead trees depends on the rest of the run If there are other behaviors in the run that deal directly with snags or create them then the run is snag aware In this case all adult trees killed are turned into snags saplings never become snags If the run is not snag aware then the trees are marked as dead When if the dead tree remover behavior runs the dead trees will be removed at that time These dead trees are available as input to Substrate The actual amount of trees killed may not be exactly what was specified since the Episodic Mortality behavior can t remove part of a tree to get the numbers right The behavior stores how much it actually cut each timestep in the Mortality Episode Results grid To optimize the accuracy of the behavior use larger kill ranges and high proportions of the plot area to make sure there is a big pool of trees to choose from How to apply it To define planned mortality episodes use the Edit Episodic Events Window Random browse This behavior simulates random browsing from herbivores Parameters for this behavior Parameter name Description Random Browse Annual Browse Probability 0 1 The annual probability from 0 to 1 of being browsed This is the mean probability if the probability is being varied each timestep The PDF used to vary the browse probability None means the same probability i
65. function for trees with medium damage Storm Medium Damage Survival Prob DBH Coeff b The b value in the probability of survival logit function for trees with medium damage Storm Prop Heavy The proportion of those heavily damaged trees that are killed in the storm Damage Dead Trees that tip up as a value between 0 and 1 For how a tipped up tree is that Tip Up treated see the behavior description How it works Trees that have received medium or heavy damage from the Storm damage applier behavior have a certain probability of survival Undamaged trees and any trees with a DBH smaller than the values set in the Minimum DBH for Storm Damage in cm parameter are ignored The probability is mn expla 4 j ry H 4 4 tt pen l ezp a h Z BH t where e pis the tree s probability of survival between 0 and 1 e a is either the Storm Medium Damage Survival Prob Intercept a or the Storm Heavy Damage Survival Prob Intercept a parameter depending on the tree s damage category e bis either the Storm Medium Damage Survival Prob DBH Coeff b or the Storm Heavy Damage Survival Prob DBH Coeff b parameter depending on the tree s damage category e DBH is the tree s DBH in cm Once the survival probability has been calculated this behavior uses a random number to determine whether it lives or dies Damaged trees are only at risk of dying at the time of the storm that damages them if
66. grid cell area Fresh logs X timesteps ago Substrate favorability Grid This grid is created by either the Substrate Dependent Seed Survival No Gap Status or the Substrate Dependent Seed Survival With Gap Status behavior It holds the proportion of seeds expected to germinate on the substrate composite of the grid cell The cell resolution must match the Substrate grid above Data in the grid Data member name Description Favorability Index Species The proportion of seeds of Species X expected to germinate in X that cell Temperature Dependent Neighborhood Survival Grid This grid is created by the Temperature dependent neighborhood survival behavior It holds the timestep survival rate for each species in each grid cell Data in the grid Data member Description name The survival rate for Species X for that cell The rate is per timestep not annual aor Note that the value may be 1 if there were no trees of Species X in the grid cell Species X for that timestep Neighbor The adult neighbor basal area in square meters basal area Weibull Climate Quadrat Growth Grid This grid is created by one of the Weibull climate quadrat growth behaviors It holds the number of neighbors and the growth rate for each species Set this grid to the resolution you desire for neighborhood growth calculations This grid may not be set up with initial values Data in the grid Data member Description name Growth
67. is repeated until the harvest cut target has been reached If removing a tree will cause the harvest to overshoot its cutting target a random number is compared to the amount of overshoot to determine if the tree will be removed then harvest ends If species are to be cut in a certain proportion then separate cut targets are maintained for each species If the highest COE individual is of a species whose cut target has been reached it is not cut and Harvest Competition searches for the highest COE individuals of other species Only trees to which you have applied the Competition Harvest behavior are considered for harvesting You can only apply the behavior to saplings and adults You can specify a size range to cut using the Competition Harvest Minimum DBH to Harvest and Competition Harvest Maximum DBH to Harvest parameters The Competition Harvest behavior stores how much it actually cut each timestep in the Competition Harvest Results grid Additionally and optionally you can give the behavior a filename with the Competition Harvest Filename for List of Harvested Trees parameter If a filename is present Competition Harvest will write to this file a list of the individuals harvested each timestep for the entire run The file is a tab delimited text file with a header line and five columns X Y Species DBH and Timestep cut How to apply it Apply this behavior to saplings and or adults of any species Generalized Harvest Regim
68. is 135 cm the tallest possible seedling height Seedling Height Class 1 Upper Bound in cm The upper bound of the first seedling height class in cm for specifying seedling initial densities The lower bound of the size class is 0 Seedling Height Class 2 Upper Bound in cm The upper bound of the second seedling height class in cm for specifying seedling initial densities The lower bound of the size class is the Seedling Height Class 2 Upper Bound in cm parameter There is a third size class whose lower bound is this parameter s value and whose upper bound is 135 cm Tree Map To Add As Text External tree map file to add Basic tree population parameters required Minimum Adult DBH The minimum DBH at which trees are considered adults See more about tree life history stages here Max Seedling Height meters The maximum seedling height in meters Trees taller than this height are saplings See more about tree life history stages here e New Seedling Diameter at 10 cm The average diameter at 10 cm height value for newly created seedlings when another size is not specified Actual values are randomized slightly around this value In addition to the values listed in the parameter window the tree population also keeps the list of species and size classes These can be edited in the Tree population edit species list window and Tree population edit initial density size classes window Tree initial conditions Tree initia
69. is applied must also have a light behavior applied You can choose either a diam with auto height diam only or height only version Linear bi level growth This behavior increments growth according to a simple linear equation with the possibility of two sets of parameters for each species one for high light conditions and one for low light conditions This can also be used alone without the light levels Parameters for this behavior Parameter name Linear Bi Level Intercept for High Light Growth a Linear Bi Level Intercept for Low Light Growth a Linear Bi Level Slope for High Light Growth b Linear Bi Level Slope for Low Light Growth b Linear Bi Level Threshold for High Light Growth 0 100 How it works Description The intercept of the linear growth function used in high light conditions The intercept of the linear growth function used in low light conditions The slope of the linear growth function used in high light conditions The slope of the linear growth function used in low light conditions The threshold between low light and high light parameters as a value between 0 and 100 The equation used by this behavior to increment growth is where Y a b diam T e Y amount of diameter growth in cm e a growth intercept in high light conditions this is the Linear Bi Level Intercept for High Light Growth a parameter in low light conditions this is the Linea
70. is rooted light filter Years released E Years suppressed B Bole Vol Tree Bole Volume The absolute growth behaviors The length of the current release period in years The absolute growth behaviors The length of the current suppression period in years A flag for whether a tree has died and why Integer of one of the following 0 not dead 1 harvest 2 natural causes 3 disease 4 fire 5 insects or 6 storm This is used by the dead tree remover behavior to find the trees it should remove Any of the mortality behaviors An integer value with the damage level of a storm and how long it has been damaged A value of 0 means no damage a value starting with 1 means medium damage a value starting with 2 means complete damage The digits at the end count how many years since the damaging event For example a value of 1005 is a tree that received medium damage 5 years ago Tree bole volume calculator The volume of a tree in cubic feet Tree Biomass of the tree in metric tons Dimension Biomass Float nee oeerreee Biomass Mg analysis Tree Age Age of the tree in years Tree age Snag Decay aie Pedy SnagDecayClass Integer Snag decay class Class Dynamics New Break Snag break height if the break Snag Decay NewBreakHeight Float occurred this timestep 1 if the Class Height snag is unbroken Dynamics Snag Old Snag break height if the break Snag De
71. it is applied must also have a Disperse behavior applied as well Neighborhood seed predation This simulates seed predation as a function of tree neighborhood and masting events The same equations are used to calculate the amount of seed eaten but there are different parameters for masting and non masting timesteps Masting events can be determined in one of two ways by seed levels rising above a threshold that you set or by masting having occurred as defined by one of the masting disperse behaviors Parameters for this behavior Parameter name Description Neighborh ore hor opd Determines which species are included when totaling up seed numbers to Predation Counts determine whether or not masting has occurred For Masting Neighborhood Determines how masting is decided If this is set to Seed threshold Predation Mast then masting events occur when seed levels are above a set threshold If Event Decision this is set to Ask disperse then masting has occurred if any of the Method Neighborhood Predation Masting po Neighborhood Predation Species i Masting pn Neighborhood Predation Masting Seed Density m2 yr Neighborhood Predation Minimum Neighbor DBH cm Neighborhood Predation Neighbor Search Radius m Neighborhood Predation Non Masting p0 Neighborhood Predation Species i Non Masting pn How it works applicable species masted as determined by the
72. lignin Foliar Chemistry N Goncenttion The proportion of foliar dry weight 0 1 that is N Foliar Chemistry P COO The proportion of foliar dry weight 0 1 that is P Foliar Chemistry Phenolics The proportion of foliar dry weight 0 1 that is phenolics Concentration Foliar Chemistry A Coan The proportion of foliar dry weight 0 1 that is specific leaf area Foliar Chemistry Tannins The proportion of foliar dry weight 0 1 that is tannins Concentration How it works For each tree the foliar dry weight is calculated as F a DBH where e F foliar dry weight in kg e a the Foliar Chemistry Foliar Weight a parameter e b the Foliar Chemistry Foliar Weight b parameter e DBH tree s DBH in cm For each component the amount is the tree s foliar dry weight multiplied by the parameter for that component s concentration The weight of each component in metric tons is summed for each species and saved in a grid called Foliar Chemistry You can save these values in a detailed output file for analysis You of course can skip any of the components by entering 0 s for their concentration parameter values How to apply it Apply this behavior to saplings adults or snags of any species This behavior does not automatically create output Once you have added this behavior to your run the Detailed output grid setup window will list the Foliar Chemistry grid You can then view the contents of this grid a
73. mounds area to the grid cell where it was rooted Saplings never create tip up mounds Fallen adults create new tip ups with the probability specified in the Proportion of Fallen that Uproot parameter snags contribute at the probability in Proportion of Fallen that Uproot Relationship 7 results from harvests only Scarified soil creation results from the use of machinery and skidding during a harvest Parameters for this behavior Parameter name Description Clear Cut Proportion The proportion of substrate that is decayed logs in areas that had a clear of Decayed Logs cut harvest event as a value between 0 and 1 This is not required if the Clear Cut Proportion of Fresh Logs Clear Cut Proportion of Scarified Soil Clear Cut Proportion of Tip Up Mounds Decayed Log Annual Decay Alpha Decayed Log Annual Decay Beta Fresh Log Annual Decay Alpha Fresh Log Annual Decay Beta Gap Cut Proportion of Decayed Logs Gap Cut Proportion of Fresh Logs Gap Cut Proportion of Scarified Soil Gap Cut Proportion of Tip Up Mounds Clear Cut Proportion of Scarified Soil Harvest behavior is not used The proportion of substrate that is fresh logs in areas that had a clear cut harvest event as a value between 0 and 1 This is not required if the Harvest behavior is not used The proportion of substrate that is scarified soil in areas that had a clear cut harvest event as a value between 0 and 1 This is not required if
74. os fics fan fossa m fie pa f f e fs reo arr fn s o fio re fs foe pr aeo feco ron Joos eo Yo fs is faz fasas sor irre zos 2307 aos Form Class 85 oes ee e fs6 efi o fos rw o m fo e pe awe f ies pe fpr fase is fo fas foe E wo pr por ps E fas f2 fee af s pas foss oss i f fo or as fous feo fro fes How to apply it Apply this behavior to saplings adults or snags of any species and enter parameters in the Parameter edit window This behavior does not automatically create output Once you have added this behavior to your run the Detailed output setup window for trees will have a tree data member called Merchantable Value Add this to your detailed output file to output volume in cubic feet You can also use the Detailed output grid setup window to save the data members in the Merchantable Timber Value grid which contains the total value for each species You can then view the contents of this grid as a table using SORTIE s data visualization system Partitioned DBH Biomass This behavior calculates biomass as a linear function of DBH partitioned into leaf branch and bole biomass Parameters for this behavior Parameter name Description lt th Partitioned DBH Biomass Bole The slope in the linear biomass equation for boles Slope a Partitioned DBH Biomass Bole The intercept in the linear biomass equation for boles Intercept b
75. plot Actual sizes are chosen randomly from a uniform distribution within each size class Tree maps Tree maps are lists of individual trees You can add one or more maps to your parameter file The maps can come from detailed output files from other runs or you can make your own tab delimited tree maps The preferred method of incorporating a tree map to a run is to add it directly into a parameter file However if the number of trees is very large it may make the XML file too big to read In this case a text tree file s filename can be added to the parameter file instead and SORTIE can read the trees directly from the file Choosing how to set up the initial conditions In most cases you would define your initial conditions using DBH size classes They are simple to define and describe There are cases where you would need a tree map For example e You intend to model a particular real life plot e You want to use a mid run timestep of another simulation as the starting point of a new simulation e You want a particular spatial pattern of trees instead of a random distribution e You want to do a set of simulations that all start out exactly the same way You can mix the two methods as well If you have a tree map of adults you d like to use you can add seedlings and saplings using size classes It is important to consider initial conditions for juveniles It can take awhile for seed dispersal establishment and recruitment to cr
76. plot as a whole not for individual cells of the seed grid This offtake rate is then available for use by the Neighborhood seed predation behavior inked behavior and no further action is taken This behavior can be used in the same run with the non linked version of this behavior The two sets of species are kept completely separate and there are two separate sets of parameters How to apply it This behavior may be applied to seeds of any species Any species to which it is applied must also have a Disperse behavior applied as well Presumably the Neighborhood seed predation behavior linked behavior will be applied to the same set of species and should be placed after this behavior in the ordered list of model behaviors Neighborhood seed predation linked Parameters for this behavior Parameter name Description Neighborhood Predation p0 The pO term in the seed offtake equation when in linked mode Mienborkood The pn term for species i in the seed offtake equation when in linked Predation Species i nan mode pn Neighborhood Predation The minimum DBH of trees to be included when calculating the basal Minimum Neighbor area composition of the neighborhood when in linked mode DBH cm Neighborhood Predation Neighbor Search Radius m The radius to search for trees when calculating the basal area composition of the neighborhood when in linked mode How it works This behavior is used tog
77. season 1 The seed predator population demographic efficiency for season 2 The coefficient describing the effect that density dependent factors have on the predator population instantaneous rate of change in season 1 The coefficient describing the effect that density dependent factors have on the predator population instantaneous rate of change in season 2 The predator population foraging efficiency for each seed species If true this means that the final predator density at the end of the behavior mini model run is the initial density for the next mini model run If false every time the behavior mini model runs it is re initialized with the value of the Predator initial density num sq m parameter The maximum rate of decline in the predator population in the absence of any food in predators per week for season 1 The maximum rate of decline in the predator population in the absence of any food in predators per week for season 2 The maximum number of seeds of each species that can be eaten by one predator in one day The number of weeks at the beginning of the behavior mini model run that seedfall occurs Seedfall Occurs Func Resp Predator Initial Density num sq m Func Resp Proportion of Seeds Germinating Each Week Func Resp Seed Predation Output Filename If Desired Func Resp Week Germination Begins Func Resp Week Season 2 Begins Func Resp Weeks to Run Seed Predation Model 1
78. second age class of snag light transmission Snags with an age greater than the upper limit for size class 1 but less than or equal to this age have a light transmission coefficient matching Snag Age Class 2 Light Transmission Coefficient Snags with an age greater than this value are in age class three If your run does not work with snags you can ignore this This behavior calculates a Sail Light index value for each individual of each tree type to which it is assigned Sail Light values go from 0 full sun to 1 full shade How to apply it This behavior may be applied to seedlings saplings and adults of any species Storm Light behavior This behavior calculates light levels as a function of number of trees damaged in storms Light levels are stored in a grid for later retrieval by other behaviors this behavior does not directly assign light to trees Parameters for this behavior Parameter name Storm Light Intercept of Light Function Storm Light Max Radius m for Damaged Neighbors Storm Light Max Years Damaged Trees Affect Light Storm Light Max Years Snags Affect Light Storm Light Minimum Trees For Full Canopy Storm Light Slope of Light Function Storm Light Standard Deviation Storm Light Stochasticity Description Intercept of the function to determine light level The maximum distance in meters within which the Storm Light behavior searches for damaged trees The m
79. seeds are assumed to be equally available however each species can have its own parameters for actual consumption rate The initial number of predators is calculated from the Predator initial density num sq m parameter or if the mini model has run before and the Preserve predator densities between SORTIE timesteps parameter is set to true from the final density of the last mini model run The behavior mini model run begins at the part of the year in which seedfall occurs The number of seeds in the seed rain is the total seed pool which is evenly divided over the user defined seed rain length The predator population has as a food source the number of seeds added during the current week s rain if the rain is going on plus any leftover seeds from previous weeks which have not been consumed Beginning at a certain week in the spring the number of seeds available to the mice is further reduced by a certain percentage each week to simulate germination Once germination begins it continues until the predator model finishes running In order to correctly calculate mouse consumption and ensure that the seeds which germinate are actually available later the behavior keeps track of the seeds actually consumed it is this number which is subtracted from total seeds at the end Seed offtake for each week is calculated as O X IR N where e Ois offtake total number of seeds consumed e IR is per capita seed offtake for each species e Nis the nu
80. species even if they don t all use light Fraction of light transmitted through the snag tree crown for each species Applies to those snags whose age is less than or equal to Upper Age Yrs of Snag Light Transmission Class 1 Expressed as a fraction between 0 and 1 If your run does not work with snags you can ignore this Otherwise a value must be provided for all species Fraction of light transmitted through the snag tree crown for each species Applies to those snags whose age is greater than Upper Age Yrs of Snag Light Transmission Class 1 but is less than or equal to Upper Age Yrs of Snag Light Transmission Class 2 Expressed as a fraction between 0 and 1 If your run does not work with snags you can ignore this Otherwise a value must be provided for all species Fraction of light transmitted through the snag tree crown for each species Applies to those snags whose age is greater than Upper Age Yrs of Snag Light Transmission Class 2 Expressed as a fraction between 0 and 1 If your run does not work with snags you can ignore this Otherwise a value must be provided for all species The upper age limit in years defining the first age class of snag light transmission Snags with an age less than or equal to this age have a light transmission coefficient matching Snag Age Class 1 Light Transmission Coefficient If your run does not work with snags you can ignore this The upper age limit in years defining the
81. species of tree to which it is being applied The increment is calculated as described in the Constant radial growth behavior Note that the increment parameter specifies radial growth the behavior makes all necessary conversions How to apply it This behavior can be applied to seedlings saplings and adults of any species Any tree species type combination to which it is applied must also have a light behavior applied You can use either the diam with auto height or diam only version Relative growth limited to basal area increment How it works This behavior calculates an amount of diameter growth according to the relative growth equation Growth is limited to a maximum of a constant basal area increment The amount of diameter increase is calculated by dividing the annual basal area increment of the tree s species by the diameter of the tree The increment is calculated as described in the Constant basal area growth behavior How to apply it This behavior can be applied to seedlings saplings and adults of any species Any tree species type combination to which it is applied must also have a light behavior applied You can use either the diam with auto height or diam only version Non limited relative growth How it works The amount of increase returned by the relative growth equation is applied to the tree How to apply it This behavior can be applied to seedlings saplings and adults of any species Any tree species type
82. square meter for a species has been calculated it is multiplied by the grid cell area and number of years per timestep to determine the final number of seeds to add to the grid cell How to apply it Apply this behavior to adults of the species you wish to use Seed predation behaviors Seed predation occurs after seed dispersal has occurred and serves to reduce the number of seeds by simulating seed consumption by predators Behavior Description Functional response seed Simulates functional response seed predation where the number of predators is predation a function of the amount of food that has been consumed behavior Neighborhood seed predation behavior Simulates seed predation as a function of tree neighborhood and masting events Functional response seed predation behavior linked Neighborhood seed predation Works together with the Neighborhood seed predation behavior linked behavior to model seed predation Works together with the Functional response seed predation behavior linked behavior to model seed predation behavior linked Functional response seed predation This behavior simulates functional response seed predation where the number of predators is a function of the amount of food that has been consumed Since seed predator life cycles are often very short this behavior runs as a mini model within the context of the larger simulation It simulates weekly timesteps of seed fal
83. substrate that is scarified soil in areas that had a clear cut harvest event as a value between 0 and 1 This is not required if the Harvest behavior is not used Clear Cut Proportion of Tip Up Mounds Decayed Log Annual Decay Alpha Decayed Log Annual Decay Beta Fresh Log Annual Decay Alpha Fresh Log Annual Decay Beta Gap Cut Proportion of Decayed Logs Gap Cut Proportion of Fresh Logs Gap Cut Proportion of Scarified Soil Gap Cut Proportion of Tip Up Mounds Initial Conditions Proportion of Decayed Logs Initial Conditions Proportion of Fresh Logs Initial Conditions The proportion of substrate that is tip up mounds substrate in areas that had a clear cut harvest event as a value between 0 and 1 This is not required if the Harvest behavior is not used oer The a exponent in the decay equation logs Note that this is annual decay as applied to decayed p The B exponent in the decay equation as applied to decayed logs Note that this is annual decay Pen The a exponent in the decay equation logs Note that this is annual decay as applied to fresh aro as applied to fresh The B exponent in the decay equation logs Note that this is annual decay The proportion of substrate that is decayed logs in areas that had a gap cut harvest event as a value between 0 and 1 This is not required if the Harvest behavior is not used The proportion of substrate t
84. t matter where you put your parameter files or where you write your output but if you move parameter files around SORTIE ND may not be able to find them when it runs your batch Once all of your parameter files are ready create and save your batch file Batch runs and output Parameter files being run in batches can write output files If you are running a parameter file more than once SORTIE ND will automatically rename each run s output files so that they will be numbered sequentially For instance if your parameter file saves a file called my_out out and you use a batch to run the file three times you will get the following output files my out _1 out my out 2 out and my out 3 out Running a batch Once you have created a batch file you can run it by choosing Model gt Run Batch This allows you to select the batch file you have created Once you have selected it SORTIE ND will begin running your batch You do not have to have a parameter file of any kind loaded into SORTIE ND to begin a batch run If you have a parameter file currently loaded it will have no effect on the batch run You cannot view output during a batch run like you can with a single run This is because of the difficulty SORTIE ND would have in managing the many possible output files You also cannot pause a batch run only stop it However if you do stop a batch run any output that was created before you stopped it will still be present and available
85. that number back to the Dispersed Seeds grid cell If there is only one seed in a grid cell it always survives How to apply it Apply this behavior to seeds of your desired species Any species to which it is applied must also have any disperse behavior applied Establishment with Microtopography This behavior germinates seeds into seedlings It simulates microtopography in the plot and assigns new seedlings a rooting height as a function of the type of substrate on which they land from the Substrate behavior This behavior is designed to work with both the Substrate and the Beer s law light filter behaviors to simulate shading by ferns The rooting height that seedlings get influences the amount of light they receive Seeds that land on fresh logs in addition are eligible for a respite from the Beer s law light filter behavior Parameters for this behavior Parameter name Description Mean Height of Fresh Log Substrate The mean height of fresh log substrate in meters inm Mean Height of The mean height of mounded areas in meters Mounds in m Years Respite from Fern Shading for Seeds on Fresh Logs The maximum number of years that seeds can get respite from fern shading as implemented by the Beer s law light filter behavior Proportion of Plot A Mond Proportion of the plot area that is mound area between 0 and 1 Standard Deviation of Fresh Log Substrate Height in m The standard deviation of heig
86. the Michaelis Menton growth function at high light function term A for height growth Slope of the Michaelis Menton growth function at zero light function term S below The exponent to be used with diameter when calculating relative growth Relative growth is calculated with the equation where Axte FT FT AFG Ae 777 oe TTL fa e Yis the amount of annual relative growth e Ais the Asymptotic Diameter Growth A or Asymptotic Height Growth A parameter e Sis the Slope of Growth Response S or Slope of Height Growth Response S parameter e GLI is the global light index calculated by a light behavior Diameter growth is compounded over multiple timesteps with the equation G Y 1 1 diam where e Gis the amount of diameter growth for the timestep in cm e diam is the diameter of the tree in cm at 10 cm height if seedling or sapling or DBH if adult e Tis the number of years per timestep e Xis the Relative Michaelis Menton Growth Diameter Exponent parameter Relative height growth is calculated slightly differently The details are discussed in the section for the Relative growth height only behavior below Relative growth is discussed in Pacala et al 1996 Relative growth limited to radial increment How it works This behavior calculates an amount of diameter growth according to the relative growth equation Growth is limited to a maximum of the constant radial growth increment for the
87. the Tree Age Calculator behavior applied Temperature dependent neighborhood survival This behavior assesses tree survival as a function of mean annual temperature and neighbor adult basal area For efficiency it calculates survival rates for cells in a grid and assigns trees the survival probability of the grid cell in which they are found Trees killed by this behavior will have a mortality reason code of natural Parameters for this behavior Parameter name Description Temp Dependent Neighborhood Surv A in the survival function A Temp Dependent Neighborhood Surv B in the survival function B Temp Dependent Neighborhood Surv M in the survival function M Temp Dependent Neighborhood Surv N in the survival function N Temp Dependent Neighborhood Surv Neigh Search Radius m Maximum radius to search for crowding neighbors in meters How it works This behavior uses the Temperature Dependent Neighborhood Survival grid to keep track of survival rates The annual probability of survival for a given species and given grid cell is calculated as 2 _ _ A BAT os Surv e e N where e Surv is the annual probability of survival e A is the Temp Dependent Neighborhood Surv A parameter e Bis the Temp Dependent Neighborhood Surv B parameter e Mis the Temp Dependent Neighborhood Surv M parameter e Nis the Temp Dependent Neighborhood Surv N parameter e Tis the mean annual temperature
88. the behavior represents the probability of falling during the timestep as ee Pr fall __ fix Sx a Pspp Yde In DBH y In DBH x BAy where e Pr fall is the probability of the snag falling e ais the Snag Decay Class Dynamics Snag Fall Alpha parameter Pspp is the Snag Decay Class Dynamics Snag Fall Beta parameter for the tree s species e Yac is the Snag Decay Class Dynamics Snag Fall Gamma X parameter where X is the snag s decay class e DBH is the DBH in cm e Cis the Snag Decay Class Dynamics Snag Fall Zeta parameter e 7 is the Snag Decay Class Dynamics Snag Fall Eta parameter e xis the Snag Decay Class Dynamics Snag Fall Kappa parameter e BAzis the basal area m2 ha of harvested trees in the current snag s cell of the Snag Decay Class Dynamics Basal Area grid Trees and snags that fall are removed completely from SORTIE and are not available for processes such as substrate If a tree or snag does not fall it s condition at the end of the timestep will be represented by a snag decay class Decay class 1 is the least decayed condition and decay class 5 is the most decayed Parameters should be entered to specify the probability of going from a live tree or one of five decay classes to each of the higher decay classes over a five year timestep given that the snag is still standing The transition probabilities for each initial condition must sum to 1 For all models parameter values should correspo
89. the effects of climate change If the run does not have a behavior that uses temperature this will have no effect Parameters for this behavior Parameter name Description Temperature Change B B in the function for varying temperature through time Temperature Change C C in the function for varying temperature through time Temperature Change Temp Lower The lower bound for allowed temperature values Bound Temperature Change a Ulnar Bema The upper bound for allowed temperature values How it works The value for plot temperature is a function of time elapsed since the start of the run as follows T T B where e Tis the mean annual temperature in degrees C at time t e Tis the mean annual temperature value at the start of the run as assigned in the Plot parameters e Bis the Temperature Change B parameter e Cis the Temperature Change C parameter e tis the time elapsed in years since the start of the run This value is then given to the Plot object which makes it available to other behaviors in the run You can set bounds on the possible temperature values using the Temperature Change Temp Lower Bound and Temperature Change Temp Upper Bound parameters Values are not allowed to go outside these limits How to apply it Add this behavior to the run You can use it alone or in addition to the Precipitation Climate Change behavior You do not need to assign this behavior to trees Disturb
90. the first canopy cell it reaches How to apply it Apply this behavior to all trees of at least the minimum reproductive age for your chosen species If the minimum reproductive age is less than the Minimum adult DBH be sure to apply this behavior to saplings as well as adults In the parameters choose the appropriate probability distribution function for each species for each forest cover type This behavior can be used to simulate the suckering of stumps Apply this behavior to tree type stump of your chosen species Stumps reproduce like other parent trees except they always assume they are in a gap They use the same probability distribution function and parameters as live members of their species but they get their own B and STR values so that they can produce different numbers of seeds Masting spatial disperse behavior This behavior is a variant of the Non gap spatial disperse behavior that adds masting and more stochasticity in seed production Parameters for this behavior Parameter name Description The probability distribution function to be used to distribute seeds in canopy conditions For the behaviors Non gap spatial disperse and Masting spatial disperse these PDFs are always the ones used Canopy Function Used The mean of the lognormal function under canopy conditions or under Lognormal Canopy non masting conditions in the case of Masting spatial disperse see Xo equation below This is only required if the can
91. the last or current period of suppression in years Details of this model are published in Wright et al 2000 Absolute growth limited to radial increment How it works This behavior calculates an amount of diameter growth according to the absolute growth equation Growth is limited to a maximum of the constant radial increment for the species of tree to which it is being applied The increment is calculated as described in the Constant radial growth behavior Note that the increment parameter specifies radial growth the behavior makes all necessary conversions How to apply it This behavior can be applied to seedlings saplings and adults of any species Any tree species type combination to which it is applied must also have a light behavior applied You can use either the diam with auto height or diam only version Absolute growth limited to basal area increment How it works This behavior calculates an amount of diameter growth according to the absolute growth equation Growth is limited to a maximum of a constant basal area increment The amount of diameter increase is calculated by dividing the annual basal area increment of the tree s species by the diameter of the tree The increment is calculated as described in the Constant basal area growth behavior How to apply it This behavior can be applied to seedlings saplings and adults of any species Any tree species type combination to which it is applied must also have
92. the size dependent annual growth potential for diameter growth Shape parameter 1 for shade reduction of annual growth for diameter growth Shape parameter 2 for shade reduction of annual growth for diameter growth Slope of the size dependent annual growth potential for diameter growth Intercept of the size dependent annual growth potential for height growth Shape parameter for shade reduction of annual growth for height growth Shape parameter 2 for shade reduction of annual growth for height growth Slope of the size dependent annual growth potential for height growth This behavior calculates annual diameter or height increases as where a b t dian e a GLI 1 e Y amount of diameter increase in mm or the amount of height increase in cm e a Size Dep Logistic Diam Intercept a parameter for diameter growth or the Size Dep Logistic Height Intercept a parameter for height growth e b Size Dep Logistic Diam Slope b parameter for diameter growth or the Size Dep Logistic Height Slope b parameter for height growth e c Size Dep Logistic Diam Shape Param 1 c parameter for diameter growth or the Size Dep Logistic Height Shape Param 1 c parameter for height growth e d Size Dep Logistic Diam Shape Param 2 d parameter for diameter growth or the Size Dep Logistic Height Shape Param 2 d parameter for height growth e GLI global light index as
93. the standard deviation of the function in seeds per m If you have not chosen these PDFs then this parameter is not required Non spatial disperse calculates how many seeds to distribute as where A u BA K e Ais the mean number of seeds per m e is the Slope Mean Non Spatial Seed Rain seeds m2 ha of BA yr parameter e BA is the basal area of the parent species in m e xis the Intercept of Mean Non Spatial Seed Rain seeds m2 yr parameter From this the number of seeds per grid cell of the Dispersed Seeds grid is calculated and then that number is added to each grid cell In the equation above u is the basal area dependent seed rain term Setting this value to zero turns off density dependent seed rain x is the bath seed rain term Setting this value to zero turns off bath seed rain How to apply it Apply this behavior to adults of the species you wish to use non spatial disperse Masting non spatial disperse behavior This behavior adds stochasticity to basic seed rain by simulating masting and basic inter year variation in seed production Parameters for this behavior Parameter name Description ee p value for the binomial distribution used to randomly decide whether to mast each timestep Chance P Species in the same group always mast together If all the group numbers are different then each species masts separately The actual numbers do not matter just whether species have identical numbers
94. to Diameter at 10 cm Relationship The slope of the linear relationship between the DBH in cm and the diameter at 10 cm height in cm in small trees Used by all species DBH and diamyo are related as follows DBH diamjo R I where e DBH is the DBH in cm e diam ois the diameter at 10 cm height in cm e Ris the Slope of DBH to Diameter at 10 cm Relationship parameter e Iis the Intercept of DBH to Diameter at 10 cm Relationship parameter The standard diameter height relationships Standard is one of the names used to describe a set of allometric functions relating height to diameter There is one for adults and saplings and one for seedlings These are called standard because they were the original SORTIE functions and until recently were the only choices Parameters Parameter name Description The maximum tree height for a species in meters No tree no matter what allometric function it uses is allowed to get taller than this Used by all species Maximum Tree Height in meters Slope of Asymptotic Exponential decay term in the adult and sapling standard function for Height DBH and height S10 pe or Heihi The slope of the seedling standard function for diameter at 10 cm and Diameter at 10 cm height Relationship The standard sapling and adult DBH height function is height 1 35 H 1 35 1 8 PB where e height is tree height in meters e H is the Maximum Tree Height in m parameter
95. tree even if the allometric equations would produce a different result This feature is useful if you intend to use growth behaviors that separately increment diameter and height for your trees When in doubt use 0 Adding extra data to the tree map You can add additional data to the tree map beyond the first six columns You can add extra columns for any item in the Tree data member list Put the short code name in the column header There must be a value for each tree for each column but if that data piece does not apply to that tree it will be ignored Even data that will be ignored must be of the proper type don t use a value such as NA in a column of integers for example Using tree maps Tree maps can be loaded into SORTIE ND only if there is a parameter file loaded as well The data in the tree map is expected to match the parameter file all species in the tree map must be present in the parameter file and height values must not exceed the maximum height limits The the Once you have prepared a tree map file according to the format below and once you have loaded a compatible parameter file use the File gt Open file command to load your tab delimited tree map file If you save your parameter file after this point the tree map will be included in it To work with the tree map trees further including removing them use the Manage tree maps window SORTIE ND will not alter your tab delimited tree map file Converting pr
96. 0 for Low Light Growth parameter e X in high light conditions this is the Lognormal Bi Level Xb for High Light Growth parameter in low light conditions this is the Lognormal Bi Level Xb for Low Light Growth parameter e H tree height in meters e T number of years per timestep Light levels come from the Storm Light grid produced by the Storm Light behavior The threshold between the use of high light and low light parameters is set in the Lognormal Bi Level Threshold for High Light Growth 0 100 parameter This behavior can also be used without Storm Light In this case only the low light growth parameters are used How to apply it This behavior can be applied to seedlings saplings and adults of any species Any tree species type combination to which it is applied must also have a diam only growth behavior applied If you wish to use the light level parameter switch also use the Storm Light behavior Lognormal with exponential shade reduction This behavior does either diameter or height growth as a function of tree size and GLI Parameters for this behavior Parameter name Description Lognormal Diam Effect of Shade Effect of shade for diameter growth Lognormal Diam Growth Increment at Diam 36 in mm yr a Lognormal Diam Shape Parameter b Annual growth increment at diameter 36 in mm yr for diameter growth Shape parameter for diameter growth Lognormal Height Eiee oi Sha
97. 1 The grid resolution default is 8 m X 8 m You can change this to whatever you wish but if you are also using the grid Storm Susceptibility the resolutions must match Data in the grid Data member Description name The mean storm damage index for all storms occurring in the past timestep omae i from 0 no damage to 1 total damage Time Since Last The number of years since the last storm occurred in this cell The last storm Storm is any storm at all of any strength Packages Data member name Description Single Storm Damage Index Storm damage index for a single storm event Storm Killed Partitioned Biomass Grid This grid is created by the Storm Killed Partitioned DBH Biomass and Storm Killed Partitioned Palm Biomass behaviors This is where the amount of biomass is stored partitioned into leaf bole and branch if applicable biomass All data is stored raw no conversion to per hectare amounts The grid cell resolution is set to 8 m X 8 m You can change this to whatever you wish The grid is shared by the two behaviors mentioned above so changing it for one changes it for both Data in the grid Data member name Description Mg Leaf Biomass for species X Amount of storm killed leaf biomass for species X in Mg Mg Bole Biomass for species X Amount of storm killed bole biomass for species X in Mg Amount of storm killed branch biomass for species X in Mg Branch Biomass for species X Mg Mg Leaf Palm
98. Analysis behaviors Analysis behaviors are those whose only purpose is to prepare data for output They do not change model state such as growing trees or updating grid values They assemble calculate or analyze data for the user Behavior Description Carbon Value Calculates the amount of carbon per species and its value Dimension Calculates the biomass of trees based on DBH This approach comes from Analysis Jenkins et al 2004 Foliar Chemie Calculates chemistry components as a function of DBH Merchantable z Calculates the value of merchantable timber Timber Value e Calculates biomass as a linear function of DBH partitioned into leaf branch and bole biomass Biomass oa Calculates biomass as a linear function of tree height partitioned into leaf and bole biomass Biomass Ripley s K Calculates the Ripley s K function for all trees in the plot as well as for the Calculator members of each species Relative Neighborhood Calculates the relative neighborhood density index Q as described in Condit et Density al 2000 Calculator State Reporter Reports the values of state variables Storm Killed Partitioned Calculates biomass of trees killed in storms as a linear function of DBH DBH partitioned into leaf branch and bole biomass Biomass Storm Killed Partitioned Calculates biomass of trees killed in storms as a linear function of tree height Height partitioned into leaf and bole biomass Bio
99. BH for its species it becomes an adult Tree life history stage transitioning death Death also produces tree life history stage transitions Behaviors can request to a tree population that a tree be killed How the tree population responds to this request depends on the type of tree the reason for death and the type of run Mortality reasons The reasons why a tree is killed are e Natural mortality e Harvest e Insects e Fire e Disease Check the documentation for your chosen disturbance behaviors and mortality behaviors for more information on which codes will apply to your run There are life history stages for dead trees but a run may not be set up to handle them The tree population takes this into account It examines the run to see if any behaviors directly deal with stumps and snags If either is the case the run is classified as stump aware and or snag aware Here s what happens to a tree to be killed in different situations e Ifa tree is a seedling it is deleted from memory no matter why it died e Ifa tree is a sapling or adult killed in a harvest and the run is stump aware the tree is converted to a stump e Saplings killed for any other reason or by harvest in a run that is not stump aware are deleted from memory e Ifthe tree is an adult killed by harvest and the run is not stump aware it is deleted from memory e Ifthe tree is an adult killed for any reason other than harvest and the run
100. CI is calculated as DBH S N fq NCI X gt i ee ee j 1 k 1 ik where e the calculation sums over j 5 species and k N neighbors of each species of at least a DBH of NCI Minimum Neighbor DBH in cm out to a distance of NCI Max Radius of Crowding Neighbors in m e ngis the storm damage parameter of the kth neighbor depending on the damage status optional If the neighbor is undamaged the value is 1 If the neighbor has medium damage the value is the NCI Neighbor Storm Damage eta Medium 0 1 parameter for the target species If the neighbor has complete damage the value is the NCI Neighbor Storm Damage eta Complete 0 1 parameter for the target species To omit the storm damage term set all values for the above two parameters to 1 e ais the NCI Alpha parameter for the target tree s species e fis the NCI Beta parameter for the target tree s species e DBH is the DBH of the kth neighbor in cm e qis the NCI DBH Divisor q parameter Set this to a value greater than 1 to rescale the competitive effects of neighbors e Aix is the Species j NCI Lambda parameter for the target species relative to the kth neighbor s species e distance 1s distance from target to neighbor in m The value of Damage Effect is optional If you elect not to use storms in your run set all values in the NCI Damage Effect Medium Storm Damage 0 1 and NCI Damage Effect Complete Storm Damage 0 1 parameters to 1 If you are us
101. I Weibull d or Height GLI Weibull Browsed d parameter e H tree height in meters e GLI light level between 0 and 100 of full sun If the timestep length is not one year the actual probability of mortality for the timestep is calculated as p 1 1 p where p is the annual probability of mortality p is the timestep probability of mortality and T is the number of years per timestep Once the mortality probability for the timestep is known for a tree then a random number is compared to this probability to determine if the tree lives or dies Light levels can come from any of the light behaviors that directly assign a tree its light level It is expected that this is a GLI value from 0 to 100 of full sun Whether or not a tree is browsed is determined by the Random browse behavior If the Random browse behavior does not apply to a tree or is not present in the run the unbrowsed parameters are always used The other parameters can be ignored How to apply it This behavior can be applied to seedlings saplings and adults of any species You must also use a light behavior If you wish to include the effects of herbivory also include the Random browse behavior in the run Insect Infestation Mortality This behavior causes mortality in trees that are infested with insects as determined by the Insect Infestation behavior Trees killed by this behavior will have a mortality reason code of insect Parameters for this be
102. If it is autocorrelated the previous year s stochastic factor SF is added to Y to determine height growth If it is not autocorrelated a new value for SF is drawn If you do not wish to use autocorrelation set the value of the autocorrelation parameter to zero Autocorrelation is ignored if there is no growth stochasticity If the timestep is more than one year long growth is recalculated for each year of the timestep increasing the height each time Stochasticity and autocorrelation are also evaluated on a yearly basis How to apply it This behavior can be applied to seedlings saplings and adults of any species Any tree species type combination to which it is applied must also have a light behavior and a diameter growth behavior applied Michaelis Menton with photoinhibition height only This behavior uses a modified Michaelis Menton function to do height growth Parameters for this behavior Parameter name Description Michaelis Menton with Photoinhibition Alpha parameter Alpha Michaelis Menton with Photoinhibition Beta parameter Cannot be equal to zero Beta Michaelis Menton with Photoinhibition D parameter D Michaelis Menton Phi parameter with Photoinhibition Phi How it works The amount of height growth is calculated as a 1 BsGu a i en 0 ou where e Yis the amount of height growth for one year in cm e GLI is the light level e ais the Michaelis Menton with Photoinhibition
103. It loads much faster and contains raw data in a format you can use outside of SORTIE without any kind of conversion If you want to look at changes in tree basal area and density through time save a summary output file and use it to look at these charts When you are first setting up new runs you are likely to be testing your parameters to make sure they are all right You will probably be doing several short runs until you are confident that you have chosen the correct behaviors and entered your parameters correctly At this point you might want to save a lot of data and run for small numbers of timesteps so you can examine all aspects of a run to make sure it is progressing the way you want Create a detailed output file and have it save at least X Y and diameter information for all trees save grids for things such as substrate conditions and dispersed seeds so you can look at maps and save a summary output file so you can quickly examine line graphs and tables of basal area and density through time Do short runs and examine output until you are confident that your parameter file is set up correctly When you are doing a set of research runs OR you are doing long runs save the bare minimum of data that you require in order to make your output files as small as possible and to make working with them quicker and easier If all you care about is plotwide amounts of basal area and density use a summary file only If you want that plus a DBH dis
104. Minimum DBH parameter Any target tree whose DBH is less than this value will get a size effect based on the minimum DBH instead This allows you to avoid problems with very small trees that can occur because of the shape of the lognormal function Precipitation Effect is calculated as T r o PE where e Ais the Weibull Climate Survival Precip Effect A parameter e Bis the Weibull Climate Survival Precip Effect B parameter e Cis the Weibull Climate Survival Precip Effect C parameter e Ps the plot s annual precipitation in millimeters as entered for the Plot Temperature Effect is calculated as ae ec Oy A TE where e Ais the Weibull Climate Survival Temp Effect A parameter e Bis the Weibull Climate Survival Temp Effect B parameter e Cis the Weibull Climate Survival Temp Effect C parameter e Tis the plot s annual mean temperature in degrees Celsius as entered for the Plot Crowding Effect is calculated as CE e C DBHY ND where e Cis the Weibull Climate Survival Competition Effect C parameter e DBH is of the target tree in cm e yis the Weibull Climate Survival Competition Effect gamma parameter e Dis the Weibull Climate Survival Competition Effect D parameter e ND is the number of neighbors with a DBH greater than the target tree s DBH The ND value is a count of all larger neighbors with a DBH at least that of the Weibull Climate Survival Minim
105. NCI Maximum Potential Growth cm yr parameter Size Effect Shading Effect Crowding Effect and Damage Effect are all factors which act to reduce the maximum growth rate and will vary depending on the conditions a tree is in Each of these effects is a value between 0 and 1 In the Competition mortality behavior the following measure is used as predictor variable for probability of mortality Relative increment Growth PG The relative increment is the ratio between the growth for an individual tree and the maximum growth possible for that tree The Growth is the tree s growth for the previous timestep PG is calculated as follows PG Max Growth SE where Max Growth is the NCI growth parameter NCI Maximum Potential Growth cm yr and SE is the Size Effect Size Effect is calculated as follows 0 5 SE e Xb In DBH where e DBH 1s of the target tree in cm e Xo is the NCI Size Effect Mode in cm X0 NCI growth parameter e Xis the NCI Size Effect Variance in cm Xb NCI growth parameter Once the relative increment for an individual tree has been calculated the probability of mortality for that individual is calculated in the following way Prob Z relative increment max where e Prob is the probability of mortality e Zis the Competition Mortality Shape Parameter Z parameter e maxis the Competition Mortality Maximum Parameter max parameter which indicates the maximum relative increment subjec
106. Otherwise a value must be provided for all species The upper age limit in years defining the first age class of snag light extinction Snags with an age less than or equal to this age have a light extinction coefficient matching Snag age class 1 light extinction coefficient If your run does not work with snags you can ignore this The upper age limit in years defining the second age class of snag light extinction Snags with an age greater than the upper limit for size class 1 but less than or equal to this age have a light extinction coefficient matching Snag age class 2 light extinction coefficient Snags with an age greater than this value are in age class three If your run does not work with snags you can ignore this The effects of light levels on seed survival is graphed as Light Effect Proportion Established 0 GLI 100 To assess the effects of light level on the number of seeds that survive this behavior calculates the GLI at the center of each grid cell in the Dispersed Seeds grid at the height specified in the Height in m At Which to Calculate GLI parameter value is in meters The calculation proceeds exactly as described in the Light Behaviors In order to perform these GLI calculations this behavior requires its own copy of the key GLI setup parameters If you wish to use storms in your run this behavior can take into account the fact that storm damaged trees may have different light extinctio
107. SORTIE ND User Manual Version 7 01 Beta October 18 2012 Author Lora E Murphy Cary Institute of Ecosystem Studies SORTIE ND User Manual e SORTIE ND License e What s new in the latest version e Basic SORTIE modeling concepts e Setting up SORTIE ND for your site e The SORTIE ND plot e Timesteps and run length e Trees O Oo 0 0 0 0 O What is a tree Tree population how trees are organized Tree life history stages and transitions Tree allometry Setting up trees parameters Setting up tree initial conditions Tree data member list e Behaviors 2 Oo 0 0 0 What is a behavior The relationship of behaviors to trees and grids Choosing behaviors for a run Setting up behaviors parameters Complete behavior documentation State change behaviors Harvest and disturbance behaviors Management behaviors Light behaviors Growth behaviors Mortality behaviors Substrate behaviors Epiphytic establishment behaviors Mortality utility behaviors Snag dynamics behaviors Disperse behaviors Seed predation behaviors Establishment behaviors Planting behaviors Analysis behaviors What is a grid How grids are created and used Grid cell size Setting up grid initial conditions Individual grid documentation e Creating a parameter file e Setting up output Types of output files Output strategies Tree output Gri
108. Species 1 NCI Lambda Include Snags in NCI Calculations How it works The fraction to which a neighbor s competitive effect is reduced when the neighbor has sustained complete storm damage The fraction to which a neighbor s competitive effect is reduced when the neighbor has sustained medium storm damage The coefficient in the shading effect equation Set this value to 0 if you do not wish to use shading The exponent in the shading effect equation If you set the NCI Shading Effect Coefficient m parameter to 0 this value is ignored The mode of the size effect curve The variance of the size effect curve The sensitivity of a tree s survival probability to its DBH The fraction by which a tree s survival probability is reduced when it has sustained complete storm damage The fraction by which a tree s survival probability is reduced when it has sustained medium storm damage The scale of the competitive effect of a neighbor tree s species on the target tree s species Whether or not to include snags when finding competitive neighbors for NCI For a tree the annual probability of survival is calculated as Prob Survival Max Survival Size Effect Shading Effect Crowding Effect Storm Effect Max Survival is the NCI Max Survival Probability 0 1 parameter Storm Effect Shading Effect Size Effect and Crowding Effect are all optional factors which act to reduce the maximum survival probability and will
109. Survival Minimum Neighbor DBH cm The minimum DBH for trees of that species to compete as neighbors Used for all species not just those using Weibull Climate growth Weibull Climate Survival Size The minimum possible DBH for size effect Trees with a DBH less than Effect Minimum this value will use this value in the size effect calculation instead DBH How it works For a tree the annual probability of survival is calculated as Survival Probability Max Survival Probability Size Effect Precipitation Effect Crowding Effect Temperature Effect Max Survival Probability is the maximum possible annual survival probability entered in the Weibull Climate Survival Max Survival Prob 0 1 parameter Size Effect Precipitation Effect Crowding Effect and Temperature Effect are all factors which act to reduce the maximum survival probability and will vary depending on the conditions a tree is in Each of these effects is a value between 0 and 1 Size Effect is calculated with a lognormal function as follows In DBH be i Xb 0 5 SE where e DBH is of the target tree in cm e Xo is the Weibull Climate Survival Size Effect X0 parameter this is the mode of the function expressed in cm e X is the Weibull Climate Survival Size Effect Xb parameter this is the variance of the function expressed in cm You can set a minimum DBH for the size effect in the Weibull Climate Survival Size Effect
110. The behavior then goes through each grid cell in the Dispersed Seeds grid and assesses the survival for the seeds of those species to which it applies This behavior starts by giving each seed a random temporary location within the Dispersed Seeds grid cell Then it retrieves the substrate favorability at that point from the Substrate Favorability grid It then compares a random number to the substrate favorability to determine whether the seed lives This method ensures that we can assess substrate favorabilities correctly when the Dispersed Seeds and Substrate grids have different grid cell resolutions Once this process is complete the number of surviving seeds for each species is assigned back to the Dispersed Seeds grid How to apply it This behavior may be applied to seeds of any species A species to which this is applied must also have a Disperse behavior applied Also the Substrate behavior must be used in the run Substrate Dependent Seed Survival No Gap Status This behavior assesses seed survival based on substrate conditions Parameters for this behavior Parameter name Fraction Seeds Germinating on Canopy Decayed Logs Fraction Seeds Germinating on Canopy Fresh Logs Fraction Seeds Germinating on Canopy Forest Floor Litter Fraction Seeds Germinating on Canopy Forest Floor Moss Fraction Seeds Germinating on Canopy Scarified Soil Description The proportion of those seeds that land on decayed lo
111. You must also use the Storm disturbance and Storm Light behaviors Relative growth behaviors Several behaviors apply a relative growth version of the Michaelis Menton function Parameters for these behaviors Parameter name Description Adult Constant Area The constant amount of basal area by which to increase a tree s basal Growth in sq cm yr area Applies to basal area increment limited behaviors adni l an The constant value by which to increase a tree s radius at breast height Radial Growth in wee a Applies to radial increment limited growth behaviors mm yr A yop us Asymptote of the Michaelis Menton growth function at high light Diameter Growth A function term A below for diameter growth Asymptotic Height Asymptote of the Michaelis Menton growth function at high light Growth A function term A for height growth Slope of Growth Slope of the Michaelis Menton growth function at zero light function Response S term S below Relative Michaelis Menton Growth The exponent to be used with diameter when calculating relative growth Diameter Exponent Relative growth is calculated with the equation where e Yis the amount of annual relative growth e Ais the Asymptotic Diameter Growth A or Asymptotic Height Growth A parameter e Sis the Slope of Growth Response S or Slope of Height Growth Response S parameter e GLI is the global light index calculated by a light behavior Diameter growth is
112. a grid object called Gap Light to determine the basic position of plot gaps If a grid cell contains no adult trees it is considered a gap If there are any adults of any species then it is non gap The trees to which this behavior has been applied get their GLI values based on the gap status of the grid cell in which they are located If the gap status is TRUE then they receive a GLI value of 100 If it is FALSE they receive a value of 0 How to apply it This behavior may be applied to seedlings saplings and adults of any species GLI light For more on what GLI is and how it is calculated see here Parameters for this behavior Parameter name Height of Fisheye Photo Minimum Solar Angle for GLI Light in rad Number of Altitude Sky Divisions for GLI Light Calculations Number of Azimuth Sky Divisions for GLI Light Calculations Description When a fish eye photo is simulated for a tree this positions the photo at either the top of the crown or at mid crown Seedlings always get fisheye photos at top of crown no matter what this value is This is the minimum angle at which sunlight is seen in radians Below this value the sky is assumed to be dark due to shading neighbors Number of grid cells into which the sky is divided from horizon to zenith for the purpose of calculating light direction Number of grid cells into which the sky is divided around the horizon for the purpose of calculating light direc
113. a light behavior applied You can use either the diam with auto height or diam only version Non limited absolute growth diam with auto height How it works The amount of diameter increase returned by the absolute growth equation is applied to the tree How to apply it This behavior can be applied to seedlings saplings and adults of any species Any tree species type combination to which it is applied must also have a light behavior applied You can use either the diam with auto height or diam only version Absolute growth behaviors Several behaviors apply an absolute growth version of the Michaelis Menton function Parameters for these behaviors Parameter name Adult Constant Area Growth in sq cm yr Adult Constant Radial Growth in mm yr Asymptotic Diameter Growth A Slope of Growth Response S Length of Current Release Factor Length of Last Suppression Factor Mortality Threshold for Suppression Years Exceeding Threshold Before a Tree is Suppressed Description The constant amount of basal area by which to increase a tree s basal area Applies to basal area increment limited behaviors The constant value by which to increase a tree s radius at breast height Applies to radial increment limited growth behaviors Asymptote of the Michaelis Menton growth function at high light function term A below Slope of the Michaelis Menton growth function at zero light function term S below Cont
114. a neighbor tree s size on its sensitivity to competition The value by which target DBHs are divided when calculating competitive effects This can be used to make units adjustments Divisor Gen Harvest ee ee 7 NOTRE The amount by which it is acceptable to deviate from the harvest target T basal area removal without triggering a second harvest pass Expressed Deviation From Cut Target as a proportion of the target basal area between 0 and 1 How it works Competition Harvest performs harvests when specific conditions are met in the plot The amount harvested is also based on conditions in the plot There are three ways to specify the timing and amount of harvesting The desired method is set in the Competition Harvest Harvest Type parameter The harvest types are e Fixed basal area threshold cutting a specific amount of basal area Set the harvest type parameter to Fixed BA Amt A harvest occurs whenever the plot s basal area exceeds a certain threshold set in the Competition Harvest Fixed BA Harvest Threshold m2 ha parameter The same amount of basal area is harvested every time set in the Competition Harvest Amount to Harvest parameter To make sure that harvests do not happen too frequently set a minimum interval between harvests in the Competition Harvest Min Years Between Fixed BA Harvests parameter e Fixed basal area threshold cutting a proportion of the plot basal area Set the harvest type parameter to Fixed BA
115. ability that the tree will expose an area of tip up mounds substrate Any new substrate created this way is added in to the existing substrate but does not completely replace it like harvest does Substrate relationships Substrate Creation and Decay Schematic Fresh logs Tip up mounds Scarified sail Decayed logs Relationships 1 2 4 and 6 represent the decay of the different substrates as a function of substrate age according to the equation where t is time in years Graphed this equation looks like this Hypothetical Substrate Loss Function 0 9 ba eT in im 5 o a Remaining 4 4 3 Lostiyr 3 EN t t 4 4 6 4 6 4 10 15 20 Time Steps In this diagram there are two kinds of substrate A and B A decays into B according to the equation above The amount of A and B together sum to 1 for this diagram The curve for Remaining is the amount of A The curve for Lost yr is the amount of B When gt 1 the rate of loss time step increases over time giving an initial lag period when there is little loss of the substrate When lt 1 the substrate disappears most rapidly immediately after substrate creation less likely 6 1 gives a constant loss per time step i e exponential decline In this example a 0 0002 and 4 Relationship 3 governs the amount of fresh logs created each time step as a result of tree mortality For the purposes of adding new subst
116. ages can be attached to individual cells to add to the amount of information a grid can carry There is no limit to the number of packages that can be attached to a cell An example of data which might come in packages is a grid holding data on harvest events with each package representing a discrete harvest How grids are created and used Which grids are used for a run depends entirely on which behaviors are used All grids are created automatically by a behavior A grid that is not needed in a run will not be created Behaviors use grids for three primary reasons e To map spatial variation in some aspect of the plot as with a storm damage susceptibility map e To pass information from behavior to behavior as with a substrate map which is updated by one behavior and used by another to determine likelihood of seed establishment e To report something for output number of trees harvested amount of biomass Grid cell size Grids are always exactly the same size as the plot Grids have an X and a Y axis which match the orientation and size of the plot s axes Grids are divided along the X and Y axes separately so that each cell within the grid is a rectangle If the chosen grid cell sizes do not divide evenly into the X and Y plot lengths the length of the cells in the last rows in each direction will be the remainder value Grids can carry more than one value per cell Grid cell size applies to all values in the grid The amount of memor
117. al Cut Proportion of Scarified Soil Partial Cut Proportion of Tip Up Mounds Partial Cut Proportion of Scarified Soil Partial Cut Proportion of Tip Up Mounds Proportion of Dead that Fall Proportion of Fallen that Uproot Proportion of Forest Floor Litter Moss Pool that is Moss as a value between 0 and 1 If a map of substrate values is included in the parameter file see Grid initial conditions for information on how to do this then the map values will be used for the initial conditions and this number will be ignored The proportion of plot substrate that is tip up mounds substrate when the run starts as a value between 0 and 1 If a map of substrate values is included in the parameter file see Grid initial conditions for information on how to do this then the map values will be used for the initial conditions and this number will be ignored The number of years that a substrate disturbance event has effect before it is deleted the lifetime of a substrate cohort The proportion of substrate that is decayed logs in areas that had a partial cut harvest event as a value between 0 and 1 This is not required if the Harvest behavior is not used The proportion of substrate that is fresh logs in areas that had a partial cut harvest event as a value between 0 and 1 This is not required if the Harvest behavior is not used The proportion of substrate that is scarified soil in areas that had a partial cut harves
118. al chance of becoming infested no matter where they are in the plot This behavior uses a tree data member called Years Infested to track which trees are infested and how long they have been so How to apply it Apply this behavior to saplings and or adults of any species Episodic Mortality Trees removed by this behavior will have a mortality reason code of disease Parameters for this behavior This behavior does not have its parameters entered through the Parameters Window Set up these behaviors using the Edit Episodic Events Window How it works The Episodic Mortality behavior allows you to replicate tree killing events with the same level of control you have when defining Harvest events A planned mortality episode can simulate disease an insect outbreak fire or the like The main difference between Harvest and Episodic Mortality is that the Episodic Mortality behavior can create snags or standing dead trees A large snag proportion can significantly affect the light and substrate dynamics of a SORTIE run Defining a mortality episode is like defining a partial cut harvest Mortality episodes have no automatic impact on substrate dynamics like harvest events do although the newly dead trees may be a source of harvest input You can define up to four size classes and specify the amount of trees to kill in one of four ways as a percentage of total basal area as an absolute amount of basal area as a percentage of tota
119. alls in the pool of trees that die How to apply it This behavior can be applied to seedlings saplings and adults of any species Suppression Duration Mortality This behavior evaluates mortality as a function of tree age This is particularly useful for simulating suppression in seedlings Trees killed by this behavior will have a mortality reason code of natural Parameters for this behavior Parameter name Description Suppression Duration Mortality 2 Max Mortality Rate The maximum mortality rate for suppressed trees 0 1 SUPP E AS XO in the suppression mortality function This is the age at which half of Duration Mortality x0 the maximum mortality rate is reached Suppression Duration Mortality Xb in the suppression mortality function Xb How it works A tree s probability of mortality is Max p a T E where e pis the probability of mortality e Maxis the Suppression Duration Mortality Max Mortality Rate 0 1 parameter e Xois the Suppression Duration Mortality X0 parameter e Xis the Suppression Duration Mortality Xb parameter e Age is the tree s age in years The value for Xo is the age at which half of the maximum mortality rate is reached Tree age is tracked using the Tree Age Calculator behavior Initial conditions trees get a mortality of zero because their age is unreliable How to apply it This behavior can be applied to trees of any species Trees must also have
120. ameter in the equation for calculating tree diameter outside bark below The height at which volume calculations begin For merchantable volume calculations this can be thought of as the stump height The height is height off the ground in cm The trunk diameter inside the bark at which volume calculations end For merchantable volume calculations this is the minimum usable trunk diameter The diameter is in cm The length in m of segments into which the tree trunk is divided for volume calculations A smaller value means a greater degree of accuracy a larger value means a faster processing time Tree volume is estimated by dividing the trunk into segments and calculating the volume of each segment You control where the trunk starts and stops and the length of segments used Trunks start at the value in the Height to Begin Calculating Trunk Volume in cm parameter To calculate merchantable volume set this to the average stump height To calculate total volume set this to zero Trunks end when their diameter inside the tree bark becomes smaller than the volume in the Minimum Trunk Diameter for Volume Calculations in cm parameter For merchantable volume set this to the minimum usable diameter For total volume set this to Zero Trunks are divided into segments for volume calculations The length of these segments is set in the Trunk Segment Length for Volume Calculations in m parameter Setting this to a smaller value increa
121. an or Size Class 1 equal to the value in Upper DBH of snag size class 1 Mortality Weibull Annual a Parameter for Snag Size Class 2 Mortality Weibull annual a parameter for those trees whose DBH is greater than the value in Upper DBH of snag size class 1 but less than or equal to the value in Upper DBH of snag size class 2 Weibull Annual a Parameter for Snag Weibull annual a parameter for those trees whose DBH is greater than Size Class 3 the value in Upper DBH of snag size class 2 Mortality Weibull Annual b Parameter for Snag Weibull annual b parameter for those trees whose DBH is less than or Size Class 1 equal to the value in Upper DBH of snag size class 1 Mortality Weibull Annual b Parameter for Snag Size Class 2 Mortality Weibull annual b parameter for those trees whose DBH is greater than the value in Upper DBH of snag size class 1 but less than or equal to the value in Upper DBH of snag size class 2 Weibull Annual b Parameter for Snag Weibull annual b parameter for those trees whose DBH is greater than Size Class 3 the value in Upper DBH of snag size class 2 Mortality Weibull Upper DBH afore cine Cine The upper DBH value of trees in size class 1 Weibull Upper DBH The upper DBH value of trees in size class 2 Trees with a value greater of Snag Size Class 2 than this are considered to be in size class 3 How it works The behavior uses a Weibull function to determi
122. an this value are in age class three If your run does not work with snags you can ignore this This behavior calculates a Global Light Index GLI value for each individual of each tree type to which it is assigned GLI values range from 0 no sun to 100 full sun How to apply it This behavior may be applied to seedlings saplings and adults of any species GLI Map Creator For more on what GLI is and how it is calculated see here Parameters for this behavior Parameter name Height at Which GLI is Calculated for GLI Map in meters Minimum Solar Angle for GLI Map Creator in rad Number of Altitude Sky Divisions for GLI Map Creator Calculations Number of Azimuth Sky Divisions for GLI Map Creator Calculations Description Height at which GLI is calculated This is the minimum angle at which sunlight is seen in radians Below this value the sky is assumed to be dark due to shading neighbors Number of grid cells into which the sky is divided from horizon to zenith for the purpose of calculating light direction Number of grid cells into which the sky is divided around the horizon for the purpose of calculating light direction General light parameters used by this behavior Parameter name Beam Fraction of Global Radiation Clear Sky Transmission Coefficient First Day of Growing Season Last Day of Growing Season Amount Canopy Light Transmission 0 1 Snag Age Class 1 Amount Canopy
123. ance behaviors Disturbance behaviors simulate different kinds of forest disruption These behaviors cause tree damage and death due to a variety of processes Behavior Competition Harvest Generalized Harvest Regime Harvest Harvest interface Insect Infestation Episodic mortality Random browse Storm disturbance Storm damage applier Storm damage killer Storm direct killer Selection harvest Windstorm Description Performs harvests in a way that preferentially removes the most competitive individuals in a plot The behavior itself decides when harvests will occur and how much to cut based on total plot adult biomass then chooses trees to cut with the help of a preference algorithm Implements complex silvicultural treatments Allows SORTIE to work directly with an external harvesting program Simulates an insect outbreak by choosing and marking infested trees Allows you to replicate tree killing events with the same level of control you have when defining Harvest events Simulates random browsing from herbivores Simulates the effects of wind damage from storms Decides which trees are damaged when a storm has occurred and how badly Kills trees damaged in storms Kills trees based on storm severity without an intervening damage step Allows you to specify target basal areas for a tree population as a method of harvest input instead of designing specific harvest events K
124. and no database of tree species sites and parameters to draw from SORTIE was intended to study real locations and that tends to mean starting by finding out how trees behave at a study site This does not mean that you must start with field studies Neither does it mean that you have to study real places SORTIE has also been used for purely theoretical work What it means is that you will need to gather a lot of information before you start Look at the example provided on the SORTIE website read some of the SORTIE related publications and begin to build your parameter file You ll quickly see what information you need Plot The plot in SORTIE is the simulation of the physical space in which the model runs It has a size a climate and a geographical location Plot size You can think of the plot as a rectangle although it s not really more on that later You tell the plot what its east west and north south dimensions are It s useful to keep your plot size in mind when you are setting up your parameters and viewing your output since many SORTIE values are per hectare units The size of your plot also makes a difference in run time the larger the plot the longer the run The absolute minimum size of a plot is 100 meters by 100 meters 200 meters by 200 meters is a more realistic minimum It is a careful balance to find a plot size big enough to see the effects you are interested in but not so big that your runs take too long to b
125. ap Calculates GLI values for individual points in the plot Calculates GLI for grid cells and assigns trees the GLI of their cell Calculates a Sail Light index value for each individual Calculates light levels as a function of number of trees damaged in storms Average Light This behavior averages GLI values to produce a set of values with a coarser spatial resolution How it works This behavior does not actually calculate GLI It averages the GLI values in the GLI Map grid which is created by the GLI Map Creator behavior This behavior creates its own map called Average Light The value for each cell in this grid is an average of the cells of GLI Map in the same area If the size of the cells of Average Light is an exact multiple of the size of the cells of GLI Map then a straight average is calculated If the size is not an exact multiple each Average Light cell value is an average of the values of all the cells of GLI Map that overlap it in area even if only partially Trees to which this behavior are applied get the value of their location in the Average Light grid How to apply it This behavior may be applied to seedlings saplings and adults of any species The GLI Map Creator behavior must also be used and must come before Average Light in the run order Once both behaviors have been added to your run set up the cell sizes of the two grids the way you want them using the Grid Setup window Basal Area Light behavior
126. ases to the east Y to the north There are no negative numbers If there are trees outside the plot boundaries you are warned of this if you elect to continue loading the file those trees are discarded The third column is species The species names must match those that appear in the parameter file including case EXCEPT that spaces in the species name must be replaced with underscores For instance if the species name is Red Maple in the file the species is Red_Maple SORTIE ND will reject a tree map with an unrecognized species name To find out what the species names are for your parameter file use the Edit species list window to view the list The fourth column is tree life history stage Possible values are Seedling Sapling Adult and Snag Case is unimportant The fifth column is tree diameter in cm If the life history stage is Seedling this value is the diameter at 10 cm height For all other types this is DBH If the diameter value and the life history stage do not match diameter takes precedence For instance if the parameter file specifies that the minimum adult DBH is 10 cm and the tree map contains a tree designated as a sapling with a diameter of 15 cm then SORTIE ND will create an adult with a DBH of 15 The sixth column is tree height in meters If this value is set to 0 SORTIE ND will use the allometry equations to calculate tree height If this value is non zero then this height is assigned to the
127. astic Bi Level Applies a constant rate of mortality to trees with different rates for high light Mortality and low light conditions This works with the GLI behavior GLI Stochastic Produces background mortality by randomly choosing trees to die according to a Mortality specified rate Suppression Duration Mortality Evaluates mortality as a function of tree age This is particularly useful for simulating suppression in seedlings Temperature dependent neighborhood survival Assesses tree survival as a function of mean annual temperature and neighbor adult basal area For efficiency it calculates survival rates for cells in a grid and assigns trees the survival probability of the grid cell in which they are found Weibull Climate Assesses tree survival as a function of climate and larger neighbor trees Survival Weibull Snag Mortalit Controls snag fall according to a Weibull function of snag age Aggregated Mortality Aggregated Mortality is similar to the Stochastic Mortality behavior in that it kills trees randomly to match a predetermined mortality rate However Aggregated Mortality clumps together the deaths in both time and space Trees killed by this behavior will have a mortality reason code of natural Parameters for this behavior Parameter name Description Aggregated Mortality Annual Kill Amount 0 1 The annual mortality rate for a mortality episode as a proportion between 0 and 1 Aggre
128. avior can be applied to saplings and adults of any species Linear growth This behavior does either diameter or height growth as a linear function of GLI Parameters for this behavior Parameter name Description Simple Linear Diam Intercept in mm yr a Intercept of the linear growth function or growth at no light in mm yr for diameter growth Simple Linear 3 Diam Slope Slope of the linear growth function for diameter growth Simple Linear Height Intercept in cm yr a Intercept of the linear growth function or growth at no light in cm yr for height growth Simple Linear Height Slope b Slope of the linear growth function for height growth How it works This behavior calculates an amount of diameter or height growth as Y a b GLI T where e Y amount of radial increase in mm or amount of height increase in cm e a Simple Linear Diam Radial Intercept in mm yr a parameter for diameter growth or the Simple Linear Height Intercept in cm yr a parameter for height growth e b Simple Linear Diam Radial Slope b parameter for diam growth or the Simple Linear Height Slope b parameter for height growth e GLI global light index as a percentage between 0 and 100 calculated by a light behavior e T number of years per timestep How to apply it This behavior can be applied to seedlings saplings and adults of any species Any tree species type combination to which it
129. aximum amount of time in years after storm damage that a tree will still be counted in the number of damaged trees The maximum amount of time in years after death that a snag will still be counted in the number of damaged trees The minimum number of adult trees and snags within the value in Storm Light Max Radius m for Damaged Neighbors for the point to be considered under full canopy Slope of the function to determine light level If the value in the Storm Light Stochasticity parameter is Normal or Lognormal the standard deviation of the probability distribution function If stochasticity is Deterministic this value is ignored What method to use for randomizing light values if desired How it works This behavior uses a grid called Storm Light to manage light levels Each timestep it calculates the light level at the center of each grid cell and places it in the grid The light level is calculated as follows GLA 1 T M 100 a b N where e GLA is the light level as a value between 0 and 100 e Tis the number of adult trees and snags within the search radius e Mis the Storm Light Minimum Trees For Full Canopy parameter e ais the Storm Light Intercept of Light Function parameter e bis the Storm Light Slope of Light Function parameter e Nis the proportion of trees that are dead or were heavily damaged in recent storms This behavior calculates the light levels at the center of each grid
130. ay alter the values in this grid The survival probability as calculated above is an annual probability For multi year timesteps the timestep probability is AP where AP is the annual probability and X is the number of years per timestep Once a tree s timestep survival probability has been calculated it is compared to a random number to determine whether the tree lives or dies How to apply it This behavior can be applied to seedlings saplings and adults of any species Any tree species type combination to which it is applied must also have a growth behavior applied You must also enter a map of second resource values into the Resource grid Height GLI Weibull Mortality with Browse This behavior calculates the probability of mortality using a Weibull function of tree height and GLI light level It can also simulate the effects of herbivory by using different parameters for browsed and unbrowsed trees Trees killed by this behavior will have a mortality reason code of natural Parameters for this behavior Parameter name Height GLI Weibull a Height GLI Weibull b Height GLI Weibull c Height GLI Weibull d Height GLI Weibull Max Mortality 0 1 Height GLI Weibull Browsed a Height GLI Weibull Browsed b Height GLI Weibull Browsed c Height GLI Weibull Browsed d Height GLI Weibull Browsed Max Mortality 0 1 How it works Description The a parameter in the Weibull funct
131. b D lt exzpla o where e pis the tree s probability of mortality between 0 and 1 e ais the Storm Direct Killer a parameter e bis the Storm Direct Killer b parameter e Dis the storm damage at the tree s location Once the mortality probability has been calculated this behavior uses a random number to determine whether it lives or dies If more than one storm has occurred in the current timestep each storm gets a separate independent chance to kill trees Trees that die have a dead flag set to true and are treated in the rest of the run like trees that have died due to natural mortality How to apply it Apply this behavior to the trees that can be killed in storms You must also use the Storm disturbance behavior and have any kind of mortality behavior applied to each tree species and life history stage to which this behavior is applied Selection harvest This behavior allows you to specify target basal areas for a tree population as a method of harvest input instead of designing specific harvest events Trees removed by this behavior will have a mortality reason code of harvest Parameters for this behavior Parameter name Selection Harvest Cut Range 1 Lower DBH cm Selection Harvest Cut Range 1 Upper DBH cm Selection Harvest Cut Range Target Basal Area m2 ha Selection Harvest Cut Range 2 Lower DBH cm Selection Harvest Cut Range 2 Upper DBH cm Selection Harvest Cut Range 2 Tar
132. basal area in sq m per ha within a radius set by the Post Harvest Skid Mort Crowding Effect Radius parameter e 1 18 the Post Harvest Skid Mort Snag Recruitment Rate Param parameter e His the number of timesteps since the last harvest in this tree s grid cell e tis the number of years per timestep e cis the Post Harvest Skid Mort Snag Recruitment Background Prob parameter How to apply it This behavior can be applied to saplings and adults of any species In order for the harvest intensity term to have an effect the float data member HarvInten must be registered for all species type combos to which this behavior is applied by using the HARP external harvesting program along with the Harvest Interface Self thinning Self thinning is a behavior that uses a pseudo density dependent function designed to increase the death rate in dense uniform age stands You specify a maximum DBH at which to apply it above this DBH a tree will not die Trees killed by this behavior will have a mortality reason code of natural Parameters for this behavior Parameter name Description Self Thinning Intercept of the self thinning linear function Intercept Self Thinning Slope Slope of the self thinning linear function Maximum DBH for Maximum DBH at which self thinning applies Above this value no Self Thinning mortality occurs How it works Self thinning uses a simple linear function of probability of mortality as a function of DBH
133. bination to which it is applied must also have a light behavior applied You must also enter a map of second resource values into the Resource grid You can use either the diam with auto height or diam only version Juvenile NCI growth This behavior uses the effects of neighbor competitiveness to influence growth rates for juvenile trees NCI stands for neighborhood competition index A tree s maximum potential growth rate is reduced due to competitiveness and other possible factors This is very similar to NCI growth but adapted for juveniles Parameters for this behavior Parameter name Description Juvenile NCI Alpha NCI function exponent Juvenile NCI Beta NCI function exponent Juvenile NCI Crowding Effect The slope of the curve for the crowding effect equation Slope C Juvenile NCI Crowding Effect The steepness of the curve for the crowding effect equation Steepness D Juvenile NCI The value by which neighbor djs are divided when calculating NCI Diam 10 Divisor q Juvenile NCI Include Snags in NCI Calculations Species i Juvenile NCI Lambda Neighbors Juvenile NCI Maximum Crowding Distance in meters Juvenile NCI Maximum Potential Growth cm yr Juvenile NCI Minimum Neighbor Diam 10 in cm Juvenile NCI Size Effect a Juvenile NCI Size Effect b How it works This can be used to make units adjustments Whether or not to include snags when finding competitive neighbors for NCI T
134. ble using Path and filename of the executable on the Edit Harvest Interface window Each harvest timestep SORTIE writes a text file with a list of trees eligible for harvest The trees in the list are those to which the Harvest Interface behavior is applied You choose which trees those are in Behavior currently assigned to on the Edit Harvest Interface window Once the file is written SORTIE then launches your executable Your executable writes a file in response with the list of trees it wishes SORTIE to kill Trees that are cut are treated exactly like those in SORTIE harvest That is they disappear completely and do not become snags See the documentation on Harvest for more details The cut details for each timestep are written to the Harvest Results grid Warning if you put both the Harvest and Harvest Interface behavior in the same run they will overwrite each other s results in the grid Because the process can be slow you can set harvests to occur less often than every timestep To do this use How often to harvest in years on the Edit Harvest Interface window Optionally you can also add new tree data members that are controlled by the executable The executable can write a file with a list of trees to update and the new values for those variables for each tree File formats Each harvesting timestep SORTIE begins by writing a file of all trees eligible for harvest You give SORTIE the path and name of that file in Tree fil
135. can be applied to saplings and adults of any species It cannot be applied to seedlings You can use either the diam with auto height or diam only version Weibull climate quadrat growth This behavior calculates tree growth as a function of climate and neighbor trees For processing efficiency growth is calculated for each species on a per grid cell basis There is a maximum potential growth rate that is reduced due to several possible factors Parameters for this behavior Parameter name Description Weib Clim Quad Growth The C parameter for the competition effect Competition Effect IES Weib Clim Quad Growth Competition Effect De Weib Clim Quad Growth Max Neighbor Search Radius m Weib Clim Quad Growth Max Potential Growth cm yr Weib Clim Quad Growth Minimum Neighbor DBH cm Weib Clim Quad Growth Precip Effect A Weib Clim Quad Growth Precip Effect B Weib Clim Quad Growth Precip Effect C Weib Clim Quad Growth Temp Effect A Weib Clim Quad Growth Temp Effect B Weib Clim Quad Growth Temp Effect C How it works The D parameter for the competition effect The maximum distance in m at which a neighboring tree has competitive effects on a target tree Maximum potential diameter growth for a tree in cm yr The minimum DBH for trees of that species to compete as neighbors Used for all species not just those using this growth behavior The A paramet
136. cay Break SnagOldBreakHeight Float occurred in a previous timestep Class Height 1 if the snag is unbroken Dynamics Whether a tree that has died this Snag Decay Fall Fall Boolean timestep has fallen true or Class remains standing as a snag false Dynamics g Lagged post Pe narvon Growth prior to the last harvest harvest growth growth Michaelis Last PT Float The previous year s stochastic ae stochastic growth factor growth height only Years Vanrsintesiad Thier The number of years that a tree Insect Infested 8 has been infested with insects Infestation Whether a tree is vigorous or not Ares Quality Vigorous vigorous Boolean Vigor true or false Classifier Whether a tree is sawlog quality Sawlog sawlog Boolean Vigor or not true or false A Classifier Tree Quality Tree class treeclass Integer Tree class number 1 6 Vigor Classifier What is a behavior Behaviors are the active part of a SORTIE simulation Nothing in the model is pre defined default or automatic Everything that happens is done by a behavior and all behaviors are under user control Behaviors fall into two categories The first category is behaviors that act on trees and roughly correspond to biological and environmental processes These behaviors calculate how much individual trees grow select trees that will die distribute seeds and perform other similar jobs The second category is behaviors that perform
137. ccording to Beer s Law Parameters for this behavior Parameter name Description longi olan Height in meters at which the Beer s law light filter hangs Filter in m Light Filter Light Transmission Amount of light that is blocked by the light filter Coefficient How it works Imagine a fog that hangs out on the forest floor and ends abruptly at a certain height All trees shorter than the top of the fog layer will have their light attenuated but not blocked completely The closer they get to the top of the fog the more light is let in The amount of light which actually gets through is calculated according to Beer s Law where transmission e where a is the Light Filter Light Transmission Coefficient parameter and z thickness of the filter in meters which is the distance from the light point to the top of the filter the Height of Light Filter in m parameter This filter behavior can be used to for instance replicate the effects of an herbaceous layer in reducing light to young seedlings The height of the filter is randomized slightly each time the thickness of the filter over the light point is calculated to introduce a stochastic element Trees can be given a respite from the effects of the filter This behavior does not set the respite counter but it will respect any values which another behavior has put in Trees can be given a rooting height in addition to their normal height This value is added to their existing height t
138. ce increment This is not Omega Value necessarily the distance in meters Resource Grid This grid holds values for a second growth resource for use by the Double resource relative growth and Growth and Resource Based Mortality behaviors The actual identity of the resource is unknown and unimportant The grid holds a value for resource level in each cell and it is assumed that the units scale appropriately to the parameters for the growth behavior The grid cell resolution defaults to 8 m X 8 m You can set whatever new resolution you wish Data in the grid Data member name Description Resource Resource amount in whatever units are appropriate Ripley s K Grid This grid holds values for the Ripley s K statistic as calculated by the Ripley s K Calculator behavior The grid holds a K value for each distance increment for each species This can be a great many values The grid cell resolution is always set to one cell covering the entire plot You cannot change this Data in the grid Data member Description name Maximum distance to which to calculate K in meters Including this in the a Dr anie output is not necessary but will improve the SORTIE graphing capability How often to calculate K in meters Including this in the output is not Laseno Be necessary but will improve the SORTIE graphing capability All Species Dist The K value for all plot trees at the Yth distance increment This is not Y K Value necessarily t
139. ch individual has been infested How to apply it Apply this behavior to saplings and or adults of any species Any tree to which this behavior is applied must also have the Insect Infestation behavior applied Logistic bi level mortality This behavior calculates the probability of survival according to a logistic equation with the possibility of two sets of parameters for each species one for high light conditions and one for low light conditions This can also be used alone without the light levels Trees killed by this behavior will have a mortality reason code of natural Parameters for this behavior Parameter name Description Logistic Bi Level ae ve Bardem 2 The a parameter used in low light conditions Logistic Bi Level ae cae EL The b parameter used in low light conditions Logistic Bi Level ae eens oe High Light a The a parameter used in high light conditions Logistic Bi Level nae ee D Hini The b parameter used in high light conditions Logistic Bi Level High Light Mortality Threshold 0 100 The threshold between low light and high light parameters as a value between 0 and 100 How it works The equation used by this behavior to calculate survival probability is expla b D 1 exp fat b D where e p annual probability of survival e a inhigh light conditions this is the Logistic Bi Level High Light a parameter in low light conditions this is the L
140. ch is the distance from the top to the bottom of the crown cylinder in meters e Cy is the Slope of Asymptotic Crown Height parameter e height is the tree s height in meters e bis the Crown Height Exponent parameter The Chapman Richards crown depth and radius relationships Crown Depth Parameters Parameter name Description Chapman Richards Asymptotic Crown Height Chapman Richards Crown Height Intercept Chapman Richards Crown Height Shape 1 b Chapman Richards Crown Height Shape 2 c The asymptotic crown depth or length in m of the Chapman Richards crown depth equation The intercept of the Chapman Richards crown depth equation This represents the crown depth in m of the smallest possible sapling The first shape parameter b of the Chapman Richards crown depth equation The second shape parameter c of the Chapman Richards crown depth equation Crown Radius Parameters Parameter name Chapman Richards Asymptotic Crown Radius Chapman Richards Crown Radius Intercept Chapman Richards Crown Radius Shape 1 b Chapman Richards Crown Radius Shape 2 c Description The asymptotic crown radius in m of the Chapman Richards crown radius equation The intercept of the Chapman Richards crown radius equation This represents the crown radius in m of the smallest possible sapling The first shape parameter b of the Chapman Richards crown radius equation The second shape parame
141. ch piece of data has its own save frequency You can use this to cut down on detailed output file size Data you are less interested in can be saved less frequently You can also save data separately for just a portion of the plot by defining subplots Viewing the data in a detailed output file The data visualization capabilities of the model interface allow you to see your data graphically If you want the data raw to do your own analysis you can save the contents of individual maps within the detailed output files as tab delimited text The easiest way to write tree data is to use the Timestep tree writer tool listed in the Tables options after a detailed output file has been loaded for data visualization Grid map data can be written from any grid map display Detailed output files as input to other runs The maps in a detailed output timestep file can be used as initial conditions on a subsequent run provided that they are compatible with the parameter file being used See the Using output as input to a new run topic Copying and renaming detailed output files Because of their structure detailed output files cannot be renamed like ordinary files If you change the file name the file will be broken Use the Copy detailed output file tool in the Tools menu to safely make a copy of the file with a new name You can safely copy and move detailed output files to different file locations as long as the name stays the same Summary
142. chosen from the normal distribution and D is the previous diameter This means that growth can be negative The effect is to create a tree population with normally distributed diameters where any individual tree may jump from place to place within the distribution How to apply it This function can be applied to seedlings saplings or adults of any species Any tree using this behavior must also use a height only growth behavior Puerto Rico storm bi level growth diam with auto height Puerto Rico storm bi level growth diam with auto height This behavior increments growth according to two possible growth equations one to be used in low light conditions and the other to be used in high light conditions This behavior was originally created for the Puerto Rico model Parameters for this behavior Parameter name Description PR Storm Bi Level Threshold for High The threshold between low light and high light equations as a value Light Growth 0 between 0 and 100 100 PR Storm Bi Level High Light a The a value in the high light growth function PR Storm Bi Level High Light b The b value in the high light growth function PR Storm Bi Level Intercept for Low The intercept of the linear growth function used in low light conditions Light Growth a PR Storm Bi Level Slope for Low Light The slope of the linear growth function used in high light conditions Growth b How it works Light levels
143. cies X X Neighbors NCI Crown Radius Max Potential The maximum possible value for crown radius in m Radius m NCI Crown Radius Max Search Distance for Neighbors m The maximum distance in m at which a neighboring tree has competitive effects on a target tree Ne oe Rann The minimum DBH for trees of that species to compete as neighbors SUE Taine ISeegin ren Values are needed for all species DBH cm aaa a NCI Crown Radius Sre Biia T Size effect function exponent The crown dimensions are calculated as CR CD Max CR Max CD Size Effect Crowding Effect where e CR is the crown radius in m e CD is the crown depth in m e Max CR is the NCI Crown Radius Max Potential Radius m parameter e Max CD is the NCI Crown Depth Max Potential Depth m parameter Size Effect is calculated as SE 1 exp d DBH where e SE is the size effect between 0 and 1 e dis either the NCI Crown Depth Size Effect d parameter or the NCI Crown Radius Size Effect d parameter e DBH is the tree s DBH in cm Crowding Effect is calculated as CE exp n NCT where CE is the crowding effect between 0 and 1 n is the NCI Crown Radius Crowding Effect n parameter or the NCI Crown Depth Crowding Effect n parameter NCI is calculated as below NCI is calculated as where SO N DBH p NCI ba oa Ay IF amp d se T a distance the calculation sums over j S specie
144. class Y All partial cut values added together must be less than or equal to 1 This is not required if the Harvest behavior is not used After a partial cut harvest the proportion of substrate area that is small logs of species group X decay class Y All partial cut values added together must be less than or equal to 1 This is not required if the Harvest behavior is not used co Bey The a exponent in the decay equation as applied to tip up mounds substrate Note that this is annual decay ate The exponent in the decay equation aS applied to tip up mounds substrate Note that this is annual decay The amount by which to multiply the tree s radius when calculating the size of the new tip up mounds soil exposed by fallen trees see equation below This is meant to allow for the effects of roots If true dead trees fall in a random direction and possibly contribute new fresh log across several Substrate grid cells If false dead trees collapse vertically and contribute all their fresh log area to the cell in which they are rooted The relative proportions of each kind of substrate are tracked in the Detailed Substrate grid Within each cell the grid keeps track of each substrate s area as a proportion of the total area as well as volume for each type of log substrate in m ha The behavior also summarizes and copies values into the Substrate grid for compatibility with other behaviors that use that grid
145. combination to which it is applied must also have a light behavior applied Relative growth height only This behavior uses the Michaelis Menton function to do height growth How it works After the Michaelis Menton function is used to calculate Y as described in the section above the amount of height growth is calculated as G Y Height where e Gis the amount of height growth for one year in cm e Height is the height of the tree in cm e Xis the Relative Michaelis Menton Growth Height Exponent parameter If the timestep is more than one year long growth is recalculated for each year of the timestep increasing the height each time How to apply it This behavior can be applied to seedlings saplings and adults of any species Any tree species type combination to which it is applied must also have a light behavior and a diameter growth behavior applied Stochastic Gap Growth This behavior uses a shortcut for simulating gap dynamics with very competitive conditions This behavior causes rapid growth in high light with a unique winner low light produces no growth at all How it works This behavior simulates high growth in gap conditions It relies on the Gap Light grid created by the Gap Light behavior to tell it where the gaps are In this grid each cell is either in gap with 100 GLI or not in gap with 0 GLID If a cell is in gap a tree in that cell is randomly chosen out of all the trees to which the behavior
146. come from the Storm Light grid produced by the Storm Light behavior The threshold between the use of the high light and low light functions is set in the PR Storm Bi Level Threshold for High Light Growth 0 100 parameter The function used in low light conditions is Y a b diam T where e Y amount of diameter growth in cm e a PR Storm Bi Level Intercept for Low Light Growth a parameter e b PR Storm Bi Level Slope for Low Light Growth b parameter e diam diameter diameter at 10 cm for seedlings and saplings DBH for adults e T number of years per timestep The function used in high light conditions is H T a diam e where e H amount of height growth in cm e a PR Storm Bi Level High Light a parameter e b PR Storm Bi Level High Light b parameter e diam diameter diameter at 10 cm for seedlings and saplings DBH for adults e N number of years since the last storm from the Storm Damage grid produced by the Storm disturbance behavior e T number of years per timestep H is expressed in centimeters of height growth This is transformed into a number of cm of diameter growth which is what this behavior passes along This means that during tree life history stage transitions the height the tree ends up with is not guaranteed to match the height calculated by the high light growth function How to apply it This behavior can be applied to seedlings saplings and adults of any species
147. crease is calculated as follows Y g diam 100 T where e Yis the amount of diameter increase in cm e gis the Adult Constant Area Growth in sq cm yr parameter e diam is the tree s diameter in cm e Tis the number of years per timestep How to apply it This behavior can be applied to seedlings saplings and adults of any species Any tree species type combination to which it is applied must also have a light behavior applied You can use either the diam with auto height or diam only version Browsed relative growth behavior This behavior simulates herbivory by allowing trees to grow at different rates when browsed versus unbrowsed Parameters for this behavior Parameter name Description Asymptotic eee Dance Crain Asymptote of the Michaelis Menton growth function at high light function term A below A Slope of Growth Slope of the Michaelis Menton growth function at zero light function Response S term S below Relative Michaelis Menton Growth The exponent to be used with diameter when calculating relative growth Diameter Exponent Browsee sympioue Asymptote of the Michaelis Menton growth function at high light when a Diameter Growth plant has been browsed A Browsed Slope of Slope of the Michaelis Menton growth function at zero light when a Growth Response S plant has been browsed Browsed Diameter The diameter exponent for growth when a plant has been browsed Exponent How it wor
148. croll around the map in each of the four directions by clicking the arrow buttons surrounding the map Grid maps Maps are available for almost any kind of grid value The values are shown in grayscale Maps of boolean values true false will be displayed as black false and white true any other kind of numerical value allows you to adjust the grayscale for best viewing with the controls to the left of the map e Min brightness the darkest color that shows up on the map as a value between 0 and 255 This defaults to pure black value of 0 e Min value the minimum grid value where the grayscale starts Any grid values below this value will show up the min brightness color This defaults to the smallest value for the map e Knee brightness the color that corresponds to the knee value as a value between 0 and 255 The knee brightness defaults to gray halfway between black and white e Knee value the grid value corresponding to the knee brightness color This defaults to halfway between the minimum and maximum grid values If the map does not show a lot of contrast this may be because the values are not evenly distributed between the minimum and the maximum grid values If the map is too dark set the knee value lower if it s too light set it higher e Max brightness the lightest color that shows up on the map as a value between 0 and 255 This defaults to pure white value of 255 e Max value the maximum grid value where th
149. cutable How often to harvest in years How often SORTIE will perform the harvest process This number must be a positive integer value Behavior currently assigned to This is the tree types and species to which the harvest interface behavior are applied Only these trees will be written to the text file that is passed to the executable Use the Edit button to add or remove from the list File columns The columns in the text files written by both SORTIE and the executable in the order that they will appear The text in this list matches the text in the column headers Parameters file for batch run optional If you want SORTIE to manage input files for the executable when in SORTIE batch mode this is the full path and filename of the file that contains the executable s input parameters for each run in the entire batch Single run parameters file for batch run optional If you want SORTIE to manage input files for the executable when in SORTIE batch mode this is the full path and filename of the file that SORTIE will write with the executable s input parameters for a single run in the batch Arguments to pass to the executable optional SORTIE will pass this string value to the executable when launching it Tree update file that the executable will write If extra tree data members have been created for the executable to control this is the full path and filename of the file the executable will write with updates to these data memb
150. d PR Height The tree height threshold in meters between deterministic and stochastic Threshold for growth Stochastic Growth m PR Mean DBH cm for Stochastic Growth The mean for DBH values in cm when a tree uses stochastic growth This is the mean of the DBH value NOT the amount of growth PR DBH Standard Standard deviation for DBH values when a tree uses stochastic growth Deviation for This is the standard deviation of the DBH value NOT the amount of Stochastic Growth growth How it works The divide between the two growth functions is defined in the PR Height Threshold for Stochastic Growth m parameter Trees shorter than this use the following function Y A exp B Height Diam where e Y diameter growth for the timestep in cm e a PR a Parameter for Deterministic Growth parameter e b PR b Parameter for Deterministic Growth parameter e Height tree height in cm AFTER height growth in the current timestep e diam diameter of the tree at which to apply growth before growth in cm Above the height cutoff trees are assigned random diameters drawn from a normal distribution The normal distribution is defined by the PR Mean DBH cm for Stochastic Growth and PR DBH Standard Deviation for Stochastic Growth parameters and represents the distribution of DBH values NOT growth values The amount of growth for a tree is Y D D where Y is the amount of growth D is the new diameter
151. d This behavior can be combined with other mortality behaviors but for best results it should be the first one to occur BC mortality BC mortality is a growth based mortality behavior Trees killed by this behavior will have a mortality reason code of natural Parameters for this behavior Parameter name Description Light Dependent Mortality Light dependent mortality Mortality at Zero Mortality rate at zero growth Growth y 8 How it works The BC mortality model evaluates the following function to determine the probability of a tree s mortality y aa y ma _ Tm le me jl e Ml Je where e mis the probability of mortality e Tis the number of years per timestep e mis the Mortality at Zero Growth parameter e mz is the Light Dependent Mortality parameter e Gis amount of radial growth in mm yr added to the tree s diameter during T BC mortality is described in Kobe and Coates 1997 How to apply it This behavior can be applied to seedlings saplings and adults of any species Any tree species type combination to which it is applied must also have a growth behavior applied Browsed Stochastic Mortality This simulates the effects of herbivory by allowing different background mortality rates for browsed and unbrowsed trees Trees killed by this behavior will have a mortality reason code of natural Parameters for this behavior Parameter name Description Bache oud The proportion of trees that die
152. d Years parameter e dis the Storm Storm Cyclicity Sine Curve d parameter which controls the sine curve s amplitude e fis the Storm Storm Cyclicity Sine Curve f parameter which controls the sine curve s frequency e gis the Storm Storm Cyclicity Sine Curve g parameter which controls where on the sine curve storms start occurring e mis the Storm Storm Cyclicity Trend Function Slope m parameter e iis the Storm Storm Cyclicity Trend Function Intercept i parameter To turn off all cyclicity and use constant storm probabilities set Storm Storm Cyclicity Sine Curve d to 0 Storm Storm Cyclicity Trend Function Slope m to 0 and Storm Storm Cyclicity Trend Function Intercept i to 1 The other values are unimportant To use only the sine portion with no trend line set both Storm Storm Cyclicity Trend Function Slope m and Storm Storm Cyclicity Trend Function Intercept i to 0 To use only the trend portion set Storm Storm Cyclicity Sine Curve d to 0 To decide whether storms occur the behavior compares a random number to the annual probability of each storm severity class For timesteps that are longer than one year the behavior repeats the random number test for each year in the timestep This process is repeated for each storm severity class separately This means that multiple storms can occur in a single timestep and if the timestep is longer than one year there can be multiple storms in the same severity cla
153. d absolute data types also include a total across species For a definition of the different tree types see the Tree life history stages topic You can define subplots within the plot to track separately Output files are saved as tab delimited text files with a out extension You can open them in almost any spreadsheet or word processing program There is a column for each species for each data type Each timestep is one row If you have defined subplots there is a row for each subplot for each timestep You can view graphs of summary output files using SORTIE s data visualization functions See the Loading and displaying data from an output file topic Tab delimited tree maps You can use tab delimited tree maps to create your own tree map data You can save files of this type in many programs particularly spreadsheet programs like Microsoft Excel You can use these maps to create tree initial conditions Files must be in plain text with a txt extension Tree map format Here is an example of a tree map os Jozi ape sceana fo2 o 9 31396 14 82 The first six columns are required and must be in that order The first row is column headers Each subsequent row is the data for one tree Trees can appear in any order There is no limit to the number of trees The first two columns are the X and Y coordinates of the tree In the SORTIE ND coordinate system the origin is at the southwest corner of the plot X incre
154. d distribution this is the clumping parameter of the function in seeds per m If you have not chosen that PDFs then this parameter is not required If you have chosen the normal or lognormal probability distribution functions for Seed distribution this is the standard deviation of the function in seeds per m If you have not chosen these PDFs then this parameter is not required The annual STR value Standardized Total Recruits or all seeds produced by a 30 cm DBH tree in one year for stumps Stumps use the same probability distribution function as the live members of their species Only required if a behavior is being applied to stumps The annual STR value Standardized Total Recruits or all seeds produced by a 30 cm DBH tree in one year for the Weibull function under canopy conditions see equation below This is only required if the canopy probability distribution function is Weibull The for the Weibull function under canopy conditions see equation below This is only required if the canopy probability distribution function is Weibull Weibull Canopy Dispersal Weibull Canopy Theta Weibull Gap Annual STR Weibull Gap Beta Weibull Gap Dispersal Weibull Gap Theta How it works The dispersal value for the Weibull function under canopy conditions or under non masting conditions in the case of Masting spatial disperse see equation below This is only required if the canopy probability distributio
155. d output Subplots in output Setting up output o Using output as input to a new run Viewing output o Loading and displaying data from an output file o Extracting chart data into text format o Batch extracting chart data into text format o Viewing output data while a run is still in progress Output chart types o Line graphs o Histograms o Tree map o Grid maps o Tables Starting and managing a run Batching Files in SORTIE ND o Parameter files o Detailed output files o Summary output files o Tab delimited tree map files The SORTIE ND menu o File menu Batch setup window o Edit menu Parameters window Harvest interface window Schedule storms window Tree population set allometry functions window Tree population edit species list window Tree population edit initial density size classes window Tree population manage tree maps window Grid setup window Grid value edit window Model flow window Current run behaviors window Tree behavior edit window Tree assignments window Episodic events window Edit harvest window Edit mortality episode window Edit planting window o Oo Qa 6 0 Edit harvest interface window Edit diameter at 10 cm window Output options window Setup detailed output file window Setup tree save options window Setup grid save options window Summary output file setup window Edit subplots window
156. da parameter Tree fall theta parameter Probability of a snag that did not fall moving from live killed this timestep to decay class 1 Snag Decay Class Dynamics Live To Class 2 Prob 0 1 Snag Decay Class Dynamics Live To Class 3 Prob 0 1 Snag Decay Class Dynamics Live To Class 4 Prob 0 1 Snag Decay Class Dynamics Live To Class 5 Prob 0 1 Snag Decay Class Dynamics Class 1 To Class 1 Prob 0 1 Snag Decay Class Dynamics Class 1 To Class 2 Prob 0 1 Snag Decay Class Dynamics Class 1 To Class 3 Prob 0 1 Snag Decay Class Dynamics Class 1 To Class 4 Prob 0 1 Snag Decay Class Dynamics Class 1 To Class 5 Prob 0 1 Snag Decay Class Dynamics Class 2 To Class 2 Prob 0 1 Snag Decay Class Dynamics Class 2 To Class 3 Prob 0 1 Snag Decay Class Dynamics Class 2 To Class 4 Prob 0 1 Snag Decay Class Probability of a snag that did not fall moving from live killed this timestep to decay class 2 Probability of a snag that did not fall moving from live killed this timestep to decay class 3 Probability of a snag that did not fall moving from live killed this timestep to decay class 4 Probability of a snag that did not fall moving from live killed this timestep to decay class 5 Probability of a snag that did not fall remaining in decay class 1 Probability of a snag that did not fall moving from decay class 1 to decay class 2 Probability of a snag that did not fall movi
157. de Effect of shade for height growth Lognormal Height Growth Increment at Diam 36 in cm yr a Lognormal Height Shape Parameter b Annual growth increment at diameter 36 in cm yr for height growth Shape parameter for height growth How it works This behavior calculates annual diameter or height increases as 100 _ if infdiam 36 0 3 arre iv Fe b x Hh r F 2 sis where e Y amount of diameter increase in mm or the amount of height increase in cm e a Lognormal Diam Growth Increment at Diam 36 in mm yr a parameter for diameter growth or the Lognormal Height Growth Increment at Diam 36 in cm yr a parameter for height growth e b Lognormal Diam Shape Parameter b parameter for diameter growth or the Lognormal Height Shape Parameter b parameter for height growth e c Lognormal Diam Effect of Shade c parameter for diameter growth or the Lognormal Height Effect of Shade c parameter for height growth e GLI global light index as a percentage between 0 and 100 calculated by a light behavior e diam diameter diameter at 10 cm for seedlings and saplings DBH for adults For diameter growth Assume that the number of years per timestep is X In order to find the total amount of diameter increase for a timestep the lognormal growth equation is calculated X times with the diameter incremented by the amount of diameter increase for t
158. depth and radius relationships This calculates crown dimensions as a function of tree size and local crowding The equations are the same for crown depth and crown radius but they each have separate parameters NCI Crown Depth Parameters Parameter name NCI Crown Depth Alpha NCI Crown Depth Beta NCI Crown Depth Crowding Effect n NCI Crown Depth Gamma NCI Crown Depth Lambda for Species X Neighbors NCI Crown Depth Max Potential Depth m NCI Crown Depth Max Search Distance for Neighbors m NCI Crown Depth Minimum Neighbor DBH cm NCI Crown Depth Size Effect d Description NCI function exponent NCI function exponent Crowding effect exponent NCI function exponent The competitive effect of neighbors of species X The maximum possible value for crown depth in m The maximum distance in m at which a neighboring tree has competitive effects on a target tree The minimum DBH for trees of that species to compete as neighbors Values are needed for all species Size effect function exponent NCI Crown Radius Parameters Parameter name NCI Crown Radius Alpha NCI Crown Radius Beta NCI Crown Radius Crowding Effect n NCI Crown Radius Gamma Description NCI function exponent NCI function exponent Crowding effect exponent NCI function exponent NCI Crown Radius Lambda for Species The competitive effect of neighbors of spe
159. dex is stored in the grid Substrate Favorability The behavior then goes through each grid cell in the Dispersed Seeds grid and assesses the survival for the seeds of those species to which it applies This behavior starts by giving each seed a random temporary location within the Dispersed Seeds grid cell Then it retrieves the substrate favorability at that point from the Substrate Favorability grid It then compares a random number to the substrate favorability to determine whether the seed lives This method ensures that we can assess substrate favorabilities correctly when the Dispersed Seeds and Substrate grids have different grid cell resolutions Once this process is complete the number of surviving seeds for each species is assigned back to the Dispersed Seeds grid How to apply it This behavior may be applied to seeds of any species A species to which this is applied must also have the Gap spatial disperse behavior applied Also the Substrate behavior must be used in the run Planting behaviors Planting Planting directly creates new seedlings When you create a new planting you specify the timestep in which to plant the species to plant and the relative amount of each whether new seedling spacing is gridded or random how many seedlings to plant and how far apart if gridded and the area of the plot to plant You can create as many plantings as you like How it works Planting keeps track of planting events to per
160. disappears The actual amount of tree harvest may not be exactly what was specified since the Harvest behavior can t remove part of a tree to get the numbers right The behavior stores how much it actually cut each timestep in the Harvest Results grid To optimize the accuracy of the Harvest behavior use larger cut ranges and high proportions of the plot area to make sure there is a big pool of trees to choose from How to apply it To add harvesting to a SORTIE run use the Edit Episodic Events Window Harvest interface The harvesting interface allows SORTIE to work directly with another program SORTIE tells the other program what trees are eligible for harvesting and the other program replies with its choices This lets users write code for harvesting without having to modify SORTIE itself Warning this link between SORTIE and another program is inefficient It may be very slow when there are large numbers of trees It is for convenience not speed Trees removed by this behavior will have a mortality reason code of harvest How it works You set up the Harvest Interface behavior using the Edit gt Harvest Interface window Parameters in this documentation are defined by their names on that screen You either create or find a separate program an executable that reads a text file of trees makes decisions about which to kill then writes those trees to kill to another text file You tell SORTIE where to find this executa
161. distribute seeds in gap conditions The annual STR value Standardized Total Recruits or all seeds produced by a 30 cm DBH tree in one year for the lognormal function under canopy conditions see equation below This is only required if the canopy probability distribution function is lognormal The for the lognormal function under canopy conditions see equation below This is only required if the canopy probability distribution function is lognormal The mean of the lognormal function under canopy conditions or under non masting conditions in the case of Masting spatial disperse see equation below This is only required if the canopy probability distribution function is lognormal The standard deviation of the lognormal function under canopy conditions or under non masting conditions in the case of Masting spatial disperse see equation below This is only required if the canopy probability distribution function is lognormal The annual STR value Standardized Total Recruits or all seeds produced by a 30 cm DBH tree in one year for the lognormal function under gap conditions see equation below This is only required if the gap probability distribution function is lognormal The for the lognormal function under gap conditions see equation below This is only required if the gap probability distribution function is lognormal The mean of the lognormal function under gap conditions see equation below This is only re
162. divided by X Then the logistic growth equation is calculated X times with the diameter incremented by the amount of diameter increase per timestep each time The total height increment is the sum of the X individual height increments How to apply it This behavior can be applied to seedlings saplings and adults of any species Any tree species type combination to which it is applied must also have a light behavior applied You can choose either a diam with auto height diam only or height only version Logistic growth This behavior does either diameter or height growth as a function of GLI Parameters for this behavior Parameter name Description Logistic Asymptotic Diam Growth Full Light in mm yr a Asymptotic annual growth at full light in mm yr for diameter growth Logistic Diam Shape Param 1 b Shape parameter 1 for diameter growth Logistic Diam Shae kaan Shape parameter 2 for diameter growth Logistic Asymptotic annual growth at full light in cm yr for height growth Asymptotic Height Growth Full Light in cm yr a Logistic Height Shape Param 1 b Shape parameter 1 for height growth Logistic Height Shape Par Shape parameter 2 for height growth How it works The amount of diameter increase is calculated as a y xT 7 Pr Y b fe GLI o L l g where e Y amount of diameter increase in mm or the amount of height increase in cm e a Logistic
163. dling Linear The slope of the seedling linear function for DBH and height Function Slope The linear diam height function is where height a b diam e height is tree height in m e ais the appropriate linear intercept parameter either Adult Linear Function Intercept Sapling Linear Function Intercept or Seedling Linear Function Intercept e bis the appropriate linear slope parameter either Adult Linear Function Slope Sapling Linear Function Slope or Seedling Linear Function Slope e diam is DBH in cm for saplings and adults or diamjo in cm for seedlings The reverse linear diameter height relationship The reverse linear diameter height relationship is the same for all life history stages but each stage can use a different set of parameter values The name comes from the fact that it is almost the same as the linear function but with height and diameter switched In other words in the linear function height is a linear function of diameter In the reverse linear function diameter is a linear function of height Parameters Parameter name Maximum Tree Height in meters Adult Reverse Linear Function Intercept Adult Reverse Linear Function Slope Sapling Reverse Linear Function Intercept Sapling Reverse Linear Function Description The maximum tree height for a species in meters No tree no matter what allometric function it uses is allowed to get taller than this Used by all species T
164. dow will list the Partitioned Biomass grid You can then view the contents of this grid as a table using SORTIE s data visualization system Ripley s K Calculator This behavior calculates the Ripley s K function for all trees in the plot as well as for the members of each species Parameters for this behavior Parameter name Description lt th Ripley s K Maximum Distance The maximum distance out to which to calculate K values m Ripley s K Distance The distance increments at which K will be calculated Smaller Increment m increments mean a smoother curve but also more processing time How it works The Ripley s K function is a measure of the way trees are spatially distributed across the plot K values are calculated repeatedly for a succession of distances out to a maximum giving a curve The Ripley s K statistic for a given distance t is calculated as K n where e K t is the K value at distance t e Ais the plot area in square meters e Xis the number of pairs of trees in the plot less than t meters apart e nis the total number of trees in the plot The size of the distance increment is given in the Ripley s K Distance Increment m parameter The maximum distance out to which to calculate K is given in the Ripley s K Maximum Distance m parameter Most Ripley s K formulas come with a term for edge correction which is not needed in SORTIE ND as the plot has no edges See the SORTIE ND Plot topic for
165. dstorm Storm Cyclicity Sine Curve 8 Windstorm Storm Cyclicity Trend Function Intercept i Windstorm Storm Cyclicity Trend Function Slope m Windstorm Storm Intensity Coefficient c Windstorm Timestep to Start Storms The severity of storms with a 640 year return interval as a value between 0 no mortality and 1 complete devastation The severity of storms with a 1280 year return interval as a value between 0 no mortality and 1 complete devastation The severity of storms with a 2560 year return interval as a value between 0 no mortality and 1 complete devastation Parameter that controls the cyclicity of storm frequency For no cyclicity set this value to 0 This value is part of the sine curve term and controls the sine amplitude Parameter that controls the cyclicity of storm frequency This value is part of the sine curve term and controls the sine frequency Parameter that controls the cyclicity of storm frequency This value is part of the sine curve term and controls where on the sine curve storms start occurring Parameter that controls the trend of cyclicity of storm frequency This value is part of the trend term and is the intercept of the function controlling the increase or decrease of overall frequency cycling For no cyclicity at all set this term to 1 For no trend in cyclicity set this term to 0 Parameter that controls the trend of cyclicity of storm frequency This valu
166. duced STR stochasticity The STR value may be randomized each timestep Use the Masting Disperse STR Draw PDF parameter to choose from a normal or lognormal probability distribution You can then set the mean and standard deviations for each species which are different in masting and non masting timesteps You can also leave the STR value deterministic in which case the mean STR value is used directly If you choose to use a stochastic STR the STR value can be generated once per species per timestep or once per tree per timestep If the value is generated once per species all individuals of that species use the same STR value that timestep Once the behavior has decided whether masting occurs and what the STR values are then disperse proceeds exactly as described in the Non gap spatial disperse behavior How to apply it Apply this behavior to all trees of at least the minimum reproductive age for your chosen species If the minimum reproductive age is less than the Minimum adult DBH be sure to apply this behavior to saplings as well as adults Temperature dependent neighborhood disperse behavior This behavior calculates seed density based on annual mean temperature and the basal area of neighborhood adults Parameters for this behavior Parameter name Description Minimum DBH for The minimum DBH at which a tree can reproduce This value does not Reproduction incm have to match the Minimum adult DBH The distribution me
167. e This behavior can perform harvest very flexibly depending on the parameters used The behavior itself decides when harvests will occur and how much to cut based on total plot adult biomass then chooses trees to cut with the help of a preference algorithm Trees removed by this behavior will have a mortality reason code of harvest Parameters for this behavior Parameter name Description Gen Harvest Regime RE A in the function that calculates cut preference of individual trees Cut Preference A Gen Harvest Regime SAR B in the function that calculates cut preference of individual trees Cut Preference B Gen Harvest Regime acai C in the function that calculates cut preference of individual trees Cut Preference C Gen Harvest Regime Cut Preference Alpha in the function that calculates cut preference of individual trees Alpha Gen Harvest Regime Cut Preference Beta in the function that calculates cut preference of individual trees Beta Gen Harvest Regime Cut Preference Beta in the function that calculates cut preference of individual trees Beta Gen Harvest Regime Cut Preference Gamma in the function that calculates cut preference of individual trees Gamma Gen Harvest Regime Cut Preference Mu Gen Harvest Regime Gamma Scale Parameter Gen Harvest Regime Harvest Probability Ae Gen Harvest Regime Harvest Probability B Gen Harvest Regime Harvest Probability M Gen Harvest Re
168. e practical Since the length of the run depends on many other factors in addition to plot size you may need to tweak plot size a bit until you ve found a good value The SORTIE Coordinate System SORTIE uses X Y coordinates starting at 0 0 which is at the southwest corner of the plot Positive Y coordinates increase to the north positive X coordinates increase to the east There are no negative plot location values The coordinate values are in meters Plot shape the torus forest When you are working with the plot you think of it as a rectangle In fact it is a torus donut Each edge connects to the edge on the opposite side To picture this imagine a sheet of paper Roll the sheet of paper into a tube then bend the tube around so its ends meet This is what the SORTIE forest looks like The purpose of this shape is to eliminate edges in the forest Trees near the edges of the plot torus see trees on the far edge as being right next to them The torus shape is what controls the minimum plot size in SORTIE Some processes in SORTIE require searching a portion of the plot for instance to find all the trees in a given circle If that search took place over too great an area compared to the size of the plot it would run the risk of searching around the world It would work its way around the torus and back to and past the place it started finding the same trees multiple times Plot climate and location
169. e 6 0 SORTIE tree map files If you have a tree map file from before SORTIE 6 0 you can simply copy and paste the columns with the following exception The old version of SORTIE has reversed coordinate axes So paste the old X values into the new Y column and vice versa Last updated File menu New parameter file Use this option to be led through the first steps of creating a new parameter file from scratch You start with the Edit species list window then move to the Edit simulation flow window Once you have completed these steps you can save your new file and then enter parameters for it For more on creating a new parameter file see Creating a parameter file New batch file Use this option to create a new batch file You can read more about batch runs here This option opens the batch file setup window Open file Use this option to open parameter batch and data files in SORTIE ND You can open parameter files this way and then use this option again to add data from detailed output files to the run Save parameter file Use this option to save a parameter file You have to specify the filename each time The filename of the file currently loaded is visible in the bottom left corner of the main SORTIE window You can save a parameter file even if it is not complete or valid If this is the case you will get a warning message that tells you of the file s problem and asks you if you want to continue with the save Clicking y
170. e chosen biomass equation requires a correction factor to be multiplied by the result The paper above outlines 9 different biomass equations in Table 6 as follows DOO r biomass a b dia c dia biomass a b dia c dia arg E dia a biomass a exp b c In dia d dia T biomas a b dia 9 dia 4 8 1og100 biomass a b log O dia 9 In biomass In a b In dia In all equations dia is DBH You choose the equation ID that you wish to use for each species There are many different published parameters using the equation forms above which use a range of different units Thus you specify what units dia that is DBH is in and what units of biomass the equation is expected to produce The possible DBH units are millimeters mm centimeters cm and inches in the possible biomass units are grams g kilograms kg and pounds lb This behavior handles all unit conversions so that biomass is appropriately calculated The final biomass values are reported in metric tons Mg For those equations that calculate log10 log100 or In biomass some papers specify a correction factor to remove bias that may be introduced when biomass is calculated If you wish you may use such a correction factor Set the value of the Dimension Analysis Use Correction Factor parameter to true then specify the appropriate correction factor in the Dimension Analysis Correcti
171. e grayscale ends Any grid values above this value will show up the max brightness color This defaults to the largest value for the map The color lightness increases linearly with map value from the minimum to the knee and linearly again from the knee to the maximum Once you have adjusted your display values click the Update button Updating can be slow If you can t see a difference try minimizing and then restoring the chart window this guarantees that it has refreshed Tables There are several different kinds of tables available in SORTIE The only thing they have in common is their format Plot tables An overview table is available for both summary output files and detailed output files This table shows basal area and density information for each tree life history stage In the case of a summary output file only the data that you saved in the summary output file setup window are shown For a detailed output file data is shown for each tree species and life history stage for which you have saved at least DBH or diameter at 10 cm for seedlings If you know you want to look at this table type you should save a summary output file The graphing performance will be significantly better Stand tables When you save DBH data and optionally height you can also view stand tables These show density or basal area data broken out by DBH size classes that you define When you first choose a stand table you will be given a windo
172. e in the equation used to determine the mortality of an individual tree as a result of a storm Parameter that controls the cyclicity of storm frequency This value cannot be 0 The severity of storms with a 1 year return interval as a value between 0 no mortality and 1 complete devastation The severity of storms with a 5 year return interval as a value between 0 no mortality and 1 complete devastation The severity of storms with a 10 year return interval as a value between 0 no mortality and 1 complete devastation The severity of storms with a 20 year return interval as a value between 0 no mortality and 1 complete devastation The severity of storms with a 40 year return interval as a value between 0 no mortality and 1 complete devastation The severity of storms with a 80 year return interval as a value between 0 no mortality and 1 complete devastation The severity of storms with a 160 year return interval as a value between 0 no mortality and 1 complete devastation The severity of storms with a 320 year return interval as a value between 0 no mortality and 1 complete devastation Year Return Interval Storm Windstorm Severity for 640 Year Return Interval Storm Windstorm Severity for 1280 Year Return Interval Storm Windstorm Severity for 2560 Year Return Interval Storm Windstorm Storm Cyclicity Sine Curve d Windstorm Storm Cyclicity Sine Curve f Win
173. e increment parameter specifies radial growth the behavior makes all necessary conversions How to apply it This behavior can be applied to seedlings saplings and adults of any species Any tree species type combination to which it is applied must also have a light behavior applied You can use either the diam with auto height or diam only version Absolute growth limited to basal area increment How it works This behavior calculates an amount of diameter growth according to the absolute growth equation Growth is limited to a maximum of a constant basal area increment The amount of diameter increase is calculated by dividing the annual basal area increment of the tree s species by the diameter of the tree The increment is calculated as described in the Constant basal area growth behavior How to apply it This behavior can be applied to seedlings saplings and adults of any species Any tree species type combination to which it is applied must also have a light behavior applied You can use either the diam with auto height or diam only version Non limited absolute growth diam with auto height How it works The amount of diameter increase returned by the absolute growth equation is applied to the tree How to apply it This behavior can be applied to seedlings saplings and adults of any species Any tree species type combination to which it is applied must also have a light behavior applied You can use either the diam with
174. e individuals and making sure specific species targets are met When selecting trees for harvesting Competition Harvest removes the individuals that have the greatest competitive effects on their neighbors The neighbors of an individual are all sapling and adult trees within the radius specified in the Competition Harvest Max Radius of Competitive Effects m parameter Seedlings snags and dead trees never count as neighbors The competitive effect COE of tree i on the N neighbors surrounding it is l N y DBH k dist where e Cis the Competition Harvest C parameter for the species of neighbor j e Dis the Competition Harvest D parameter for the species of neighbor j e ais the Competition Harvest DBH Effect of Targets alpha parameter for the species of neighbor j e fis the Competition Harvest Distance Effect of Targets beta parameter for the species of neighbor j e yis the Competition Harvest Size Sensitivity gamma parameter for the species of neighbor j e DBH is the DBH in cm of neighbor j e Ais the Competition Harvest Species i Target Lambda parameter for the species of neighbor j where Species i is the target s species e DBH is the DBH in cm of target i e dist is the distance between target and neighbor in meters Competition Harvest removes the tree with the highest COE value in the plot then updates the COE of each tree in the vicinity so that the removed tree is no longer a neighbor This process
175. e is part of the trend term and is the slope at which frequency cycling increases or decreases For no cyclicity or no trend in cyclicity set this term to 0 The c value in the equation used to determine the mortality of an individual tree as a result of a storm The first timestep that storms are allowed to occur How it works Using the parameters you provide a general shape of storm intensity SORTIE then decides which storms occur each timestep and which trees die as a result This behavior defines 11 storm return intervals 1 5 10 20 40 80 160 320 640 1280 and 2560 years Each has a set annual probability for example an 80 year return interval storm has an annual probability of 1 80 or 0 0125 For each year of each timestep for each return interval SORTIE generates a random number to decide whether a storm of that return interval will occur This means that there can be multiple storms in a timestep or no storms at all In a multi year timestep a storm of a given return interval can happen more than once You give each return interval a storm severity value between 0 and 1 These are defined in the Windstorm Severity for X Year Return Interval Storm parameters A severity of 0 means no tree mortality a severity of 1 approaches 100 mortality The overall frequency of storms can remain constant or it can change through time It has been reported in Goldenburg et al 2001 that storm activity in the North Atlantic
176. e mean in a negative binomial probability distribution function You must then supply a clumping parameter If you have chosen the negative binomial probability distribution Parameter Neg function for Seed distribution this is the clumping parameter of the Binomial function in seeds per m If you have not chosen that PDFs then this parameter is not required If you have chosen the normal or lognormal probability distribution functions for Seed distribution this is the standard deviation of the function in seeds per m If you have not chosen these PDFs then this parameter is not required Seed Dist Std Deviation Normal or Lognormal How it works Deciding when to mast Each timestep each species may mast or not Mast is determined by making a random draw from a binomial distribution with the p value for the distribution set using the Mast NS Disperse Binomial P Mast Chance parameter Masting decisions are made completely independently for each species except in the case of masting groups more on those later The number of seeds in seeds per square meter is then drawn from a second probability distribution The distribution choices are normal and inverse Gaussian A species can use different distributions for mast and non mast timesteps You choose the distributions using the Mast NS Disperse PDF Masting Conditions and Mast NS Disperse PDF Non Masting Conditions parameters You then set up the values f
177. e ms is the probability of mortality e a Senescence Mortality Alpha parameter and f Senescence Mortality Beta parameter control the magnitude of the uptick e DBH is the tree s DBH in cm e DBH is the DBH at Onset of Senescence in cm parameter The probability is compared to a random number to determine whether the individual tree will die How to apply it Senescence may be applied to saplings and adults of any species It cannot be applied to seedlings Stochastic Bi Level Mortality This behavior applies a constant rate of mortality to trees with different rates for high light and low light conditions There are two versions designed to work with different behaviors that calculate light levels Stochastic Bi Level Mortality Storm Light and Stochastic bi level mortality GLI Trees killed by this behavior will have a mortality reason code of natural Parameters for this behavior Parameter name Description Stochastic Bi Level High Light Mortality Probability 0 1 The annual probability of mortality under high light conditions as a proportion between 0 and 1 Stochastic Bi Level High Light Mortality Threshold The threshold between low light and high light mortality rates as a value between 0 and 100 Stochastic Bi Level Low Light Mortality Probability 0 1 The annual probability of mortality under low light conditions as a proportion between 0 and 1 How it works In the version of the behav
178. e not including storms in your run The coefficient in the shading effect equation Set this value to 0 if you do not wish to use shading The exponent in the shading effect equation If you set the NCI Shading Effect Coefficient m parameter to 0 this value is ignored The mode of the size effect curve NCI Size Li The variance of the size effect curve Variance in cm Xb NCI Size Sensitivity The sensitivity of a tree s growth rate to its DBH Set this to O to remove to NCI gamma the DBH term altogether Include Snags in Whether or not to include snags when finding competitive neighbors for NCI Calculations NCI How it works For a tree the amount of growth per year is calculated as Growth Max Growth Size Effect Shading Effect Crowding Effect Damage Effect Max Growth is the maximum diameter growth the tree can attain in cm yr entered in the NCI Maximum Potential Growth cm yr parameter Size Effect Shading Effect Crowding Effect and Damage Effect are all optional factors which act to reduce the maximum growth rate and will vary depending on the conditions a tree is in Each of these effects is a value between 0 and 1 Size Effect is calculated as 0 5 SES P Xb In 2B m where e DBH 1s of the target tree in cm e Xo is the NCI Size Effect Mode in cm X0 parameter e X is the NCI Size Effect Variance in cm Xb Shading Effect is calculated as ShE e where e mis the NCI
179. e peli psf 2f er os foo fra faa a2 as How to apply it Apply this behavior to saplings adults or snags of any species and enter parameters in the Parameter edit window This behavior does not automatically create output Once you have added this behavior to your run the Detailed output setup window for trees will have a tree data member called Tree Bole Volume Add this to your detailed output file to output volume in cubic feet You can then view charts and graphs with the resulting volume data using data visualization on your detailed output file Tree Age This behavior calculates tree age How it works The age of a tree in years is kept in a tree data member called Tree Age and updated each timestep If this behavior is after the establishment behaviors new seedlings will have an age equal to one timestep on the timestep they are created Some trees can be created at the beginning of a run either in a tree map or to provide a specified initial tree density These trees are given an age of 10000 so they can be easily distinguished from trees created during a run If a tree map is provided and the trees are specifically given an age in the map that age is kept and they are not re assigned an age of 10000 This behavior may not be applied to snags since they have a different age counter How to apply it Apply this behavior to the trees for which you want to track age You can then save the Tree Age data in a de
180. e that SORTIE will write on the Edit Harvest Interface window SORTIE does not care what the filename nor file extension is The file is tab delimited text It has the following format Line 1 two columns Current timestep total number of timesteps Line 2 column names 6 n columns X Y Species Type Diam Height Subsequent lines 6 n columns one line per tree X Y species number type number DBH diam10 height Species is given as a number from 0 to x 1 where x is the number of species The number counts the species in the order in which they are listed in the parameter file which is the same as the order they are listed in the Edit Species window Type is given as a number as well The type numbers are 1 Seedling 2 Sapling 3 Adult 4 Stump 5 Snag Stumps are not available for harvesting The Diam value is diameter at 10 cm if the tree type is seedling and DBH in all other cases Both of these values are in cm The Height value is the height of the tree in meters The represents additional columns that you can ask SORTIE to include You set this up using the File columns section of the Edit Harvest Interface window You can choose any other tree data member that applies to all of the kinds of trees to which the harvest interface is applied including new ones that you add The list of tree data members depends on the other behaviors in the run The column header matches the inte
181. e the storm frequency over time using either a sinusoidal pattern a constant linear change or both together In the figure below curve 1 is a basic sine wave Curve 2 has a sinusoidal pattern plus an upwards trend 4 e Curve 1 Curve 2 kd he J k A N K a n gt ky j A 2 a ie 7 x r st K N N A N A id EN a 1 r oo tk a i P4 es ka s 8 T T A a T i 1 Mi 1 2 J 4 5 The actual probability of an individual storm that takes place in a storm regime with a cyclical frequency is P F P F d sin m x 8 2f mx iJ Note that the new probability is a baseline probability P F multiplied by a value that adjusts the probability according to where the model is at the given time in the frequency cycle The frequency cycle multiplier is itself made up of two terms added together The first term is the sine curve cycling and the second term is the overall trend upwards or downwards Terms in the equation e P F is this timestep s annual probability of a storm of the ith return interval adjusted according to the frequency cyclicity e P F is the baseline probability of a storm of the ith return interval that is the reciprocal of the values specified in the Return Interval for Severity Storm Class X parameters e x 4 t Sr where tis the number of years since the run started and Sr is the Storm Sea Surface Temperature Cyclicity Perio
182. e tree in cm e Xis the Relative Michaelis Menton Growth Height Exponent parameter If the timestep is more than one year long growth is recalculated for each year of the timestep increasing the height each time How to apply it This behavior can be applied to seedlings saplings and adults of any species Any tree species type combination to which it is applied must also have a light behavior and a diameter growth behavior applied Relative growth behaviors Several behaviors apply a relative growth version of the Michaelis Menton function Parameters for these behaviors Parameter name Adult Constant Area Growth in sq cm yr Adult Constant Radial Growth in mm yr Asymptotic Diameter Growth A Asymptotic Height Growth A Slope of Growth Response S Relative Michaelis Menton Growth Diameter Exponent Description The constant amount of basal area by which to increase a tree s basal area Applies to basal area increment limited behaviors The constant value by which to increase a tree s radius at breast height Applies to radial increment limited growth behaviors Asymptote of the Michaelis Menton growth function at high light function term A below for diameter growth Asymptote of the Michaelis Menton growth function at high light function term A for height growth Slope of the Michaelis Menton growth function at zero light function term S below The exponent to be used with diameter whe
183. e trees to which it is assigned The grid cells are the quadrats in this case this is a throwback to old SORTIE terminology Each grid cell in which there is a tree to which this behavior applies has a GLI value calculated at its center at a height that the user specifies All other trees to which this behavior applies that are in that same grid cell get that same GLI value This behavior saves having to calculate a different GLI value for each tree GLI values range from 0 no sun to 100 full sun For efficiency this behavior does not calculate the value of a grid cell if there are no trees in that cell In this case the light value of the cell is 1 To force it to always calculate all GLIs useful if you intend to save maps of the Quadrat GLI grid set the Quadrat GLI Always Calculate All GLIs parameter to true How to apply it This behavior may be applied to seedlings saplings and adults of any species Sail light For more on what the Sail Light index is and how it is calculated see here Parameter name Sail Light Maximum Shading Neighbor Distance in meters Sail Light Minimum Solar Angle in degrees Calculated Crown Depth Height of Fisheye Photo Beam Fraction of Description The radius in meters from a tree for which neighbors will be searched who can shade that tree The azimuth angle in degrees below which it is assumed trees will see no light When the shape of a tree s shading neighbors is
184. e used along with the detailed output file name to give the final name for each data file The directory that you specify is where all of the charts of this type will go You can put each chart in a different directory if you wish You can put any file extension on the end of the root or no extension at all Whatever extension you give will be added to each file name In addition to the file name root you may be prompted for other options required by the chart you have chosen You cannot create two different instances of the same chart even if you intend to use different options You can set up subsequent batch processes for each different set of options desired Click Finish to launch the batch extraction You ll get a progress bar telling you the amount of work completed Viewing output data while a run is still in progress You can view the output from a run as it progresses SORTIE will keep a set of open charts updated with the results of the latest timestep Here s how to use this feature Load your parameter file Make sure you have the output files set up the way you want Start the run so SORTIE has some output to display A simple way to do this is to click the Run one timestep button the one on the main window with two right facing triangles When SORTIE has completed the timestep the message bar at the bottom of the window will display a message indicating that the run has paused You can also run the model using Model gt
185. ears per timestep The absolute growth behaviors also take into account suppression status A tree is considered suppressed if its growth rate for the previous timestep falls below a certain threshold That threshold is the rate of growth at which X of juveniles die where X is a user settable parameter The threshold is calculated for each species by solving the BC mortality equation for G growth where m is the threshold growth rate A tree s suppression state is a multiplicative factor in its growth rate If a tree is not suppressed the suppression factor in the growth equation is set to 1 no effect on growth If the tree is suppressed the suppression factor is calculated as follows SF el 8 YLR d YLS where e SF is the suppression factor e gis the Length of Current Release Factor parameter e YLR is the length of the last or current period of release in years e dis the Length of Last Suppression Factor parameter e YLS is the length of the last or current period of suppression in years Details of this model are published in Wright et al 2000 Absolute growth limited to radial increment How it works This behavior calculates an amount of diameter growth according to the absolute growth equation Growth is limited to a maximum of the constant radial increment for the species of tree to which it is being applied The increment is calculated as described in the Constant radial growth behavior Note that th
186. eate juveniles in arun You may see strange behavior in your first timesteps if you re missing a whole life cycle stage in your tree population Tree data member list This is a list of the possible data that a tree can have You can save this data in a detailed output file by using the Setup tree save options window Not all data is always available Certain sets of behaviors require additional information about a tree One of the ways in which behaviors communicate with one another is by defining new pieces of data for trees and then setting and reading values for those data A piece of data created by a behavior is only attached to those tree species and tree types to which the behavior is applied Tree population always available The coordinate of the tree in meters on the X axis in the SORTIE plot Tree population always available The coordinate of the tree in meters on the Y axis in the SORTIE plot The diameter at breast height of a Tree tree in cm This does not apply to population seedlings always a S T Tree The tree s diameter at 10 cm Diameter at population always available Tree Height Height Float The tree s height in meters population always available The tree s crown radius in meters Note that this value is updated only on an as needed basis This means that the value may show up as 1 meaning that the tree s crown radius was not requested Tree Crown Cowi Ra
187. ed The proportion of plot substrate that is tip up mounds substrate when the run starts as a value between 0 and 1 If a map of substrate values is included in the parameter file see Grid initial conditions for information on how to do this then the map values will be used for the initial conditions and this number will be ignored For initial conditions the mean diameter of logs in the large size class in cm For initial conditions the mean diameter of logs in the small size class in cm The number of years that a substrate disturbance event has effect before it is deleted the lifetime of a substrate cohort After a partial cut harvest the mean diameter of logs in the large size class in cm This is not required if the Harvest behavior is not used After a partial cut harvest the mean diameter of logs in the small size class in cm This is not required if the Harvest behavior is not used The proportion of live trees entering each of the five decay classes The Entering Decay Class X 0 1 Prop Snags Entering Decay Class X 0 1 Scarified Soil Annual Decay Alpha Scarified Soil Annual Decay Beta Species Group Species Group X Large Class Y Clear Cut Log 0 1 Species Group X Small Class Y Clear Cut Log 0 1 Species Group X Large Class Y Gap Cut Log 0 1 Species Group X Small Class Y Gap Cut Log 0 1 Species Group X Large Class Y Initial Log Prop 0 1 Species Group X Sma
188. ed You can delay the introduction of windstorms into the run using the Windstorm Timestep to Start Storms parameter If this value is greater than 0 no storms will occur until that timestep is reached Information on what storms occurred during a run is saved in the Windstorm Results grid This grid lists how many storms occurred each timestep and the basal area and density killed of each species in that storm How to apply it Add this behavior to your run and apply it to saplings and or adults of any species If you wish to get results on storm events save the Windstorm Results grid data in a detailed output file You can then view the contents of this grid as a table using SORTIE s data visualization system Management behaviors Management behaviors help the process of forest management Behavior Description Tree Qualit Vigor Classifies trees according to vigor and stem quality Classifier Tree Quality Vigor Classifier The Tree Quality Vigor Classifier assigns trees to a classification system based on vigor and stem quality This classification can then be used as a criterion in other behaviors There are four classes 1 2 3 4 for deciduous species and two classes 5 6 for conifers The four classes used for deciduous species result from the combination of two possible vigor states and two stem quality levels For conifers only vigor is considered The two vigor status are vigorous and non vigorous where non vi
189. ed status There are three possible damage categories for a tree no damage medium damage and heavy damage Other behaviors can use the damage categories to determine what effects the storm damage had on a tree slow growth death etc Parameters for this behavior Parameter name Minimum DBH for Storm Damage in cm Number of Years Damaged Trees Take to Heal Storm Damage Intercept a for Medium Damage Storm Damage Intercept a for Heavy Damage Storm DBH Coefficient d Storm Intensity Coefficient b How it works Description The minimum DBH for trees that can be damaged or killed by storms Trees smaller than this are never damaged no matter what storms occur The number of years it takes a damaged tree to heal After this time it is considered undamaged The storm damage intercept parameter a for the equation calculating the probability of medium damage The storm damage intercept parameter a for the equation calculating the probability of heavy damage The storm DBH coefficient d for the equations calculating the probability of damage The storm intensity coefficient b for the equations calculating probability of damage The behavior Storm disturbance determines whether a storm has occurred When it does an individual tree can either get no damage medium damage or heavy damage The tree s probability of damage in a given damage category is where e iis the damage category ei
190. edation Note that if a seeds for species species is not subject to seed predation its value may show up here as zero x despite having seeds present Its seeds are not missing just ignored Proportion seeds eaten for species X Proportion of the seeds of species x eaten this timestep as a value between 0 and 1 Partitioned Biomass Grid This grid is created by the Partitioned DBH Biomass and Partitioned Palm Biomass behaviors This is where the amount of biomass is stored partitioned into leaf bole and branch if applicable biomass All data is stored raw no conversion to per hectare amounts The grid cell resolution is set to 8 m X 8 m You can change this to whatever you wish The grid is shared by the two behaviors mentioned above so changing it for one changes it for both Data in the grid Data member name Description Mg Leaf Biomass for species X Amount of leaf biomass for species X in Mg Mg Bole Biomass for species X Amount of bole biomass for species X in Mg Mg Branch Biomass for species X Amount of branch biomass for species X in Mg Mg Leaf Palm Biomass for species X Amount of palm leaf biomass for species X in Mg Mg Bole Palm Biomass for species X Amount of palm bole biomass for species X in Mg Planting Results Grid This grid is created by the Planting behavior This is where data on planting results is stored The data is stored raw no conversion to per hectare amounts The grid cell resolutio
191. ee It is subject to substrate dynamics snag formation or any other post mortality process being used in the run just like any other dead tree How to apply it This behavior can be applied to saplings and adults of any species The species to which it is applied are the substrate species not the establishing species It should be executed after mortality and before dead tree remover behaviors have been applied in each timestep Mortality utility behaviors This type of behavior performs cleanup by removing dead trees from memory at the appropriate time This function is very important if it did not occur then the model would slow exponentially as memory filled up and those behaviors that look at recently dead trees would start getting strange results Behavior Description Dead tree remover Removes dead trees from memory Snag dynamics behaviors Snag dynamics behaviors increase control over snag fall and decay Behavior Description ae Controls transitions among snag decay classes and snag falls There are two fall Tics models one that applies to trees that die in the current time step and may fall ASG without become a snag and one that applies to pre existing snags Snag Decay Class Dynamics This behavior controls transitions among snag decay classes and snag falls There are two fall models one that applies to trees that die in the current time step and may fall without become a snag and one that applies to pre exis
192. eighbor in m The amount of growth is in cm year For multi year timesteps the behavior will calculate total growth with a loop Each loop iteration will increment dio for one year For each year any portion of the growth equation with dio as a term is recalculated with the previous year s updated dio value NCI values are constant throughout this loop for neighbors only the djo at the start of the timestep is used The final total growth amount is added to the tree s dio How to apply it This behavior can be applied to seedlings and saplings of any species You can use either the diam with auto height or diam only version Lagged post harvest growth This behavior increments growth as a function of DBH and neighboring basal area and incorporates a lag period after harvesting during which trees acclimate to their post harvest growing conditions Parameters for this behavior Parameter name Description Post Harvest Growth DBH Growth The effect of DBH on growth Effect Post Harvest Growth _ DBH NCI Effect The effect of DBH on the neighborhood competition index Post Harvest Growth Max Growth Maximum annual radial growth in mm Constant Post Harvest Growth Gl cect A constant adjusting the effects of NCI Post Harvest Growth The maximum distance at which neighboring trees can have competitive NCI Distance m effects Post Harv T 3 ost oh A parameter controlling the rate at which the actual grow
193. er e DBH is the tree s DBH in cm OG 0 0 0 Deciduous trees are further evaluated for tree quality The probability of a tree being of sawlog quality in the current timestep is e Px 4 efx where By Po Bictass B2 DBH 63 In DBH where fo is the Quality Vigor Classifier Quality Beta 0 parameter e Pictass is one of the following depending on the current class designation of the tree o Quality Vigor Classifier Quality Beta 1 Class 1 o Quality Vigor Classifier Quality Beta 1 Class 2 o Quality Vigor Classifier Quality Beta 1 Class 3 o Quality Vigor Classifier Quality Beta 1 Class 4 e 21s the Quality Vigor Classifier Quality Beta 2 parameter f3 is the Quality Vigor Classifier Quality Beta 3 parameter e DBH is the tree s DBH in cm Note that since only deciduous trees get a quality designation there is no need for B parameters for classes 5 and 6 which only apply to conifers Once a tree s probability of vigorousness and sawlog quality have been established random numbers determine the final state Then class assignment proceeds as above This behavior creates three tree data members Vigorous Sawlog and Tree class How to apply it Apply this behavior to adults of any species It cannot be applied to any other life history stage Light behaviors Light is the key resource for trees in the SORTIE model Consequently great care is taken in SORTIE to calculate the amount of light that each tree
194. er for the precipitation effect The B parameter for the precipitation effect The C parameter for the precipitation effect The A parameter for the temperature effect The B parameter for the temperature effect The C parameter for the temperature effect This behavior tracks growth using the Weibull Climate Quadrat Growth grid Each tree gets the growth rate calculated for the grid cell in which it is found You can set the grid cell size to set the balance between neighborhood composition resolution smaller grid cells and processing time larger grid cells For a given species in a given grid cell the amount of diameter growth per year is calculated as Growth Max Growth Precipitation Effect Crowding Effect Temperature Effect Max Growth is the maximum diameter growth the tree can attain in cm yr entered in the Weib Clim Quad Growth Max Potential Growth cm yr parameter Precipitation Effect Crowding Effect and Temperature Effect are all factors which act to reduce the maximum growth rate and will vary depending on the local and plot wide conditions a tree is in Each of these effects is a value between 0 and 1 Precipitation Effect is calculated as iE ee Oy A PE where e Ais the Weib Clim Quad Growth Precip Effect A parameter e Bis the Weib Clim Quad Growth Precip Effect B parameter e Cis the Weib Clim Quad Growth Precip Effect C parameter e Pis the plot s annual precipita
195. eral other possible factors You can use certain parameter values to turn these influences on and off to reflect the conditions appropriate for your run Trees killed by this behavior will have a mortality reason code of natural Parameters for this behavior Parameter name Description NCI Crowding Effect Slope C The slope of the curve for neighbor effects NCI Crowding Ea Seepa Dy The steepness of the curve for neighbor effects NCI Max Radius of Crowding Neighbors in m The maximum distance from a target tree at which neighbors can have a competitive effect NCI Max Survival Probability 0 1 The maximum annual probability of survival as a value between 0 and 1 V a E The minimum DBH for trees of that species to compete as neighbors ee 8 Used for all neighbor species not just those using NCI mortality NCI Neighbor DBH The effect of the DBH of a neighbor tree on its competitiveness for a Effect alpha target species NCI Neighbor Distance Effect beta The effect of the distance of a neighbor tree on its competitiveness for a target species NCI Neighbor Storm Damage eta Complete 0 1 NCI Neighbor Storm Damage eta Medium 0 1 NCI Shading Effect Coefficient m NCI Shading Effect Exponent n NCI Size Effect Mode in cm NCI Size Effect Variance in cm NCI Size Sensitivity to NCI gamma NCI Storm Effect Complete Damage 0 1 NCI Storm Effect Medium Damage 0 1
196. ers If there is an update file there must also be new tree data members in the New tree data members to add section New tree data members to add Extra tree data members to be created for the executable to control if desired The names can be up to 9 characters long must not match the name of any existing data member and must not contain parentheses If there are new tree data members there must also be an update file Edit Scheduled Storms Window This window is reached from the Edit menu by selecting Scheduled Storms It allows you to schedule storms for the Storm disturbance behavior See that behavior s documentation for more on how scheduled storms work Year of storm not timestep The year the storm should occur Storm minimum severity 0 1 The minimum severity of the storm Storm maximum severity 0 1 The maximum severity of the storm After entering the data for a storm click the add button to add it to the list The order of the storms on the list does not matter since they each have a time associated with them To remove storms from the list select one or more and click Remove
197. es X is calculated as follows X p RBA n l where pn is either the Neighborhood Predation Species i Masting pn or the Neighborhood Predation Species i Non Masting pn of species n and RBA is the relative basal are of species n The eaten seeds are removed from the Dispersed Seeds grid In order to make results more verifiable Neighborhood Seed Predation produces a grid called Neighborhood Seed Predation This grid stores the pre predation seed rain and amount of seeds eaten for each cell in the Dispersed Seeds grid This grid has no effect on calculations but can be saved in the output file for review How to apply it This behavior may be applied to seeds of any species Any species to which it is applied must also have a Disperse behavior applied as well Functional response seed predation linked Parameters for this behavior Parameter name Func Resp Demographic Efficiency Season 1 Func Resp Demographic Efficiency Season 2 Func Resp Density Dependent Coeff Season 1 Func Resp Density Dependent Coeff Season 2 Func Resp Foraging Efficiency Func Resp Keep Predator Densities Between Timesteps Func Resp Max Decline Rate Season 1 predators week Func Resp Max Decline Rate Season 2 predators week Func Resp Max Intake Rate seeds per predator per day Func Resp Number of Weeks in Which Description The seed predator population demographic efficiency for
198. es will save the file Set working directory Choosing this option allows you to give SORTIE a directory you wish to work in Then all windows for working with files will automatically open to this directory Open run output Use this option to use the data visualization functions to graphically view the output of a run You can open either short output files or detailed output files this way Exit Quit SORTIE Batch file setup window This window is reached from the menu option File gt New batch file in the main SORTIE ND window or by opening a batch file using File gt Open file It allows you to set up a new batch file For more information on batch runs see the batch runs topic Batch files define a set of runs that you want SORTIE ND to do at one time The batch file can list multiple different parameter files and can run each file more than once Working with a batch file does not in any way affect any parameter files you may also be working on You can work with batch files without having a parameter file loaded However all the parameter files you want to include in your batch file should be complete before you begin Batch file name This is the path and file name of the batch file you are working with Add a new parameter file This section adds a new parameter file to the batch Parameter file name The path and file name to the parameter file s to add You should make this a fully qualified name i e C my files para
199. essed as a value between 0 and 1 The proportion of those seeds that land on decayed logs under gap conditions that survive to become seedlings Expressed as a value between 0 and 1 The proportion of those seeds that land on fresh logs under gap conditions that survive to become seedlings Expressed as a value between 0 and 1 The proportion of those seeds that land on forest floor litter under gap conditions that survive to become seedlings Expressed as a value between 0 and 1 The proportion of those seeds that land on forest floor moss under gap conditions that survive to become seedlings Expressed as a value between 0 and 1 The proportion of those seeds that land on scarified soil under gap conditions that survive to become seedlings Expressed as a value between 0 and 1 The proportion of those seeds that land on tip up mounds substrate under gap conditions that survive to become seedlings Expressed as a value between 0 and 1 How it works The behavior takes the substrate composition of each grid cell in the Substrate grid and converts it into a single number for each species called the substrate favorability index The favorability index is the sum of the proportions of each substrate multiplied by the proportion of seeds that germinate on that substrate under that cell s cover canopy or gap This index represents the proportion of total seeds of that species that are expected to survive in that area of the plot This in
200. ether with the Functional response seed predation behavior linked behavior The two behaviors work together to model seed predation The actual amount of seed eaten is calculated by the Functional response seed predation behavior linked behavior This behavior then distributes the offtake according to neighborhood composition The behavior begins by calculating the Y values for each grid cell as in the non linked version masting is ignored there is only one set of parameters Then the Y values are adjusted so that their mean is equal to the amount of whole plot offtake Z as calculated by the Functional response seed predation behavior linked The adjustments are made as follows 1 Calculate logit Z 2 Calculate the logit Ys and subtract the minimum value from each as well as the logit Z so they will all be positive 3 Average the logit Y s Divide logit Z by average logit Y to get a correction factor Multiply each logit Y by the correction factor Add back the same minimum value formerly subtracted Back transform logit Y to Y and use when removing seeds ao Then the seeds are removed according to the adjusted Y values This behavior can be used in the same run with the non linked version of this behavior The two sets of species are kept completely separate and there are two separate sets of parameters This behavior may be applied to seeds of any species Any species to which it is applied must also have a Di
201. executables that read setup parameters from a file You may wish to set up a SORTIE batch run where your executable uses different parameters for each run You can give SORTIE a file of all the parameters for the entire batch in a text file and for each run it will separate out that run s parameters and write them to a file for your executable The parameters for a single run must be on a single line of the entire batch file and will be written to a one line file for the individual run Specify the entire batch parameters file in Parameters file for batch run and the single run file in Single run parameters file for batch run on the Edit Harvest Interface window For example suppose there is an executable that takes three parameters It reads these parameters from a one line file named par txt like this parl par2 You can set up a batch of three runs then set up all the parameters in a single file like this You give SORTIE this file and tell it to write par txt for each run The first run in the batch SORTIE will write the first line to par txt the second run in the batch it will write the second line to par txt etc Tips If you are having trouble with SORTIE not finding your code s output file try explicitly writing out directories in your code i e C sortie file txt instead of just file txt How to apply it It is easiest if you add the harvest interface after the rest of your parameter file is complete so
202. f dead snags that uproot to create new tip up mound substrate as a value between 0 and 1 Not required if snags are not used in the run The proportion of fallen trees that uproot to create new tip up mound substrate as a value between 0 and 1 The fixed proportion of the forest floor litter moss pool that is moss Expressed as a value between 0 and 1 The proportion of dead snags that uproot to create new tip up mound substrate as a value between 0 and 1 Not required if snags are not used in the run eh The a exponent in the decay equation soil Note that this is annual decay as applied to scarified oy RE The B exponent in the decay equation 7 soil Note that this is annual decay as applied to scarified att The a exponent in the decay equation mounds substrate Note that this is annual decay as applied to tip up ay tp The B exponent in the decay equation mounds substrate Note that this is annual decay aS applied to tip up The amount by which to multiply the tree s radius when calculating the size of the new tip up mounds soil exposed by fallen trees see equation below This is meant to allow for the effects of roots If true dead trees fall in a random direction and possibly contribute new fresh log across several Substrate grid cells If false dead trees collapse vertically and contribute all their fresh log area to the cell in which they are rooted The relative
203. ferent length timesteps If the total plotwide average annual seed density is greater than this value the timestep is treated as a masting timestep Only those seeds of species to which this behavior applies are considered in the density If the event decision method is set to Ask disperse masting events occur whenever any of the species to which this behavior applies masts according to either the Masting non spatial disperse behavior or the Masting spatial disperse behavior You can use either of these behaviors both of them or neither in which case masting never occurs If any species to which this behavior is applied has masted with either behavior then this is a masting time step If there are no adult trees in the plot then masting does not occur according to either method The seeds in each grid cell of the Dispersed Seeds grid are treated separately for predation according to their local neighborhood composition The relative basal area of each species is calculated from the total basal area of individuals within Neighborhood Predation Neighbor Search Radius m meters of the grid cell center that have a DBH greater than Neighborhood Predation Minimum Neighbor DBH cm The amount of seed eaten for each species is calculated as where Y is the proportion of that species seed that is eaten and pO is either the Neighborhood Predation Masting p0 or the Neighborhood Predation Non Masting p0 parameter for that speci
204. file they must be updated in both places Parameter name Description Tree Fern Establishment The species of seedlings which are establishing epiphytically on the Species of New substrate species Seedlings Tree Fern Establishment Seedling Prob a The variable a in the function used to calculate the probability of the establishment of a seedling on a dead substrate tree Tree Fern Establishment Seedling Prob b The variable b in the function used to calculate the probability of the establishment of a seedling on a dead substrate tree Tree Fern Establishment Seedling Prob c The variable c in the function used to calculate the probability of the establishment of a seedling on a dead substrate tree Tree Fern Establishment The intercept in the linear function for seedling rooting height Seedling Height m Tree Fern Establishment The slope in the linear function for seedling rooting height Pe L Seedling Height n How it works There can be multiple species of epiphytic substrate trees but only one establishing species The establishing species is specified using Tree Fern Establishment Species of New Seedlings parameter When an individual of one of the epiphytic substrate tree species that is a tree fern dies there is a certain probability that one of its presumed epiphytic seedlings will root in its location This probability is P 1 I 1 exp a b Height c GLI where e P is
205. for Species The amount of diameter growth for the timestep for all trees of that species X in the grid cell Number of PANEOR The number of competing neighbors in the grid cell s neighborhood Windstorm Results Grid This grid is created by the Windstorm behavior It holds information on what windstorms happened during each timestep This grid has one cell for the whole plot It will ignore any changes you make to the resolution The data is held in grid packages There is one package for each storm event No package means no storms If this grid s data is saved in a detailed output file you can view the contents of this grid as a table using SORTIE s data visualization system Data in the grid There is one of these for each storm event Data member name Description Storm Severity The severity of the storm that occurred between 0 and 1 Basal Area Dead For Species X The basal area killed in this storm for Species X Density Dead For Species X The number of stems killed in this storm for Species X Years Since Last Harvest Grid This grid is created by the Lagged post harvest growth and Post Harvest Skidding Mortality behaviors Each grid cell holds the time since a harvest last occurred in that cell The grid cell resolution defaults to 8 m X 8 m You can set whatever new resolution you wish Data in the grid Data member name Description Time Time since last harvest LastUpdated The timestep the grid was last updated Crea
206. form in a private grid Each timestep that there is a planting the behavior begins by determining whether the planting is gridded or random If the planting is random the total number of seedlings to plant is calculated by multiplying the total seedling density by the area to plant Then that number of seedlings is scattered randomly around the plant area If the planting is gridded each grid cell in the plant area is planted individually In each cell is placed the number of seedlings that can fit at the specified spacing Since each 8 meter by 8 meter grid cell is planted individually large spacing distances may result in a very low number of seedlings being planted at a 6 meter spacing for instance only one seedling per cell would be planted For best results the distance between seedlings should divide evenly into 8 meters Each seedling s species is determined by comparing a random number to the relative abundance of each species This means that the species distribution may not be exactly what was specified but the larger the number of seedlings the more accurate the species distribution will be The plant behavior outputs what it did each timestep into the Planting Results grid If you wish to review the results of the grid save it in a detailed output file How to apply it You create new planting treatments using the Edit Episodic Events Window by choosing the Edit gt Episodic events option from the main SORTIE window
207. gated Mortality Clump Size Whether the size of a clump of trees to kill is deterministic or chosen from a negative binomial probability distribution Aggregated If the size of tree clumps to kill is drawn from a negative binomial Mortality Clumping probability distribution this is the clumping parameter for the Parameter distribution This is not required if a deterministic clump size is used Determines the size of the clumps of trees killed If the clump size is Aggregated deterministic all clumps will be this size If the size is to be drawn from Mortality Number of Bt MN ee ee RE a negative binomial probability distribution then this is the mean clump Trees To Aggregate iN Aggregated Mortality Return The return interval for mortality episodes Interval years How it works Mortality occurs in discrete episodes which have an average return interval For any timestep the probability that a mortality episode will occur is T RI where T is the number of years per timestep and RI is the Aggregated Mortality Return Interval years parameter Each timestep this behavior uses a random number to decide if a mortality episode occurs Between mortality episodes this behavior does not kill any trees If a mortality episode occurs this behavior kills some of the total pool of trees to which it has been applied The base annual mortality rate proportion is given in the Aggregated Mortality Annual Kill Amount 0 1 parameter Since t
208. get Basal Area m2 ha Selection Harvest Cut Range 3 Lower DBH cm Selection Harvest Cut Range 3 Upper DBH cm Selection Harvest Cut Range 3 Target Basal Area m2 ha Description The lower bound of the first DBH cut range in cm The upper bound of the first DBH cut range in cm The target basal area in square meters per hectare of the first cut range The lower bound of the second DBH cut range in cm The upper bound of the second DBH cut range in cm The target basal area in square meters per hectare of the second cut range The lower bound of the third DBH cut range in cm The upper bound of the third DBH cut range in cm The target basal area in square meters per hectare of the third cut range Selection Harvest Cut Range 4 Lower The lower bound of the fourth DBH cut range in cm DBH cm Selection Harvest Cut Range 4 Upper The upper bound of the fourth DBH cut range in cm DBH cm Selection Harvest Cut Range 4 Target Basal Area m2 ha The target basal area in square meters per hectare of the fourth cut range Selection Harvest intel Aes The initial age How it works You can specify up to four DBH ranges You provide the lower and upper DBH bounds of these ranges and the target amount of basal area for each Each timestep this behavior calculates the amount of basal area in each of these ranges If it is greater than the target this behavior signals to the Harvest behavio
209. gets in fact these calculations take up more processing time than any other during model runs There are two basic light index types used by SORTIE to describe the amount of light a tree receives The first is the Global Light Index or GLI GLI is the percentage of full sun received at a point The second index is the Sail Light index which is the proportion of shade seen at a point from none to total The name Sail Light comes from the fact that the shape of shading neighbor tree crowns is approximated by a 2D rectangle like a sail How light calculations work Behavior Average Light behavior Basal Area Light behavior Beer s law light filter behavior Constant GLI behavior Gap Light behavior GLI light behavior GLI Map Creator behavior GLI Points File Creator behavior Quadrat based GLI light behavior Sail light behavior Storm Light behavior Description Averages GLI values to produce a set of values with a coarser spatial resolution Calculates light levels as a function of the basal area of trees in a neighborhood Simulates a filter that reduces light according to Beer s Law Assigns a constant GLI value to all trees to which it is assigned Shortcuts the light calculation process by considering GLI to be binary either full light or no light Calculates a Global Light Index GLI value for each individual Calculates a GLI value for each cell in a grid to create a light m
210. ght in meters of conspecific neighbors to include in local density calculations The radius in meters to search for conspecific neighbors to include in local density calculations Slope of Density The slope of the density dependence function for determining how many Dependence seedlings establish per square meter c in the equations below Steepness of Density The steepness of the density dependence function for determining how Dependence many seedlings establish per square meter 6 in the equations below How it works This behavior takes the seeds that have been dispersed to each grid cell of the Dispersed Seeds grid and calculates how many will survive The survival probability is a function of the density of conspecific neighbors The density of conspecific neighbors is the number of stems per square meter of trees above the height set in the Conspecific Tree Minimum Neighbor Height m parameter within the radius set in the Conspecific Tree Search Radius m parameter The number of seeds that survives is calculated as Rsp Ssp exp c Dens where e Rs is the number of surviving seeds of a given species in the seed grid cell e Sp is the original number of seeds of that species in that grid cell e Dens is the density of conspecific neighbors number per square meter of that species in that grid cell e cis the Slope of Density Dependence parameter e ois the Steepness of Density Dependence parameter Once the
211. gime Remove Amount Alpha Gen Harvest Regime Remove Amount Beta Gen Harvest Regime Remove Amount Mu How it works Mu in the function that calculates cut preference of individual trees Scale parameter for the gamma probability distribution function A term in the function that determines the probability that the plot will be harvested this time step B term in the function that determines the probability that the plot will be harvested this time step M term in the function that determines the probability that the plot will be harvested this time step Alpha term in the function that determines percentage of adult basal area to be removed from the plot Beta term in the function that determines percentage of adult basal area to be removed from the plot Mu term in the function that determines percentage of adult basal area to be removed from the plot The behavior begins the time step by deciding whether or not a harvest will occur The probability of harvest is a function of total plot adult biomass as follows where P 1 ae Bio e P is the probability that the plot will be harvested this time step e Bio is the total plot adult biomass in Mg ha as calculated by the Dimension analysis behavior e ais the Gen Harvest Regime Harvest Probability A parameter e mis the Gen Harvest Regime Harvest Probability M parameter e bis the Gen Harvest Regime Harvest Probability B parameter
212. gorous trees are considered at high risk of dying before the next harvest The quality levels are with sawlog potential and without sawlog potential Parameters for this behavior Parameter name Quality Vigor Classifier Prob New Adults Sawlog Quality Vigor Classifier Prob New Adults Vigorous Quality Vigor Classifier Quality Beta 0 Quality Vigor Classifier Quality Beta 1 Class 1 Quality Vigor Classifier Quality Beta 1 Class 2 Quality Vigor Classifier Quality Beta 1 Class 3 Quality Vigor Classifier Quality Beta 1 Class 4 Quality Vigor Classifier Quality Beta 2 Quality Vigor Classifier Quality Beta 3 Description Probability that new adult trees will be classed as sawlog quality expressed as a value between 0 and 1 Does not apply to coniferous trees Probability that new adult trees will be classed as vigorous expressed as a value between 0 and 1 Bo in the quality probability equation Ignored for conifers Bictass in the quality probability equation for trees with a current tree class of 1 Ignored for conifers Bictass in the quality probability equation for trees with a current tree class of 2 Ignored for conifers Bictass in the quality probability equation for trees with a current tree class of 3 Ignored for conifers Bictass in the quality probability equation for trees with a current tree class of 4 Ignored for conifers B2 in the quality probability e
213. gregation of a species It is the average density of conspecific neighbors at a certain distance divided by the overall density of trees in the plot A perfectly random distribution of individuals for a species would result in Q 1 Q gt 1 at short distances indicates species aggregation Q lt 1 at short distances indicates spacing among individuals How it works Q values are calculated for each species for a succession of distances out to a maximum For each tree the conspecific neighbors are counted in an ring described by the radii x to Ax This value is divided by the area of the ring to get the density of neighbors at that distance This density is averaged over all trees of each species This average density of neighbors at a given distance is then relativized by dividing by the density of that species across the plot den where e Q is the relative neighborhood density at distance x to Ax for a species e JN is the total number of conspecific neighbors for that species found between x and Ax e Tis the total number of saplings and adults of that species in the plot e A 1s the area of the ring x Ax e denis the total plot density for trees of that species The size of the distance increment x is given in the Relative Neighborhood Density Distance Increment m parameter The maximum distance out to which to calculate Q is given in the Relative Neighborhood Density Maximum Distance m parameter Only saplings and adult
214. gs under canopy conditions that survive to become seedlings Expressed as a value between 0 and 1 The proportion of those seeds that land on fresh logs under canopy conditions that survive to become seedlings Expressed as a value between 0 and 1 The proportion of those seeds that land on forest floor litter under canopy conditions that survive to become seedlings Expressed as a value between 0 and 1 The proportion of those seeds that land on forest floor moss under canopy conditions that survive to become seedlings Expressed as a value between 0 and 1 The proportion of those seeds that land on scarified soil under canopy conditions that survive to become seedlings Expressed as a value between 0 and 1 Fraction Seeds The proportion of those seeds that land on tip up mounds substrate under Germinating on canopy conditions that survive to become seedlings Expressed as a value Canopy Tip Up between 0 and 1 How it works The behavior takes the substrate composition of each grid cell in the Substrate grid and converts it into a single number for each species called the substrate favorability index The favorability index is the sum of the proportions of each substrate multiplied by the proportion of seeds that germinate on that substrate This index represents the proportion of total seeds of that species that are expected to survive in that area of the plot This index is stored in the grid Substrate Favorability In the parameters
215. h large files and long runs this can be very time consuming If you have an idea of the charts you want to work with it will be faster if you only save the data needed to create those charts Extracting chart data into text format You can save the raw data used to make any chart to a tab delimited text file suitable for viewing in spreadsheet and word processing programs Use the File gt Save menu option that appears on all charts or press Ctrl S You can take this raw data to reproduce and adjust the chart in other graphing applications If you have saved a summary output file be aware that this file already contains all its data in a tab delimited text format you can open this file directly if you wish For most charts opened from a detailed output file you can save the chart data for either just the timestep you are currently viewing or for the whole run at once In most cases saving for the whole run places the data for each timestep in a single file You can extract the same chart data from many detailed output files at once using the Batch Extract Detailed Output Files tool This tool produces the same results as saving text data for all time steps on each chart Batch extract detailed output files tool This tool allows you to extract chart data for multiple detailed output files at once The extracted data is a text version of the chart s data for all time steps For more on extracting text data see Extracting chart data int
216. hat is fresh logs in areas that had a gap cut harvest event as a value between 0 and 1 This is not required if the Harvest behavior is not used The proportion of substrate that is scarified soil in areas that had a gap cut harvest event as a value between 0 and 1 This is not required if the Harvest behavior is not used The proportion of substrate that is tip up mounds substrate in areas that had a gap cut harvest event as a value between 0 and 1 This is not required if the Harvest behavior is not used The proportion of plot substrate that is decayed logs when the run starts as a value between 0 and 1 If a map of substrate values is included in the parameter file see Grid initial conditions for information on how to do this then the map values will be used for the initial conditions and this number will be ignored The proportion of plot substrate that is fresh logs when the run starts as a value between 0 and 1 If a map of substrate values is included in the parameter file see Grid initial conditions for information on how to do this then the map values will be used for the initial conditions and this number will be ignored The proportion of plot substrate that is scarified soil when the run starts Proportion of Scarified Soil Initial Conditions Proportion of Tip Up Mounds Maximum Number of Years that Decay Occurs Partial Cut Proportion of Decayed Logs Partial Cut Proportion of Fresh Logs Parti
217. havior Parameter name Description luisa b dengliy The mortality rate between 0 and 1 at the first timestep of infestation Intercept Insect Mortality Max Mortality Rate Maximum mortality rate between 0 and 1 0 1 Insect Mortality XO The time at which 0 5 of the maximum mortality rate occurs Insect Mortality Xb Parameter controlling the steepness of the rise of the mortality rate How it works The mortality rate of trees as a function of time infested is as follows Pi icles 1 aO P I where e P is the mortality rate between 0 and 1 e Iis the Insect Mortality Intercept parameter as a value between 0 and 1 This is the function intercept or the mortality rate at the first timestep of infestation e Max is the Insect Mortality Max Mortality Rate 0 1 parameter as a value between 0 and 1 This is the maximum mortality rate that will occur regardless of how long a tree has been infested e Tis the time in years that an individual has been infested e Xo is the Insect Mortality X0 parameter This is the time at which half of the maximum mortality rate is reached e X is the Insect Mortality Xb parameter This controls the steepness of the rise of the curve Once the mortality rate for an infested individual has been determined a random number determines whether it will live or die The Insect Infestation behavior decides which trees become infested and tracks the amount of time ea
218. he double resource Michaelis Menton equation How it works Relative growth is calculated with the equation LAO RNY GES 4 OC 2 cr T7 r 4 our fF rit where e Yis the amount of annual relative growth e Ais the Asymptotic Diameter Growth A parameter e Sis the Slope of Growth Response S parameter e Cis the Double resource Influence of Resource C parameter in units appropriate to the value of R e Ris the amount of the second resource in units appropriate to the value of C e GLI is the global light index calculated by a light behavior Growth is compounded over multiple timesteps with the equation G 1 1 diam where e Gis the amount of diameter growth for the timestep in cm e diam is the diameter of the tree in cm at 10 cm height if seedling or sapling or DBH if adult e Tis the number of years per timestep Note that setting the C parameter in the equation above to 0 eliminates the second resource and makes this equivalent to the Non limited relative growth behavior The amount of the second resource is captured in a grid object called Resource Currently it is up to you to enter a map of the values for this resource grid for instructions on how to do this see the Grid Setup Window topic This behavior does not in any way alter the values in this grid How to apply it This behavior can be applied to seedlings saplings and adults of any species Any tree species type com
219. he Apache Software Foundation http www apache org What s New Version 7 0 beta There have been some big changes in the inner workings of SORTIE ND to allow more flexibility and function These changes have been extensively tested but until they get used day to day we know problems can still appear Therefore we decided to officially release version 7 0 as a beta Please report all problems to tech support and we will resolve them as quickly as possible Note If you have a parameter file from an earlier version load your file and save it SORTIE ND will automatically make any needed adjustments to your parameter file If there are errors your file may be too old Load and save into 6 11 then into 7 1 New in version 7 0 e You can now add multiple copies of behaviors to your runs and apply them to different tree life history stages with different parameters e The user manual has been rewritten to expand on basic ideas and help guide you through run setup e Data visualization charting controls have been simplified in order to help you manage all the possible chart options for an output file e Anew menu option called Tools holds useful utilities for working with SORTIE ND e Anew option in the Tools menu allows you to copy and rename detailed output files e Anew option in the Tools menu allows you to extract data from multiple output files at the same time e A recent charts button lets you find your favorite char
220. he competitive effect of neighbors of species i on the target tree species s growth between 0 and 1 The maximum distance in m at which a neighboring tree has competitive effects on a target tree Maximum potential diameter growth for a tree in cm yr The minimum djo for trees of that species to compete as neighbors Used for all species not just those using NCI growth WEN Size effect power function scaling factor a parameter Size effect exponent b parameter For a tree the amount of diameter growth per year is calculated as Growth Max Growth Size Effect Crowding Effect Max Growth is the maximum diameter growth the tree can attain in cm yr entered in the Juvenile NCI Maximum Potential Growth cm yr parameter Size Effect and Crowding Effect are factors which act to reduce the maximum growth rate and will vary depending on the conditions a tree is in Each of these effects is a value between 0 and 1 Size Effect is calculated as where SE a dig e dj is the diameter at 10 cm height of the target tree in cm e ais the Juvenile NCI Size Effect a parameter e bis the Juvenile NCI Size Effect b parameter Crowding Effect is calculated as CE exp C NCI where e Cis the Juvenile NCI Crowding Effect Slope C parameter e Dis the Juvenile NCI Crowding Effect Steepness D parameter e NCTis this tree s NCI value equation below The NCI value sums up the competitive effect of all neighbors w
221. he distance in meters Species X Dist Y The K value for Species X at the Yth distance increment This is not K Value necessarily the distance in meters Seed Predators Grid This grid is created by the Functional response seed predation behavior It holds the number of seed predators in each seed grid at the end of the predation model run This grid s resolution must match that of Dispersed Seeds Data in the grid Data member name Description Number Predators The number of predators in each grid cell Snag Decay Class Dynamics Basal Area Grid This grid is created by the Snag Decay Class Dynamics behavior It holds the amount of basal area for live and cut trees Maps and grid resolution changes for this grid are not honored Data in the grid Data member Description name Live BA Per Ha The amount of basal area in square meters per hectare of live adults UBA Par ta The amount of basal area in square meters per hectare of trees harvested this timestep State Variables Grid This grid is created by the State Reporter behavior There is one grid cell for the entire plot which holds state variables Data in the grid Data member name Description Temperature C The plot mean annual temperature as stored in the Plot Precipitation mm The plot mean annual temperature as stored in the Plot Storm Damage Grid This grid is created by the Storm disturbance behavior Each grid cell holds a storm damage index between 0 and
222. he intercept of the adult reverse linear function for DBH and height The slope of the adult reverse linear function for DBH and height The intercept of the sapling reverse linear function for DBH and height The slope of the sapling reverse linear function for DBH and height Slope Seedling Reverse Linear Function The intercept of the seedling reverse linear function for DBH and height Intercept Seedling Reverse Linear Function The slope of the seedling reverse linear function for DBH and height Slope The reverse linear diam height function is height diam a b where e height is tree height in m e ais the appropriate reverse linear intercept parameter either Adult Reverse Linear Function Intercept Sapling Reverse Linear Function Intercept or Seedling Reverse Linear Function Intercept e bis the appropriate reverse linear slope parameter either Adult Reverse Linear Function Slope Sapling Reverse Linear Function Slope or Seedling Reverse Linear Function Slope e diam is DBH in cm for saplings and adults or diam o in cm for seedlings The power diameter height relationship The power diameter height relationship relates height and diameter with a power function Since it uses diameter at 10 cm NOT DBH it is active for saplings only Parameters Parameter name Description are The a parameter in the power function for the height diameter Power Function a relationship Power Function The exponen
223. he parameter gives an annual rate the actual mortality rate is 7 1 AD J where AD is the annual amount to kill and T is the number of years per timestep During a mortality episode this behavior kills the trees in discrete clumps The behavior uses a random number with each tree in its pool of eligible trees to decide if that tree dies If it dies the behavior also kills the trees closest to it Only trees to which this behavior has been applied are killed other neighbors are left alone The size of these clumps of dead trees can either be deterministic or drawn from a negative binomial probability distribution This option is set in the Aggregated Mortality Clump Size parameter If the size is deterministic the size of all clumps is given in the Aggregated Mortality Number of Trees To Aggregate parameter If the size is from a negative binomial distribution that parameter gives the mean u for the function y of o Tixtibf u Vy u Pix u kj 1 real ute i where k the clumping parameter is the Aggregated Mortality Clumping Parameter parameter If the Aggregated Mortality Return Interval years and Aggregated Mortality Number of Trees To Aggregate parameters are both set to 1 then this behavior functions exactly like the Stochastic Mortality behavior How to apply it This behavior can be applied to seedlings saplings and adults of any species Only those trees to which this behavior has been applied will be kille
224. he previous year The total diameter increment is the sum of the X individual diameter increments For height growth In order to find the total amount of height increase for a timestep the behavior takes as an input the amount of diameter growth increase Assume that the number of years per timestep is X The amount of diameter increase is divided by X Then the lognormal growth equation is calculated X times with the diameter incremented by the amount of diameter increase per timestep each time The total height increment is the sum of the X individual height increments How to apply it This behavior can be applied to seedlings saplings and adults of any species Any tree species type combination to which it is applied must also have a light behavior applied You can choose either a diam with auto height diam only or height only version Michaelis Menton with negative growth height only This behavior uses a modified Michaelis Menton function to do height growth You can optionally add autocorrelation and a degree of stochasticity to the growth Parameters for this behavior Parameter name Michaelis Menton Neg Growth Alpha Michaelis Menton Neg Growth Beta Michaelis Menton Neg Growth Gamma Michaelis Menton Neg Growth Phi Michaelis Menton Neg Growth Growth Standard Deviation Michaelis Menton Neg Growth Autocorrelation Prob 0 1 How it works Description Alpha parameter Beta paramete
225. helper functions for the simulation itself These behaviors do things like measure and calculate forest metrics and write output Each behavior has a clearly defined action Each behavior in a run performs its action once per timestep in a pre defined order Relationship of behaviors to trees and grids Trees and grids are the state data of SORTIE Behaviors act on this data to change it and evolve the model state Behaviors are assigned to specific data and may not act outside this scope SORTIE directly manages all the state data needed for a given simulation and automatically ensures the creation of any data that a behavior is assigned to work on Users can adjust the initial conditions of all state data at the beginning of the simulation Choosing behaviors for a run Setting up behaviors is the most important step in creating a new simulation To choose which behaviors to include in the run and how to apply them use the Model flow window There are a few general guidelines for choosing a set of behaviors from scratch Start with the trees Behaviors that act on trees are assigned to trees based on species and life history stage otherwise referred to as tree type Move through the tree life cycle for each species and pick behaviors for growth mortality and reproduction There may not be a behavior that does exactly what you want but with the creative use of behavior parameters you may be able to achieve the same effect For
226. hen all trees meeting the second priority then all meeting the third then all other trees Cutting stops when the target removal amount has been met DBH ranges are honored If there is a priority tree outside the cut DBH ranges it will not be cut under any circumstances The exception to priority ordering is in the case of a basal area cut target If a priority tree would cause too much basal area to be removed a smaller non priority tree may be cut instead to more precisely reach the target Priorities may not be applied to percent of density cuts because these cuts are stochastic in nature so prioritization is meaningless You can prioritize by the same data member more than once for instance first cut trees with growth between 5 and 10 then with growth between 0 and 5 Although seedlings are not properly harvested a harvest can kill them just the same You can specify the proportion of seedlings that are killed within the harvest area for each species The seedlings of a species can be killed even if that species is not being harvested Seedlings in the harvest area are randomly chosen to die based on the mortality rate for their species They are given harvest as a mortality reason Trees that are harvested are removed immediately When light is calculated for that timestep gaps opened up by the harvest will be visible If there are behaviors which apply to stumps a stump is created for each logged tree Otherwise the tree completely
227. her storm killed trees Saplings that are killed in storms never become snags They are killed in the manner described above for trees that die in a non snag run Existing snags are never at risk for storm damage or mortality but the behavior must be applied to the snag tree type in order to cause storm killed adults to become snags How to apply it Apply this behavior to the trees that can be killed in storms You must also apply the Storm damage applier behavior to the same trees You may not apply this behavior to seedlings If you wish to have storm killed trees become snags you must apply this behavior to the snag tree type This may cause snags to appear due to natural mortality and other causes you must use other behaviors to manage these snags You must also have any kind of mortality behavior applied to each tree species and life history stage to which this behavior is applied Storm direct killer This behavior kills trees based on storm severity without an intervening damage step Trees removed by this behavior will have a mortality reason code of storm Parameters for this behavior Parameter name Description Storm Direct Killer i The a value in the probability of mortality logit function Storm Direct Killer b The b value in the probability of mortality logit function How it works When storms occur trees to which this behavior are applied have the following probability of mortality expla t
228. his tree member you must add the Tree volume calculator behavior to your run A line graph may also be created for the contents of a few grids Histograms SORTIE can produce a histogram for most tree and grid values in a detailed output file It will offer to display any value it finds which can sometimes lead to a crowded histogram display list Tree based histograms display the number of trees per hectare for each species that fall into each of several value groupings for a piece of data For instance a height histogram that divided height into one meter increments would show how many trees of each species were from 0 meters in height from 1 2 meters in height etc Grid based histograms display the number of grid cells that fall into the groupings Grids that hold species specific data will also have a histogram option for displaying all species together The visualizer attempts to optimize the histogram for the data it is displaying You can further customize the display of the histogram to suit your data You have your choice of logarithmic or linear Y axis You can also redivide the data by specifying the number of bins into which the data is divided and the size of each bin The visualizer defaults to recalculating the bin size for each timestep in order to best display the data so keep an eye on the bin size as you step through the timesteps If you change the bin size or number of bins the visualizer will preserve your cha
229. his value will be ignored Mean Annual The mean annual temperature of the plot in degrees Celsius This Temperature information may not be needed in the run depending on the behaviors degrees C that you select if it is not needed this value will be ignored Timesteps and run length A run is a single model simulation It starts at time zero and continues until its defined endpoint is reached A run is defined by its parameter file This tells the model how long to run and what to do during the run Timesteps The basic time unit in the run is the timestep You set the length and number of the timesteps Each timestep the model asks each behavior to do its work whatever that work may be The behaviors are run in the order in which they are listed in the parameter file You can see the order using the Model flow window The model counts off the timesteps until it has finished the specified number then cleans up its memory and shuts down The length of a timestep is defined in years Setting a longer timestep means that you can simulate long stretches of time more quickly and with less computer processing time For example you could create two parameter files using the same behavior set each for a run of 100 timesteps Parameter file A has a timestep length of one year Parameter file B has a timestep length of five years Both will take about the same amount of time to run because each behavior is called upon the same number of time
230. hose snags whose age is greater than Upper Age Yrs of Snag Light Transmission Class 1 but is less than or equal to Upper Age Yrs of Snag Light Transmission Class 2 Expressed as a fraction between 0 and 1 If your run does not work with snags you can ignore this Otherwise a value must be provided for all species Fraction of light transmitted through the snag tree crown for each species Applies to those snags whose age is greater than Upper Age Yrs of Snag Light Transmission Class 2 Expressed as a fraction between 0 and 1 If your run does not work with snags you can ignore this Otherwise a value must be provided for all species The upper age limit in years defining the first age class of snag light transmission Snags with an age less than or equal to this age have a light transmission coefficient matching Snag Age Class 1 Light Transmission Coefficient If your run does not work with snags you can ignore this The upper age limit in years defining the second age class of snag light transmission Snags with an age greater than the upper limit for size class 1 but less than or equal to this age have a light transmission coefficient matching Snag Age Class 2 Light Transmission Coefficient Snags with an age greater than this value are in age class three If your run does not work with snags you can ignore this How it works This behavior uses a grid object called Quadrat GLI to help it assign GLI values to th
231. ht of fresh log substrate in meters Standard Deviation of Mound Height in The standard deviation of the height of mounded areas in meters m How it works Each timestep the behavior starts by getting the substrate proportions for each cell of the Dispersed Seeds grid The six substrate types are further divided into mound and non mound types of each according to the Proportion of Ground Area that is Mound parameter The relative proportions of the different kinds of substrate are thus the same on mound and non mound areas The seeds in the Dispersed Seeds grid cell are then divided up among the substrate types in that cell according to their proportions relative to each other so if 60 of the cell area is mound forest floor moss that s the substrate type that 60 of the seeds land on A seedling is created from each seed Seedlings are randomly placed within their seed grid cell area and have a slightly randomized value of New seedling diameter at 10 cm Each seedling then gets a rooting height according to the substrate type upon which it has germinated If it has germinated on fresh logs its rooting height is a random number drawn from a normal distribution controlled by the Mean Height of Fresh Log Substrate in m and Standard Deviation of Fresh Log Substrate Height in m parameters no distinction is made between mound and non mound fresh logs If it s on a mound substrate its rooting height is a random number drawn from a normal d
232. ialized in newly created trees If you want the new data members to be written to the file that SORTIE writes make sure you put them in the list of file columns If new data members have been created SORTIE expects the executable each time it is called to write a file with the list of trees it wishes to update and the new values for these data members You can only make changes to the new data members that you create You cannot change any other attribute of a tree The user executable The user executable launches runs and quits once per harvest timestep SORTIE waits for it to finish before resuming This means it must do any necessary initialization and setup each harvest timestep The executable can be written in any language and can do anything it wishes The only two requirements is that it be a standalone executable and that it produce the file of trees to harvest that SORTIE expects The executable should be prepared for the condition that there are no trees in the file SORTIE writes and should write empty files if it doesn t want any trees harvested or updated SORTIE s behavior cannot be guaranteed in the event of a crash in the user executable The executable probably has its own input data for setup If it takes arguments during launch you can give SORTIE a string to pass to the executable in Arguments to pass to the executable on the Edit Harvest Interface window SORTIE provides a convenience feature for those
233. ibution functions for Seed distribution this is the standard deviation of the function in seeds per m If you have not chosen these PDFs then this parameter is not required A in the seed density calculation B in the seed density calculation M in the seed density calculation N in the seed density calculation The maximum distance to search for conspecific adults B in the presence test calculation M in the presence test calculation Threshold value between 0 and 1 of the presence test function above which a species will be allowed to disperse in the absence of parents 0 always includes a species always excludes it How it works This behavior examines the neighborhood of each grid cell of the Dispersed Seeds grid to determine how many seeds to place in that cell Expected seed density in a cell for a particular species is calculated as Seeds A fec BAC where e Seeds is number of seeds per square meter e Ais the Temp Dep Neigh Disperse A parameter e BAC is the total basal area of neighborhood conspecific adults in square meters e fecis a fecundity term fec is a per capita seedling production fecundity term It is a function of temperature and is calculated as T M fec B e el N where e B isthe Temp Dep Neigh Disperse B parameter e M is the Temp Dep Neigh Disperse M parameter e Nis the Temp Dep Neigh Disperse N parameter e Tis the annual mean temperature in degrees Cels
234. ies across the plot If Uniform then all locations in the plot have an equal susceptibility If Mapped then a map is used to show the way locations in the plot vary in susceptibility The return interval in years of storms of severity 0 0 1 Set this to 0 to turn off storms of this severity The return interval in years of storms of severity 0 1 0 2 Set this to 0 to turn off storms of this severity The return interval in years of storms of severity 0 2 0 3 Set this to 0 to turn off storms of this severity The return interval in years of storms of severity 0 3 0 4 Set this to 0 to turn off storms of this severity The return interval in years of storms of severity 0 4 0 5 Set this to 0 to turn off storms of this severity The return interval in years of storms of severity 0 5 0 6 Set this to 0 to turn off storms of this severity The return interval in years of storms of severity 0 6 0 7 Set this to 0 to turn off storms of this severity The return interval in years of storms of severity 0 7 0 8 Set this to 0 to turn off storms of this severity The return interval in years of storms of severity 0 8 0 9 Set this to 0 to turn off storms of this severity The return interval in years of storms of severity 0 9 1 0 Set this to 0 to turn off storms of this severity If the Storm Damage Application parameter is set to Stochastic and the Stochastic Pattern Damage Distribution is
235. ility using TP 1 1 AP where TP is the timestep probability of browse AP is the annual probability and N is the length of a timestep in years Trees that are chosen as browsed are marked as browsed This behavior does nothing else to them Other behaviors such as growth and mortality may use this information How to apply it Apply this behavior to any species and type of tree Storm disturbance This behavior simulates the effects of wind damage from storms Its function is to assess whether or not storms have occurred in the current timestep and if they have how much damage they have caused This behavior does not actually cause any trees to be damaged that is the function of the Storm damage applier behavior Parameters for this behavior Parameter name Description Plot Storm Susceptibility Pattern Return Interval for Severity Storm Class 0 0 1 Return Interval for Severity Storm Class 0 1 0 2 Return Interval for Severity Storm Class 0 2 0 3 Return Interval for Severity Storm Class 0 3 0 4 Return Interval for Severity Storm Class 0 4 0 5 Return Interval for Severity Storm Class 0 5 0 6 Return Interval for Severity Storm Class 0 6 0 7 Return Interval for Severity Storm Class 0 7 0 8 Return Interval for Severity Storm Class 0 8 0 9 Return Interval for Severity Storm Class 0 9 1 0 Standard Deviation lognormal or normal How storm damage susceptibility var
236. ills trees due to storm events Competition Harvest Competition Harvest performs harvests in a way that preferentially removes the most competitive individuals in a plot It also decides when and how much to harvest based on criteria you give it Trees removed by this behavior will have a mortality reason code of harvest Parameters for this behavior Parameter name Competition Harvest Amount of Harvest Per Species 0 1 Competition Harvest Amount to Harvest Competition Harvest C Competition Harvest D Competition Harvest DBH Effect of Targets alpha Competition Harvest Distance Effect of Targets beta Competition Harvest Filename for List of Harvested Trees Description Trees to harvest can be treated as a common pool where species identity is not a factor in selecting trees for harvest In this case all values should be set to 1 0 Otherwise species can be harvested at a fixed proportion In this case set the proportion to harvest for each species as a value between 0 and 1 with all values adding up to 1 Amount to harvest depending on the harvest type If this is a fixed interval harvest the value in Competition Harvest Harvest Type is set to Fixed Interval this is the basal area of the plot after harvesting in m ha if this is a fixed basal area threshold harvest with a fixed amount to cut Fixed BA Amt this is the amount of basal area to cut in m ha if this is a fixed
237. imate quadrat growth Calculates an amount of diameter growth according to the Michaelis Menton relative growth equation Growth is limited to a maximum of a constant radial growth increment Calculates an amount of diameter growth according to the Michaelis Menton relative growth equation Growth is limited to a maximum of the constant basal area growth increment Calculates an amount of diameter growth according to the Michaelis Menton relative growth equation Calculates an amount of height growth according to the Michaelis Menton relative growth equation Uses a shortcut for simulating gap dynamics with very competitive conditions This behavior causes rapid growth in high light with a unique winner low light produces no growth at all Calculates tree growth as a function of climate and neighbor trees Calculates tree growth as a function of climate and neighbor trees For processing efficiency growth is calculated for each species on a per grid cell basis Absolute growth behaviors Several behaviors apply an absolute growth version of the Michaelis Menton function Parameters for these behaviors Parameter name Description Adult Constant Area The constant amount of basal area by which to increase a tree s basal Growth in sq cm yr area Applies to basal area increment limited behaviors Adult Constant Radial Growth in mm yr Asymptotic The constant value by which to increase a tree s radius at breast height Ap
238. imestep Unless explained otherwise the manner in which Detailed Substrate calculates and tracks these components is the same as for the Substrate behavior Detailed Substrate divides logs into species groups size classes and decay classes Logs in each combination of species group size class and decay class can have different initial proportions proportions after harvest and decay parameters from all other types of logs Each species to which this behavior is assigned belongs to one species group assigned with the Species Group parameter As saplings adults and snags enter the substrate pool they are added to the logs for the appropriate species group Log substrate belongs to one of two size classes defined by diameter The threshold diameter separating the two size classes is defined by the Boundary Between Log Diam Classes cm parameter When a sapling adult or snag enters the substrate pool the area input to each size class is calculated separately The species group and size class to which log substrate is added do not change over time Log substrate is also divided into 5 decay classes Over time decay class logs decay into decay class 2 logs then decay class 3 logs then decay class 4 logs then decay class 5 logs then forest floor litter and moss The relationship among these states as well as tip up mounds and scarified soil is depicted in the figure below Substrate creation and decay schematic for De
239. in degrees Celsius as entered in the Plot e BAT is the adult total basal area in the neighborhood in square meters BAT is the basal area of all adults within the distance from the center of the grid cell set in the Temp Dependent Neighborhood Surv Neigh Search Radius m parameter The probability of survival is for a single year For multi year timesteps the timestep survival probability is the annual probability raised to the power of the number of years per timestep Trees receive the survival probability calculated for the grid cell in which they are found A random number is used to determine whether a tree lives or dies How to apply it This behavior can be applied to seedlings saplings and adults of any species Weibull Climate Survival This behavior assesses tree survival as a function of climate and larger neighbor trees A tree has a maximum potential annual probability of survival that is reduced due to several possible factors Trees killed by this behavior will have a mortality reason code of natural Parameters for this behavior Parameter name Description Weibull Climate The C parameter for the competition effect Survival Competition Effect LG Weibull Climate Survival Competition Effect D n Weibull Climate Survival Competition Gamma Weibull Climate Survival Max Survival Prob 0 1 Weibull Climate Survival Precip Effect A Weibull Climate Survival Precip Effect B
240. in that it does not have an upper bound Each time new substrate is added existing log substrate proportions are reduced so that the total of all substrate proportions is still less than or equal to 1 However new inputs from tree fall and breakage do not reduce existing log volume that is logs can be on top of each other and still contribute to volume but not area The volume of logs is reduced after harvesting when scarified soil is added that is log volume is destroyed in the area that is scarified Log volume also decreases as pieces decay from decay class 5 to forest floor litter and moss Parameters for this behavior Parameter name Boundary Between Log Diam Classes cm Clear Cut Large Logs Mean Diameter cm Clear Cut Small Logs Mean Diameter cm Clear Cut Proportion of Scarified Soil Clear Cut Proportion of Tip Up Mounds Gap Cut Small Logs Mean Diameter cm Gap Cut Large Logs Mean Diameter cm Gap Cut Proportion of Scarified Soil Gap Cut Proportion of Tip Up Mounds Clear Cut Proportion of Scarified Soil Description DBH boundary between the small and large log size classes in cm After a clear cut harvest the mean diameter of logs in the large size class in cm This is not required if the Harvest behavior is not used After a clear cut harvest the mean diameter of logs in the small size class in cm This is not required if the Harvest behavior is not used The proportio
241. ing storms then the value of Damage Effect depends on the tree s damage category If the tree is undamaged Damage Effect equals 1 If the tree has medium storm damage the value is the NCI Damage Effect Medium Storm Damage 0 1 parameter If the tree has complete storm damage the value is the NCI Damage Effect Complete Storm Damage 0 1 parameter The amount of growth is in cm year For multi year timesteps the behavior will calculate total growth with a loop Each loop iteration will increment DBH for one year For each year any portion of the growth equation with DBH as a term is recalculated with the previous year s updated DBH value NCI values are constant throughout this loop for neighbors only the DBH at the start of the timestep is used How to apply it This behavior can be applied to saplings and adults of any species It cannot be applied to seedlings You can use either the diam with auto height or diam only version If the Shading Effect term is activated in the growth equation then the trees to which this behavior is applied must also have a light behavior applied the Sail light behavior is the one designed to work with the NCI behavior The use of any other light behavior is at your own risk If any storm damage parameters are set to anything other than 1 it is recommended but not required that you have the Storm damage applier behavior applied Power growth height only This behavior uses a power functio
242. instance there may be a parameter that when assigned a particular value cancels out a function term you don t need or a set of parameter values that can cause a function to mimic another function shape Carefully check the behavior assignments to particular trees Behaviors often have some rules about how they can be applied but these tend to be limited in the interests of maximum flexibility The model doesn t try to second guess what you are doing beyond making sure the simulation can run as described Make sure that you applied a complete set of lifecycle behaviors to each species and life history stage Check the dependencies Many behaviors rely on the work of other behaviors Check the documentation for the set of behaviors you have so far to see if you need to add others For instance if you have a behavior that calculates growth as a function of light level you will need to add a behavior to calculate the light level Each behavior s documentation will give you all dependency requirements Add analysis and output Forest metrics and output are handled by behaviors just like everything else in SORTIE Basic metrics like stem density and basal area are handled directly by the output behavior You can add additional behaviors called analysis behaviors to calculate extra metrics like biomass or tree spatial distribution indexes Output is one of a set of behaviors that uses a separate interface for setup in this case the Outp
243. ion in millimeters as entered for the Plot Temperature Effect is calculated as ee esc oy TE where e Ais the Weibull Climate Growth Temp Effect A parameter e Bis the Weibull Climate Growth Temp Effect B parameter e Cis the Weibull Climate Growth Temp Effect C parameter e Tis the plot s annual mean temperature in degrees Celsius as entered for the Plot Crowding Effect is calculated as CE e C DBHY ND where e Cis the Weibull Climate Growth Competition Effect C parameter e DBH is of the target tree in cm e yis the Weibull Climate Growth Competition Effect gamma parameter e Dis the Weibull Climate Growth Competition Effect D parameter e ND is the number of neighbors with a DBH greater than the target tree s DBH The ND value is a count of all larger neighbors with a DBH at least that of the Weibull Climate Growth Minimum Neighbor DBH in cm parameter out to a maximum distance set in the Weibull Climate Growth Max Neighbor Search Radius m parameter The value is a straight count it is not scaled or relativized in any way Seedlings never compete The amount of growth is in cm year For multi year timesteps the behavior will calculate total growth with a loop Each loop iteration will increment DBH for one year For each year any portion of the growth equation with DBH as a term is recalculated with the previous year s updated DBH value How to apply it This behavior
244. ion for calculating annual mortality The b parameter in the Weibull function for calculating annual mortality The c parameter in the Weibull function for calculating annual mortality The d parameter in the Weibull function for calculating annual mortality The maximum mortality probability for a species expressed as a proportion between 0 and 1 The a parameter in the Weibull function for calculating annual mortality for a browsed tree The b parameter in the Weibull function for calculating annual mortality for a browsed tree The c parameter in the Weibull function for calculating annual mortality for a browsed tree The d parameter in the Weibull function for calculating annual mortality for a browsed tree The maximum mortality probability for a browsed tree expressed as a proportion between 0 and 1 The same function is used to calculate the probability of mortality for both browsed and unbrowsed trees but the parameters are different The function is where p Mmax exp a H c GLI e p annual probability of mortality Mma the Height GLI Weibull Max Mortality 0 1 or Height GLI Weibull Browsed Max Mortality 0 1 parameter e a the Height GLI Weibull a or Height GLI Weibull Browsed a parameter e b the Height GLI Weibull b or Height GLI Weibull Browsed b parameter e c the Height GLI Weibull c or Height GLI Weibull Browsed c parameter e d the Height GL
245. ion of the type of substrate on which they land Light Dependent Seed Survival Proportional Seed Survival Seed Establishment Storm Light Dependent Seed Survival Substrate Based Seed Survival With Microtopography Substrate Dependent Seed Survival No Gap Status Substrate Dependent Seed Survival With Gap Status Assesses seed survival as a function of the Global Light Index GLD of the location in which a seed lands Reduces the number of seeds by a set amount Converts seeds into seedlings This behavior assesses seed survival as a function of the light level of the location in which a seed lands This behavior assesses seed survival based on substrate conditions allowing for site microtopography to influence seed survival This behavior assesses seed survival as a function of the substrate composition of the grid cells in which seeds land This behavior assesses seed survival as a function of both the substrate composition of the grid cells in which seeds land and the cells forest cover gap or canopy Conspecific Tree Density Dependent Seed Survival This behavior asses ses seed survival as a function of the local density of conspecific trees This behavior is very similar to Density Dependent Seed Survival Parameters for this behavior Parameter name Conspecific Tree Minimum Neighbor Height m Conspecific Tree Search Radius m Description The minimum hei
246. ion of tree height partitioned into leaf and bole biomass Parameters for this behavior Parameter name Description lt th Partitioned Height Biomass Leaf The slope in the linear biomass equation for leaves Slope a Partitioned Height Biomass Leaf The intercept in the linear biomass equation for leaves Intercept b Partitioned Height Biomass Bole The slope in the linear biomass equation for boles Slope a Partitioned Height Biomass Bole The intercept in the linear biomass equation for boles Intercept b How it works The biomass of leaves and boles is calculated using the same equation but using different parameters The equation is Bio a Height b where e Bio biomass in kg dry weight of either leaves branches or the bole e ai either the Partitioned Height Biomass Leaf Slope a or Partitioned Height Biomass Bole Slope a parameters e b either the Partitioned Height Biomass Leaf Intercept b or Partitioned Height Biomass Bole Intercept b parameters e Height tree s height in meters The amount of each type of biomass in metric tons for each species is saved in a grid called Partitioned Biomass You can save these values in a detailed output file for analysis How to apply it Apply this behavior to saplings adults or snags of any species This behavior does not automatically create output Once you have added this behavior to your run the Detailed output grid setup win
247. ior called Stochastic Bi Level Mortality Storm Light light levels come from the Storm Light grid produced by the Storm Light behavior In the version called Stochastic Bi Level Mortality GLI light levels come from any light behavior that can be applied directly to trees The threshold between the use of high light and low light parameters is set in the Stochastic Bi Level High Light Mortality Threshold parameter The units depend on which index of light is being used Check the documentation on your chosen light behavior carefully For each tree a random number is compared to that species s probability of mortality to determine if it dies If light levels qualify as high light the probability of mortality is the value in the Stochastic Bi Level High Light Mortality Probability 0 1 parameter if the light levels are low the probability of mortality is the value in the Stochastic Bi Level Low Light Mortality Probability 0 1 parameter If the timestep length is not one year the probability of mortality is adjusted from an annual mortality probability to a timestep probability How to apply it This behavior can be applied to seedlings saplings and adults of any species If you have chosen the version marked Storm Light you must also use the Storm Light behavior If you have chosen the version marked GLI you must assign a light behavior to all trees to which you assign this mortality Stochastic Bi Level Mortality This
248. iors for more information on which codes will apply to your run Grid output Grid data can only be saved in a detailed output file If a grid stores multiple types of data you can choose which ones you want to save For the chosen pieces of data the output file contains the value for each cell Saved grid data can be viewed as a map or a histogram or can be used as initial conditions input for a new run Subplots in output Sometimes you might want to track a portion of the plot separately from the rest of it You can do this by defining subplots when you set up your output files You can save separate subplots in both the detailed and summary output files Subplot data is included in the summary output file SORTIE produces a detailed output file for the whole plot and one for each subplot you define You can save up to five subplots The subplots do not have to be continuous in area The same data is saved both for subplots and the plot as a whole Only tree data can be subplotted If grid data is saved the whole grid will always be saved It is easy to work with only a portion of a grid s data by for example printing out the grid using the Grid Setup window To create subplots click the button that says Set up subplots on the output file windows This will open the Edit subplots window If you load a summary output file that contains subplot data for viewing charts and graphs in SORTIE you will automatically be g
249. iple times How to apply it This behavior does not need to be applied to trees It can stand alone as the only light behavior if you wish Quadrat based GLI light For more on what GLI is and how it is calculated see here Parameters for this behavior Parameter name Number of Altitude Sky Divisions for Quadrat Light Calculations Number of Azimuth Sky Divisions for Quadrat Light Calculations Quadrat GLI Always Calculate All GLIs Height at Which GLI is Calculated for Quadrats in meters Minimum Solar Angle for Quadrat Light in rad Description Number of grid cells into which the sky is divided from horizon to zenith for the purpose of calculating light direction Number of grid cells into which the sky is divided around the horizon for the purpose of calculating light direction Whether or not to always calculate a GLI for all cells in the Quadrat GLI grid If false GLIs are only calculated when needed by a tree Set this value to true if you are planning to save and use maps of the Quadrat GLI grid If not leaving it to false makes SORTIE run faster Height at which GLI is calculated This is the minimum angle at which sunlight is seen in radians Below this value the sky is assumed to be dark due to shading neighbors General light parameters used by this behavior Parameter name Beam Fraction of Global Radiation Clear Sky Transmission Coefficient First Day of Growing Season La
250. is snag aware the tree is converted to a snag e If the tree is an adult killed for any reason other than harvest and the run is NOT snag aware the tree is removed from memory e If the tree is already a snag it is removed from memory Stumps exist only for the timestep in which they were created and then disappear You can include information on dead trees in output files For the purposes of output dead trees are those which have been removed from memory and are no longer interacting with the model in any way In this case a snag is considered alive although a tree that produced a snag will show up in output mortality records in the timestep in which it died to become a snag Then the snag would show up again when it was finally removed from the model Allometry The allometry relationships govern a tree s size and shape Tree size attributes e DBH diameter at breast height is the diameter of a tree trunk in centimeters at 1 35 meters above the ground e Diameter at 10 cm or diamyo is the diameter of a tree trunk measured in centimeters at a height of 10 cm above the ground e Height is the distance from the ground to the top of the crown in meters e Crown radius is the distance from the trunk to the edge of the crown in meters e Crown depth is the distance from the top to the bottom of the crown in meters Attributes by life history stage e Seedlings diam and height e Saplings diamjo DBH height crow
251. is behavior Parameter name Description Exponential Growth The mortality at zero growth scaled as a function of the resource Resource a Exponential Growth Roae The light dependent mortality parameter Exponential Growth The resource dependent mortality parameter Resource c Exponential Growth Function term d Resource d How it works The probability of mortality for a tree is calculated with the following equation Prob d a R exp b c R G where e Prob is the annual probability of mortality as a value between 0 and 1 e Ris the amount of the second resource e Gis the amount of radial growth in mm yr e ais the Exponential Growth Resource a parameter the mortality at zero growth scaled as a function of the resource R e bis the Exponential Growth Resource b parameter the light dependent mortality e cis the Exponential Growth Resource c parameter the resource dependent mortality e dis the Exponential Growth Resource d parameter The amount of the second resource is captured in a grid object called Resource Currently it is up to you to enter a map of the values for this resource grid for instructions on how to do this see the Grid Setup Window topic This behavior does not in any way alter the values in this grid The mortality probability as calculated above is an annual probability For multi year timesteps the timestep probability is 1 1 AP where AP is the a
252. is behavior to your run the Detailed output setup window for trees will have a tree data member called Mg Carbon which has each tree s amount of carbon in metric tons Also the Detailed output grid setup window will list the Carbon Value grid You can then view the contents of this grid as a table using SORTIE s data visualization system Dimension Analysis This behavior calculates the biomass of trees based on DBH This approach comes from Jenkins et al 2004 Parameters for this behavior Parameter name Description lt th The units of biomass that the chosen biomass equation is expected to produce based on the parameters entered SORTIE ND will use this to convert the biomass value to metric tons Mg Dimension Analysis Biomass Units The correction factor needed by some biomass equations that calculate Dimension Analysis _In biomass logio biomass or logigo biomass This value is ignored if Correction Factor the value for the Dimension Analysis Use Correction Factor parameter for this species is false The units of DBH that are appropriate to the biomass equation coefficients being entered SORTIE ND will convert a tree s DBH to these units before calculating biomass Dimension Analysis DBH Units Dimension Analysis The biomass equation ID to use when calculating biomass for a particular Equation ID species Dimension Analysis The value for a in a biomass equation The appropriate value and units Para
253. is the Non Spatial Density Dep Inst Crown Height g parameter e his the Non Spatial Density Dep Inst Crown Height h parameter e iis the Non Spatial Density Dep Inst Crown Height i parameter e jis the Non Spatial Density Dep Inst Crown Height j parameter e DBH is the tree s DBH in cm e Height is the tree height in meters e STPH is number of stems per hectare of adult trees within the entire plot e BAPH is the basal area in m per hectare of adult trees within the entire plot e BAL is the sum of the basal area of all trees taller than the height of the target tree in m per hectare The non spatial logistic density dependent crown depth function is aH DSH e heighttd rad e STPA P BAPA e 8AL S l e e chis the crown depth in meters e height is the tree s height in m e ais the Non Spatial Log Density Dep Crown Height a parameter e bis the Non Spatial Log Density Dep Crown Height b parameter wee e cis the Non Spatial Log Density Dep Crown Height c parameter e dis the Non Spatial Log Density Dep Crown Height d parameter e eis the Non Spatial Log Density Dep Crown Height e parameter e fis the Non Spatial Log Density Dep Crown Height f parameter e gis the Non Spatial Log Density Dep Crown Height g parameter e DBH is the tree s DBH in cm e rad is the instrumental crown radius of the target tree in meters calculated using the function below e STPH is number of stems pe
254. istribution controlled by the Mean Height of Mounds in m and Standard Deviation of Mound Height in m parameters If it s on a non mound substrate its rooting height is zero If a seedling germinates on fresh log it has the chance of getting a respite from the effects of the Beer s law light filter behavior which it expects to simulate fern shading Fallen logs crash through the fern layer and it takes a while for the ferns to grow back over the top of the log This length of time is the maximum possible respite length and is set in the Years Respite from Fern Shading for Seeds on Fresh Logs parameter Substrate keeps track of the age of its fresh log cohorts so that it is possible to randomly assign the seedling to a fresh log of a specific age given the relative proportions of various aged fresh log cohorts The age of the log is subtracted from the maximum respite length and this value is assigned to the seedling Thus a log that fell this timestep would give a seedling the maximum respite whereas a much older log may not give any respite at all How to apply it Apply this behavior to seeds of your desired species Any species to which it is applied must also satisfy the following requirements e A disperse behavior must be applied e The Substrate behavior must be applied e The Beer s Law light filter behavior must be applied Light Dependent Seed Survival This behavior assesses seed survival as a function of the Global Light Inde
255. it should be applied to adults and snags of all species Substrate cannot be applied to seedlings or saplings Any tree species type combination to which it is applied must also have a mortality and snag dynamics behavior applied Epiphytic establishment behaviors Epiphytic establishment behaviors allow seeds to germinate epiphytically Behavior Description Tree Fern Establishment Simulates the establishment of seedlings epiphytically on tree ferns behavior Tree Fern Establishment This behavior was developed to simulate the establishment of seedlings epiphytically on tree ferns Rather than tracking individual seedlings that germinate and grow on a tree fern during its life this assumes that upon a tree fern s death there is a possibility that a seedling will establish in that spot For the purposes of this behavior multiple species can serve as possible epiphytic substrates but only one species will establish upon them Note this behavior is applied to the epiphytic substrate trees species and life history stage not the establishing species Parameters for this behavior Because the Tree Fern Establishment behavior makes light calculations a set of light parameters is included in its parameter list These are used in exactly the same way as the light behavior parameters However the values are independent of those which may be used for other light behaviors If updates are made to the light parameters of an existing parameter
256. ith a djo at least that of the Juvenile NCI Minimum Neighbor Diam10 in cm parameter out to a maximum distance set in the Juvenile NCI Maximum Crowding Distance in meters parameter The competitiveness of a neighbor increases with the neighbor s size and decreases with distance The neighbor s species also matters the effect depends on the relationship between the target species and the neighbor species Unlike NCI growth this competitiveness index uses dio instead of DBH so seedlings can compete For adults the dig is calculated from DBH using the DBH diameter at 10 cm relationship You set whether or not snags compete in the Juvenile NCI Include Snags in NCI Calculations parameter NCI is calculated as os e ver ange Ci distance J 71k 1 ik where e the calculation sums over j 5 species and k N neighbors of each species of at least a dio of Juvenile NCI Minimum Neighbor Diam10 in cm out to a distance of Juvenile NCI Maximum Crowding Distance in meters e ais the Juvenile NCI Alpha parameter for the target tree s species e fis the Juvenile NCI Beta parameter for the target tree s species e D110 is the dio of the kth neighbor in cm e qis the Juvenile NCI Diam10 Divisor q parameter Set this as necessary to rescale the competitive effects of neighbors e Aix is the Species j NCI Lambda parameter for the target species relative to the kth neighbor s species e distance 1s distance from target to n
257. ithin the plot have a susceptibility of 1 or Mapped meaning that you will provide a map with a susceptibility for each location in a grid called Storm Susceptibility The method of storm damage application can be either Deterministic meaning that each location receives the storm s severity index or Stochastic meaning that the storm s severity index provides a mean around which individual location severities are randomized There are two possible probability distribution functions for stochastic damage application normal and lognormal The normal distribution is where o is the function standard deviation Mean is zero in this equation the final value is reached by adding the function result to the mean The lognormal distribution is J fing x J t ye 1 204 Je XN yak where is the function mean and o is the standard deviation Combining these two parameters provides four possibilities for the way a storm s damage is applied 1 Mapped Deterministic The damage index for a location equals the susceptibility of that location multiplied by the storm s severity index 2 Mapped Stochastic The storm severity for each location is determined by performing a random draw on a probability distribution function with the overall storm severity providing the function mean Each location s severity is multiplied by its susceptibility to arrive at the final storm damage index for that location 3 Uniform Deterministic
258. ius as entered for the Plot BAC is the basal area of all conspecific adult trees found within a given radius of the grid cell center The radius is set using the Temp Dep Neigh Disperse Max Distance for Conspecific Adults m parameter Note that the A parameter is an intercept potentially allowing bath rain of seeds for species for which there are no parents present To manage this the behavior uses a presence test which is the normalized probability of finding a species on a plot as a function of temperature 2 os P e B where e P is the normalized presence probability e Bis the Temp Dep Neigh Disperse Presence B parameter which controls the width of the peak e Mis the Temp Dep Neigh Disperse Presence M parameter which is the function mean or the temperature in degrees Celsius at which the probability of finding the species equals 1 e Tis the annual mean temperature in degrees Celsius as entered for the Plot You control the acceptable threshold for the presence test using the Temp Dep Neigh Disperse Presence Threshold 0 1 parameter If the value of the presence test function is above this value the species is allowed to disperse in the absence of adults in the plot A threshold value of 0 always allows the species to disperse a value of 1 always excludes it Note that if there are adults of that species in the plot the species disperses no matter what the presence test says Once the number of seeds per
259. iven separate chart viewing options for the whole plot plus each subplot To view subplot charts and graphs for detailed output you can open the detailed output subplot files separately Setting up output You should set up output last after you have completed your parameter file What data you will have available to save will depend on how you have chosen to set up your run To set up output choose Edit gt Output options from the main SORTIE window This will lead you to windows that allow you to choose what you want to save for both summary and detailed output files Your options will depend on the setup of the run If you are working with a parameter file that was created on a different computer or by someone else remember to check the file path and name of the output files You may need to change the path to one that exists on the computer on which you intend to run the parameter file Using output as input to a new run The tree and grid map data from detailed output files may be used as initial conditions for a new parameter file This is useful when you want to generate starting conditions for future runs that start with a stable forest structure or when you want to troubleshoot a run by recreating certain conditions Here are the requirements for a detailed output map file to be loaded with a parameter file different from its original file e The parameter file must have the same species as the parameter file used to create
260. ividual cut decisions No more than two passes will be made even if the second pass does not achieve a removal rate within the tolerance Setting a high tolerance such that a second pass is not often needed eliminates a lot of calculations and will allow a run to be faster How to apply it Apply this behavior to the adults of all species You must also apply the Dimension analysis behavior to the same trees Harvest Trees removed by this behavior will have a mortality reason code of harvest Parameters for this behavior This behavior does not have its parameters entered through the Parameters Window Set up these behaviors using the Edit Episodic Events Window How it works SORTIE can implement complex silvicultural treatments Harvest events are defined by species timestep amount to remove type of cut and area of the plot You can define as many harvest events as you wish For information on planting new seedlings see the Planting behaviors topic There are three types of harvest gap cut partial cut and clear cut The primary function of entering the harvest type is to control substrate composition after the harvest occurs In a partial cut harvest though you have more flexibility in choosing which trees are cut You can define up to four size classes and specify the amount of trees to remove in one of four ways as a percentage of total basal area as an absolute amount of basal area as a percentage of total tree
261. ks Trees grow according to the relative growth version of the Michaelis Menton function The same function is used for both browsed and unbrowsed trees but the parameters are different The function is A xrar AFG AL GLI Shit where e Yis the amount of annual relative growth e Ais the Asymptotic Diameter Growth A or Browsed Asymptotic Diameter Growth A parameter e Sis the Slope of Growth Response S or Browsed Slope of Growth Response S parameter e GLI is the global light index calculated by a light behavior Growth is compounded over multiple timesteps with the equation G Y 1 1 diam where e Gis the amount of diameter growth for the timestep in cm e diam is the diameter of the tree in cm at 10 cm height if seedling or sapling or DBH if adult e Tis the number of years per timestep e X is the Relative Michaelis Menton Growth Diameter Exponent or Browsed Diameter Exponent parameter Whether or not a tree is browsed is determined by the Random browse behavior How to apply it This behavior can be applied to seedlings saplings and adults of any species Any tree species type combination to which it is applied must also have a light behavior and the Random browse behavior applied You can use either the diam with auto height or diam only version Constant radial growth Parameters for these behaviors Parameter name Description Adult Constant Radial Growth in The constant value by which to i
262. l seed consumption and predator response for as much of the year as the user desires The mini model simulates a single year which starts at the beginning of seed fall It is possible to define two seasons during the year with different parameters for seed consumption All species are assumed to drop seeds at the same time at a constant rate You set the number of weeks that seedfall should occur Once seedfall is over there are no new additions to the predator food pool There is then an optional period of germination in which the food pool of seeds is further reduced by some proportion of those remaining seeds germinating into seedlings seedlings cannot be eaten Once the model has finished running the leftover seeds that were not consumed by predators or those seeds that escaped through germination are available as input to the Establishment behaviors Parameters for this behavior Parameter name Description Func Resp Demographic The seed predator population demographic efficiency for season 1 Efficiency Season 1 Func Resp Demographic The seed predator population demographic efficiency for season 2 Efficiency Season 2 Func Resp Density Dependent Coeff Season 1 The coefficient describing the effect that density dependent factors have on the predator population instantaneous rate of change in season 1 Pun Ro po cua The coefficient describing the effect that density dependent factors have Dependent Coeff on the p
263. l conditions are the trees in the SORTIE forest when a simulation begins The initial conditions are often of vital importance to how a run develops There are two ways to add trees at the beginning of the run and they can be used together or separately The first is to ask the model to create trees for you according to your chosen species composition and size structure The second way is to directly list a particular set of trees in a tree map Defining initial conditions using species composition and size structure For saplings and adults you can set up DBH size classes and enter the desired density in each size class To set up size classes use the Edit size classes window You can define as many size classes as you want The values that you enter are the upper bounds of each class Once you have defined all of your size classes you can enter the desired number of stems per hectare for each species for each class in the tree parameters which you edit using the Parameters window There are two different ways to enter seedling densities Defining a DBH size class of zero gives you a line for entering stems per hectare of seedlings These seedlings will be brand new with sizes approximating the value in the New Seedling Diameter at 10 cm tree parameters If you would like more control over seedling sizes you can define three height classes densities for each in the tree parameters The resulting trees are randomly distributed around the
264. l juvenile tree as a function of the density and mean diameter of the neighborhood trees Calculates probability of mortality as a function of growth and some second resource Kills trees as a function of growth rate Calculates the probability of mortality of an individual tree as a function of the density of conspecific neighborhood trees Calculates probability of survival as a function of growth and some second resource Calculates the probability of mortality using a Weibull function of tree height and GLI light level It can also simulate the effects of herbivory by using different parameters for browsed and unbrowsed trees Causes mortality in trees that are infested with insects Calculates the probability of survival according to a logistic equation with the possibility of two sets of parameters for each species one for high light conditions and one for low light conditions Uses multiple effects including neighbor competitiveness to calculate mortality rates Simulates an increase in mortality after harvesting attributable to skidding damage or other effects Uses a pseudo density dependent function designed to increase the death rate in dense uniform age stands Provides for an uptick in mortality rates among large adult trees Applies a constant rate of mortality to trees with different rates for high light and low light conditions This works with the Storm Light behavior Mortality Storm Light Stoch
265. l tree density or as an absolute amount of tree density When the Episodic Mortality behavior is determining which trees to remove it starts by finding the largest tree in the area of the plot affected by the mortality episode It works its way through the trees from largest to smallest assessing whether to kill each one until it either runs out of trees or reaches its cut target This process preferentially removes the largest trees in each size range unless the event is defined by a percentage of density in which case all trees in the target size ranges have an equal probability of being killed If Episodic Mortality is removing a percentage of basal area or an absolute amount of basal area it will only kill a tree if its basal area will not cause the total to be more than the target This means that for basal area defined cuts the behavior may skip some bigger trees and cut smaller ones in order to more exactly cut its target Each species is cut separately So a request to remove 20 of three species will remove 20 of each of them no matter what their relative proportions to each other Seedlings can also be killed as part of a planned mortality episode You can specify the proportion of seedlings that are killed within the target area for each species The seedlings of a species can be killed even if that species is not otherwise participating in the episode Seedlings in the target area are randomly chosen to die based on the mortality rate
266. le Grid tables There are specialized tables for the following grids e Harvest Results e Mortality Episode Results e Carbon Value e Merchantable Timber Value e Windstorm Results e Partitioned Biomass e Storm Killed Partitioned Biomass e Storm Damage e Foliar Chemistry If you wish to view these tables set up your detailed output file to save all the data from your chosen grids Timestep tree writer This is not really a table as such This tool will write out all tree data saved for a given timestep to a tab delimited text file Starting and managing a run A run is a single model simulation It starts at time zero and continues until its defined endpoint is reached A run is defined by its parameter file This tells the model how long to run and what to do during the run Starting a run You begin by creating or opening a parameter file using the File gt Open file menu option Then you choose Model gt Run from the menu or click the Run button A file must be complete and all data in it valid if the run is to succeed so the file will be validated before the run occurs You will get an error message if there is something wrong with the parameter file If you have made changes to the parameter file you ll be prompted to save the file If you choose not to save the file a temporary file will be written so the run can proceed Checking the progress of a run At the bottom of the SORTIE window
267. list the proportions used are the canopy proportions The behavior then goes through each grid cell in the Dispersed Seeds grid and assesses the survival for the seeds of those species to which it applies This behavior starts by giving each seed a random temporary location within the Dispersed Seeds grid cell Then it retrieves the substrate favorability at that point from the Substrate Favorability grid It then compares a random number to the substrate favorability to determine whether the seed lives This method ensures that we can assess substrate favorabilities correctly when the Dispersed Seeds and Substrate grids have different grid cell resolutions Once this process is complete the number of surviving seeds for each species is assigned back to the Dispersed Seeds grid How to apply it This behavior may be applied to seeds of any species A species to which this is applied must also have a Disperse behavior applied Also the Substrate behavior must be used in the run Substrate Dependent Seed Survival With Gap Status This behavior assesses seed survival as a function of both the substrate composition of the grid cells in which seeds land and the cells forest cover gap or canopy This behavior allows for different germination favorability for substrates under the two forest covers Parameters for this behavior Parameter name Description Fraction Seeds The proportion of those seeds that land on decayed logs under canopy
268. ll Class Y Initial Log Prop 0 1 Species Group X Large Class Y Log Decay Alpha Species Group X proportion for all five classes together must add up to 1 The proportion of snags entering each of the five decay classes The proportion for all five classes together must add up to 1 as applied to scarified The a exponent in the decay equation soil Note that this is annual decay sb as applied to scarified The B exponent in the decay equation y e soil Note that this is annual decay Which species group 1 3 each species is assigned to After a clear cut harvest the proportion of substrate area that is large logs of species group X decay class Y All clear cut values added together must be less than or equal to 1 This is not required if the Harvest behavior is not used After a clear cut harvest the proportion of substrate area that is small logs of species group X decay class Y All clear cut values added together must be less than or equal to 1 This is not required if the Harvest behavior is not used After a gap cut harvest the proportion of substrate area that is large logs of species group X decay class Y All gap cut values added together must be less than or equal to 1 This is not required if the Harvest behavior is not used After a gap cut harvest the proportion of substrate area that is small logs of species group X decay class Y All gap cut values added together must be less
269. ll resolution will be ignored Data in the grid Data member name Description Type of harvest that occurred in the current timestep or 1 if Harvest Type none has occurred Cut Density species x cut Number of trees cut in the current timestep for the given species range y and cut range Cut Basal Area species x cut Total basal area cut in the current timestep for the given species range y and cut range Seedlings killed as part of a harvest event in the current timestep Cut Seedlings species x for the given species Merchantable Timber Value Grid This grid is created by the Merchantable Timber Value behavior It holds the merchantable timber value for each species This grid has one cell for the whole plot It will ignore any changes you make to the resolution If this grid s data is saved in a detailed output file you can view the contents of this grid as a table using SORTIE s data visualization system Data in the grid Data member name Description Value for Species X The merchantable timber value for Species X Mortality Episode Master Cuts Grid This grid is created by the Episodic Mortality behavior This is where directions to SORTIE for planned mortality episodes for the run are stored The actual name of the grid is mortepisodemastercuts The only thing you may change in this grid is the grid cell resolution You may set it to anything you wish You can change it with either the Grid Setup window accessible o
270. load the data from any timestep of the previous run as initial conditions in the current parameter file For more on entering the maps from a detailed output file see the Using output as input to a new run topic Types of output files There are two kinds of output files summary output files and detailed output files You can save either or both kinds of files for a run Summary output files save high level plot wide density and basal area information for a run This data is stored in a text format that is small and easy to open and read Detailed output files save information on individual grades and trees They are very flexible You can save as much or as little detail as you like You cannot directly open and read these files but you can use SORTIE to graph and chart the data and produce a wide variety of text output from the files Output strategies Choosing what output to save is a bit of an art form Save too much data and your files will be too large and very slow to process Save too little and you won t have the data you need after your run Here are some strategies to help you decide what to save What you save depends on what you want to look at Each chart that SORTIE can display requires a specific set of information There are several output types line graphs histograms tree maps grid maps and tables Also be aware that for overall data the summary output file is a better choice than the detailed output file
271. m Float this time step Also this value population Radius will almost certainly reflect the always tree s size at the beginning of the available timestep when crown dimension calculations are made rather than the end of the timestep as with the other tree dimensions This does not apply to seedlings Diam10 Float height in cm This applies only to 10cm seedlings and saplings The tree s crown depth in meters Tree Crown The same warning applies as with population Depth Crowne Dopik Bloat crown radius This does not apply always to seedlings available Tree The time since death in years population Age Age Integer Only for snags always available Reason code for why a tree died Tree Only for snags Integer of one of orilaions Why dead Why dead Integer the following 1 harvest 2 P l p natural causes 3 disease 4 aways i available fire 5 insects or 6 storm Any of the Light level for the tree This could lt a Light level Light Float be GLI or percent shade if Sail except the Light is used Beer s Law light filter Light filter If_count Integer respite counter Any of the growth behaviors that increment diameter growth Amount of radial growth per year in mm Number of years of respite for a new seedling from the effects of the light filter Beer s law light filter Rooting Float The height in mm above ground Beer s law height level at which a seedling
272. m damage You may not apply this behavior to seedlings If you wish to use the Storm damage killer behavior to create snags from storm killed trees you must apply this behavior to the snag tree type Along with this behavior you must also add the Storm disturbance behavior Storm damage killer This behavior kills trees damaged in storms It decides which damaged trees die and if they become snags it manages the snag population by causing snag tip up and removal This behavior does not decide which trees get damaged in a storm that is the job of the Storm damage applier behavior Trees removed by this behavior will have a mortality reason code of storm Parameters for this behavior Parameter name Description Minimum DBH for Storm Damage in cm The minimum DBH for trees that can be damaged or killed by storms Trees smaller than this are never damaged no matter what storms occur Number of Years Storm Damaged Snags Last The number of years snags damaged in storms last before disappearing If snags are not used in a run this is not required Storm Heavy Damage Survival Prob Intercept a The a value in the probability of survival logit function for trees with heavy damage Storm Heavy Damage Survival Prob DBH Coeff b The b value in the probability of survival logit function for trees with heavy damage Storm Medium Damage Survival Prob Intercept a The a value in the probability of survival logit
273. m of the basal areas in square cm of eligible neighbors e BADiv is the Basal Area NCI BA Divisor parameter When calculating BA this behavior uses neighbors of all species out to the distance set in the NCI Max Radius of Crowding Neighbors in m parameter The neighbors must have a DBH larger than the values set in the NCI Minimum Neighbor DBH in cm parameter If the Basal Area NCI Use Only Larger Neighbors parameter is set to true they must also have a DBH larger than the target tree s DBH Seedlings and snags never contribute to BA The amount of growth is in cm year For multi year timesteps the behavior will calculate total growth with a loop Each loop iteration will increment DBH for one year For each year any portion of the growth equation with DBH as a term is recalculated with the previous year s updated DBH value NCI values are constant throughout this loop for neighbors only the d10 at the start of the timestep is used How to apply it This behavior can be applied to saplings and adults of any species It cannot be applied to seedlings You can use either the diam with auto height or diam only version Constant basal area growth Parameters for these behaviors Parameter name Description Adult Constant Area The constant amount of basal area by which to increase a tree s basal Growth in sq cm yr area How it works The amount of diameter increase is calculated from a constant basal area increment The in
274. mass Tree Bole Volume Calculates merchantable tree volume calculator Tree Age Calculates tree age Tree Volume Calculates the volume of tree trunks to find both merchantable volume and total Calculator volume Carbon Value This behavior calculates the amount of carbon per species and its value Parameters for this behavior Parameter name Description lt th Carbon Value Carbon Amount of The percentage of biomass that is carbon as a value between 0 and 100 Biomass 0 100 Carbon Value Price Per Metric Ton The price per metric ton of carbon The currency is unimportant Carbon How it works This behavior relies on the Dimension Analysis behavior to calculate each tree s biomass in metric tons It then multiplies this value by the Carbon Value Carbon Amount of Biomass 0 100 parameter to find each tree s amount of carbon in metric tons This behavior finds the total amount of carbon in each species and then multiplies it by the Carbon Value Price Per Metric Ton Carbon to find each species carbon value Both the amount of carbon in metric tons for each species and the value of that carbon are saved in a grid called Carbon Value You can save these values in a detailed output file for analysis How to apply it Apply this behavior to saplings adults or snags of any species These trees must also use the Dimension Analysis behavior This behavior does not automatically create output Once you have added th
275. masting disperse behaviors The po term in the seed offtake equation under masting conditions The pn term for species i in the seed offtake equation under masting conditions The density of edible seed that indicates masting has occurred The minimum DBH of trees to be included when calculating the basal area composition of the neighborhood The radius to search for trees when calculating the basal area composition of the neighborhood The po term in the seed offtake equation under non masting conditions The p term for species i in the seed offtake equation under non masting conditions Masting timesteps are those with a heavy density of edible seeds The first step in a given time step is deciding whether or not masting is occurring There are two methods available for making the masting decision You set your chosen method using the Neighborhood Predation Mast Event Decision Method parameter If the event decision method is set to Seed threshold masting events occur whenever seed density rises above a certain threshold You set the threshold for this density in the Neighborhood Predation Masting Seed Density m2 yr parameter You then set which species are included in the mast count with the Neighborhood Predation Counts For Masting parameter Species which do not count towards masting may still be predated The seed density is set as an annual average so the density will be calculated the same way for dif
276. mber of predators Per capita seed offtake for a single seed species is IR c 1 g e oe Ds where e c is the Func Resp Max Intake Rate seeds per predator per day parameter for that seed species e Sis the number of seeds per predator per day e Dis the Func Resp Foraging Efficiency parameter e ps is the proportion of the total seed pool made up by that species Predator response to food availability can be different for two seasons in the year The dividing line between the seasons is given with the Func Resp Week Season 2 Begins parameter If you want a uniform response with no seasonal differences you can set this value to 1 or 52 or set the predator response parameters to be the same for both seasons The number of predators in each cell s population is calculated as N N 1 e where e Nis number of predators for the current timestep e WN is number of predators in the previous timestep e r is instantaneous rate of change in predator abundance for the previous timestep The instantaneous rate of change per week r is calculated as r at d X IR g N 12 where e ais the Func Resp Max Decline Rate Season 1 or 2 predators week parameter e dis the Func Resp Demographic Efficiency Season 1 or 2 parameter e gis the Func Resp Density Dependent Coeff Season 1 or 2 parameter e Nis number of predators per hectare How to apply it This behavior may be applied to seeds of any species Any species to which
277. mean in a Poisson probability distribution function e Normal use the number of seeds as the mean in a normal probability distribution function You must then supply a standard deviation for the function e Lognormal use the number of seeds as the mean in a lognormal probability distribution function You must then supply a standard deviation for the function e Negative binomial use the number of seeds as the mean in a negative binomial probability distribution function You must then supply a clumping parameter If you have chosen the negative binomial probability distribution function for Seed distribution this is the clumping parameter of the function in seeds per m If you have not chosen that PDFs then this parameter is not required If you have chosen the normal or lognormal probability distribution functions for Seed distribution this is the standard deviation of the function in seeds per m If you have not chosen these PDFs then this parameter is not required The annual STR value Standardized Total Recruits or all seeds produced by a 30 cm DBH tree in one year for stumps Stumps use the same probability distribution function as the live members of their species Only required if a behavior is being applied to stumps The annual STR value Standardized Total Recruits or all seeds produced by a 30 cm DBH tree in one year for the Weibull function under canopy conditions see equation below This is only
278. meter a for this parameter depend on the values entered in the Dimension Dimension Analysis Parameter b Dimension Analysis Parameter c Dimension Analysis Parameter d Dimension Analysis Parameter e Dimension Analysis Use Correction Factor How it works Analysis Equation ID Dimension Analysis DBH Units and Dimension Analysis Biomass Units parameters The value for b in a biomass equation The appropriate value and units for this parameter depend on the values entered in the Dimension Analysis Equation ID Dimension Analysis DBH Units and Dimension Analysis Biomass Units parameters The value for c in a biomass equation Whether this parameter is used and the appropriate value and units for this parameter depend on the values entered in the Dimension Analysis Equation ID Dimension Analysis DBH Units and Dimension Analysis Biomass Units parameters The value for d in a biomass equation Whether this parameter is used and the appropriate value and units for this parameter depend on the values entered in the Dimension Analysis Equation ID Dimension Analysis DBH Units and Dimension Analysis Biomass Units parameters The value for e in a biomass equation Whether this parameter is used and the appropriate value and units for this parameter depend on the values entered in the Dimension Analysis Equation ID Dimension Analysis DBH Units and Dimension Analysis Biomass Units parameters Whether or not th
279. meter file 1 xml rather than parameter file 1 xml Using the Browse button causes this to happen automatically and you can select multiple files this way This ensures that the model will be able to find the file when it comes time to run the batch You are allowed to enter parameter file names and paths which do not exist on the current computer to allow you to prepare batch files to run on other machines Double check that all of your files are in the correct place before you begin to run your batch Number of times to run this file The number of times to run this parameter file during the batch Add new parameter file This button adds a parameter file and a number of times to run to the batch list Current parameter files in this batch This displays the current parameter files in the batch list along with the number of times each should be run Remove Use this button to remove one or more parameter files from the batch list Once the batch list is the way you want it click OK to write the file Edit menu The options in this menu for editing parameter files Parameters Use this option to edit parameter values for the run The parameters needing values changes depending on the behaviors for the run For more details on this option see the Parameters window topic For details on individual parameters see the behavior to which they belong Episodic events Use this option to edit planned episodic events such as sil
280. meters parameter These values are not used by any other behavior You can save the values in the GLI Map grid into a detailed output file and view the map data later How to apply it Add the behavior to the run Be sure to save the GLI Map grid in the detailed output file in order to be able to view the results GLI Points File Creator behavior This behavior calculates GLI values for individual points in the plot Parameters for this behavior Parameter name GLI Points Input File GLI Points Output File Minimum Solar Angle for GLI Points Creator in rad Number of Altitude Sky Divisions for GLI Points Creator Number of Azimuth Sky Divisions for GLI Points Creator Description The file containing the points for which to calculate GLI This file will overwrite any existing points For best results enter a fully qualified pathname i e c sortie my_file txt The file to which results will be written each timestep Any existing data in this file will be overwritten at the start of the run This is the minimum angle at which sunlight is seen in radians Below this value the sky is assumed to be dark due to shading neighbors Number of grid cells into which the sky is divided from horizon to zenith for the purpose of calculating light direction Number of grid cells into which the sky is divided around the horizon for the purpose of calculating light direction General light parameters used by this behavior
281. model run that seedfall occurs The initial density of the predator population in numbers per m This will be used the first time this behavior is run Whether this density is used for subsequent behavior mini model runs depends on the value of the Keep Predator Densities Between Timesteps parameter During the period that germination occurs this is the fraction of the seed pool that is removed due to seed germination Expressed as a value between 0 and 1 The filename where the mini model will store its intermediate results for later analysis if desired This value is not required The week during the behavior mini model run that germination begins to occur If you do not want germination to occur set this value greater than or equal to the Weeks to run seed predation model 1 52 parameter This value must be between 0 and 52 The week that the second season begins if desired The number of weeks timesteps to run the behavior s mini model This number must be between 1 and 52 The behavior s mini model begins with the number of seeds of each species to which it is applied that are available in each cell of the Dispersed Seeds grid Each cell gets its own run of the mini model The pool of seeds in one cell for all species to which this behavior applies is treated as a single food pool for one year s time even if the model timestep length is greater than one year For all the species to which this behavior is applied the
282. more on the plot s shape Only saplings and adult trees are included in K calculations The K values are calculated for all trees in the plot as well as for individual species In the case of an individual species X is the number of pairs of trees of that species and n is the total number of trees of that species The resulting K values are stored in the Ripley s K grid How to apply it Add this behavior to your run There is no need to apply it to specific tree species or types Indeed any such specifications will be ignored This behavior does not automatically create output Once you have added this behavior to your run the Detailed output grid setup window will list the Ripley s K grid Save all the data members of this grid You can then view the K values as a line graph and use the graph to save the K values as a text file Relative Neighborhood Density Calculator Parameters for this behavior Parameter name Description lt th Relative Neighborhood The maximum distance out to which to calculate Relative Neighborhood Density Maximum Density Index Q values Distance m Relative Neighborhood Density Distance Increment m The distance increments at which the Relative Neighborhood Density Index Q will be calculated Smaller increments mean a smoother curve but also more processing time This behavior calculates the relative neighborhood density index Q as described in Condit et al 2000 Q is a measure of the ag
283. n for that species is lognormal The standard deviation of the lognormal function under masting conditions This is only required for a species if the canopy probability distribution function for that species is lognormal The mean annual STR value under masting conditions If the Masting Disperse STR Draw PDF is Deterministic then this is the STR value used The standard deviation of the STR value under masting conditions If the Masting Disperse STR Draw PDF is Deterministic then this value is not used The proportion of all adults for a species that participate in disperse during a masting timestep as a value between 0 and 1 The B value under non masting conditions The mean annual STR value under non masting conditions If the Masting Disperse STR Draw PDF is Deterministic then this is the STR value used The standard deviation of the STR value under non masting conditions If the Masting Disperse STR Draw PDF is Deterministic then this value is not used The proportion of all adults for a species that participate in disperse Non Mast Proportion Participating 0 1 Masting Disperse Masting Weibull Dispersal Masting Disperse Masting Weibull Theta Masting Disperse Stochastic STR Draw Frequency Masting Disperse STR Draw PDF Minimum DBH for Reproduction in cm Seed Distribution Seed Dist Clumping Parameter Neg Binomial Seed Dist Std Deviation Normal or Lognormal during
284. n calculating relative growth Relative growth is calculated with the equation where dwr A GEi Ad 4 Ty oo fw Shs e Yis the amount of annual relative growth e Ais the Asymptotic Diameter Growth A or Asymptotic Height Growth A parameter e Sis the Slope of Growth Response S or Slope of Height Growth Response S parameter e GLI is the global light index calculated by a light behavior Diameter growth is compounded over multiple timesteps with the equation G Y 1 1 diam where e Gis the amount of diameter growth for the timestep in cm e diam is the diameter of the tree in cm at 10 cm height if seedling or sapling or DBH if adult e Tis the number of years per timestep e Xis the Relative Michaelis Menton Growth Diameter Exponent parameter Relative height growth is calculated slightly differently The details are discussed in the section for the Relative growth height only behavior below Relative growth is discussed in Pacala et al 1996 Relative growth limited to radial increment How it works This behavior calculates an amount of diameter growth according to the relative growth equation Growth is limited to a maximum of the constant radial growth increment for the species of tree to which it is being applied The increment is calculated as described in the Constant radial growth behavior Note that the increment parameter specifies radial growth the behavior makes all necessary conver
285. n coefficients These light extinction coefficients are specified in the Light Extinction Coeff of Complete Damage Trees 0 1 and Light Extinction Coeff of Medium Damage Trees 0 1 parameters Once GLI has been calculated the proportion of seeds that survive for a given species is calculated as If GLI lt GLlop LE 1 Sto GLIop GLD e IfGLI GLI LE 1 If GLI gt GLlop LE 1 Sni GLI GLIyp e GLIis the GLI at the center of the Dispersed Seeds grid cell at the height in the Height in m At Which to Calculate GLI parameter e GLI is the GLI of Optimum Establishment 0 100 parameter e Sj is the Slope of Dropoff Below Optimum GLI parameter e Sj is the Slope of Dropoff Above the Optimum GLI parameter Once the proportion of seeds that survive at the given GLI has been calculated this value is multiplied by the number of seeds to reduce them by the proper amount The new reduced number of seeds is put back in the Dispersed Seeds grid How to apply it Apply this behavior to seeds of your desired species Any species to which it is applied must also have a Disperse behavior applied Storm damage is optional Proportional Seed Survival This behavior reduces the number of seeds by a set amount Parameters for this behavior Parameter name Description Proportion Germinating Between 0 and 1 The proportion of seeds of a species that survive germination as a value between 0 and 1 How it works In
286. n each cohort The final proportion of the moss litter pool is whatever grid cell area is left over The pool is further split into moss and litter by using the fixed proportion of each in the pool How to apply it Apply Substrate to all trees which can create substrate by becoming fallen logs This generally means that it should be applied to saplings and adults of all species Substrate cannot be applied to seedlings Any tree species type combination to which it is applied must also have a mortality behavior applied Detailed Substrate This behavior is a modification of the Substrate behavior that primarily incorporates greater detail in tracking log cover In Detailed Substrate the pool for logs is divided into up to 3 species groups 2 size classes and 5 decay classes whereas the Substrate behavior has 1 species size class and 2 decay classes for logs Also unlike Substrate Detailed Substrate is designed to work with snag dynamics behaviors that assign data members representing fall or break heights of trees and snags This way the processes of tree and snag breakage and fall are separated from their input into the log substrate pool There is also a change from Substrate to the way harvesting adds new substrate and values for log volume are calculated in addition to projected area cover Like Substrate Detailed Substrate keeps track of the relative cover of forest floor litter moss scarified soil tip up mounds and logs each t
287. n function is Weibull The 9 for the Weibull function under canopy conditions or under non masting conditions in the case of Masting spatial disperse see equation below This is only required if the canopy probability distribution function is Weibull The annual STR value Standardized Total Recruits or all seeds produced by a 30 cm DBH tree in one year for the Weibull function under gap conditions see equation below This is only required if the gap probability distribution function is Weibull The value for the Weibull function under gap conditions see equation below This is only required if the gap probability distribution function is Weibull The dispersal value for the Weibull function under gap conditions see equation below This is only required if the gap probability distribution function is Weibull The 0 value for the Weibull function under gap conditions see equation below This is only required if the gap probability distribution function is Weibull The behavior starts each timestep by updating the forest cover of each cell gap or canopy It counts all trees above the minimum DBH for reproduction in each cell and compares that number to the Maximum parent trees allowed in gap cell parameter The behavior will count trees of all species to determine gap status However if it finds a tree of a species that is not one of the ones this behavior is assigned to it will use the tree s minimum adult DBH parameter i
288. n is set to 8 m X 8 m You cannot change the grid cell resolution for this grid Data in the grid Data member name Description Planted Species X Number of trees of Species X cut in the current timestep Quadrat GLI Grid This grid is created by the Quadrat based GLI Light behavior The grid holds a GLI value in each cell quadrat being a term previously used in SORTIE to describe small grid cells The grid cell resolution defaults to 2 m X 2 m You can set whatever new resolution you wish Data in the grid Data member Description name GLI value or 1 if there were no trees to which to assign a GLI value in cu that grid cell Relative Neighborhood Density Grid This grid holds values for the Relative Neighborhood Density Q statistic as calculated by the Relative Neighborhood Density Calculator behavior The grid holds an Q value for each distance increment for each species This can be a great many values The grid cell resolution is always set to one cell covering the entire plot You cannot change this Data in the grid Data member Description name Maximum distance to which to calculate Q in meters Including this in the SHES Dae output is not necessary but will improve the SORTIE graphing capability How often to calculate Q in meters Including this in the output is not Distance Inc necessary but will improve the SORTIE graphing capability Species X Dist Y The Q value for Species X at the Yth distan
289. n meters at which to calculate GLI at the center of each grid cell The last day of the growing season as a Julian day number between 1 and 365 Seeds only get light during the growing season See more on GLI calculations The fraction of light transmitted by the crowns of trees with complete Storm damage Not required if storms are not used Expressed as a value between 0 and 1 If storms are used a value must be supplied for every species See more on GLI calculations The fraction of light transmitted by the crowns of trees with medium Storm damage Not required if storms are not used Expressed as a value between 0 and 1 If storms are used a value must be supplied for every species See more on GLI calculations The fraction of light transmitted by the crowns of regular live trees and if storms are being used trees with no Storm damage Expressed as a value between 0 and 1 A value must be supplied for every species See more on GLI calculations This is the minimum angle at which sunlight is seen in radians Below this value the sky is assumed to be dark due to shading neighbors See more on GLI calculations Number of grid cells into which the sky is divided from horizon to zenith for the purpose of calculating light direction See more on GLI calculations Number of grid cells into which the sky is divided around the horizon for the purpose of calculating light direction See more on GLI calculations The slo
290. n of substrate that is scarified soil in areas that had a clear cut harvest event as a value between 0 and 1 This is not required if the Harvest behavior is not used The proportion of substrate that is tip up mounds substrate in areas that had a clear cut harvest event as a value between 0 and 1 This is not required if the Harvest behavior is not used After a gap cut harvest the mean diameter of logs in the small size class in cm This is not required if the Harvest behavior is not used After a gap cut harvest the mean diameter of logs in the large size class in cm This is not required if the Harvest behavior is not used The proportion of substrate that is scarified soil in areas that had a gap cut harvest event as a value between 0 and 1 This is not required if the Harvest behavior is not used The proportion of substrate that is tip up mounds substrate in areas that had a gap cut harvest event as a value between 0 and 1 This is not required if the Harvest behavior is not used The proportion of substrate that is scarified soil in areas that had a clear cut harvest event as a value between 0 and 1 This is not required if the Harvest behavior is not used Clear Cut Proportion of Tip Up Mounds Gap Cut Small Logs Mean Diameter cm Gap Cut Large Logs Mean Diameter cm Gap Cut Proportion of Scarified Soil Gap Cut Proportion of Tip Up Mounds Initial Conditions Proportion of Scarified Soil
291. n radius and crown depth e Adults and snags DBH height crown radius and crown depth How size and shape attributes are used Many behaviors do their work using equations that are functions of tree size in some way Diameter is by far the most important attribute Other dimensions may or may not be used in a run depending on the set of chosen behaviors How important it is to get the allometric relationships correct depends on how they will be used Check the documentation of your chosen behaviors If for instance crown shape is not used it doesn t really matter what relationships you assign Trees are not required to conform to their allometric relationships For instance growth many cause height and diameter to vary independently of each other You choose the relationship used by each life history stage of each species for each attribute These can be freely mixed and matched Use the Edit Allometry Functions window to set the allometry functions Function Description The standard crown depth and radius relationships The Chapman Richards crown depth and radius relationships Crown dimensions are power functions of tree dimensions Uses the Chapman Richards function to calculate crown dimensions The non Uses non spatial measures of density to calculate crown radius and crown depth spatial density dependent crown depth and radius relationships The NCI crown depth and radius relationshi
292. n the instrumental crown radius equation used to calculate crown depth The h term in the instrumental crown radius equation used to calculate crown depth The i term in the instrumental crown radius equation used to calculate crown depth The j term in the instrumental crown radius equation used to calculate crown depth Non Spatial Log Density Dep Crown Height a Non Spatial Log Density Dep Crown Height b Non Spatial Log Density Dep Crown Height c Non Spatial Log Density Dep Crown Height d Non Spatial Log Density Dep Crown Height e Non Spatial Log Density Dep Crown Height f Non Spatial Log Density Dep Crown sT The a term The b term The c term The d term The e term The f term The g term 8 In addition to the use of density variables the density dependent equations for crown width uses an estimate of crown depth as a dependent variable and vice versa This estimated value of crown width and crown depth rad and ch used in the density dependent equations come from the instrumental variable equations Calculating the instrumental variables equations avoids uncoupling the crown radius crown depth relationship The non spatial exponential density dependent crown radius function is rad D1 DBH Height ch STPH BAPH BAL rad is the crown radius in meters D1 is the Non Spatial Exp Density Dep Crown Radius D1
293. n to do height growth Parameters for this behavior Parameter name Description Power Height Gree The coefficient in the power function for height growth Power Height Chromite The exponent in the power function for height growth How it works The amount of height growth is calculated as Y nH where e Yis the amount of height growth for one year in cm e nis the Power Height Growth n parameter e gis the Power Height Growth Exp parameter e His the tree s height in cm If the timestep is more than one year long growth is recalculated for each year of the timestep increasing the height each time How to apply it This behavior can be applied to seedlings saplings and adults of any species Any tree species type combination to which it is applied must also have a diameter growth behavior applied Puerto Rico semi stochastic diam only This behavior combines a deterministic growth function for small trees with completely stochastic growth for larger trees It s meant to be used when a species uses a height growth behavior as the primary growth method Parameters for this behavior Parameter name Description PR a Parameter for Deterministic Growth a parameter used to calculate deterministic growth when a tree is below the stochastic height threshold PR b Parameter for Deterministic Growth b parameter used to calculate deterministic growth when a tree is below the stochastic height threshol
294. nags are standing dead trees They can be produced when saplings and adults die due to normal tree mortality or a disturbance event such as disease Only adult trees become snags See below for more on how trees become snags e Woody debris Woody debris comes from fallen snags Currently no behavior uses woody debris and this is a placeholder stage only It is not created at this time Tree life history stage transitioning growth Seed to seedling Seeds are modeled only as aggregates not individuals Seeds become individual seedlings when they are processed by an establishment behavior Seedling to sapling When a seedling reaches the maximum seedling height set for its species it becomes a sapling The diamjo value is converted to a DBH value which is then used to calculate the rest of the sapling s new dimensions Since height is re calculated with a different equation and input parameters there may be a discontinuity in height values right around the seedling sapling transition point If a species uses different allometric relationships for its saplings and adults another discontinuity may occur at the time of this transition as well For more on the allometric relationships and how they are calculated see the Allometry topic The automatic updating of these allometric relationships during the growth phase can be overridden For more see the Growth behaviors topic Sapling to adult When a sapling s DBH reaches the minimum adult D
295. ncrease a tree s radius at breast height mm yr How it works The amount of diameter increase is calculated from the constant radial increment The increase is calculated as follows Y g4 10 2 T where e Yis the amount of diameter growth in cm to add to the tree e g4is the Adult Constant Radial Growth in mm yr parameter e Tis the number of years per timestep Note that the increment parameter specifies radial growth the behavior makes all necessary conversions to diameter growth How to apply it This behavior can be applied to seedlings saplings and adults of any species Any tree species type combination to which it is applied must also have a light behavior applied You can use either the diam with auto height or diam only version Double resource relative growth This behavior uses a double Michaelis Menton function to calculate relative growth based on two resources light and a second resource The identity of the second resource is unimportant and could be anything from exchangeable calcium levels to soil moisture Parameters for this behavior Parameter name Description SUED aes Asymptote of the Michaelis Menton growth function at high light Diameter Growth function term A below A Slope of Growth Slope of the Michaelis Menton growth function at zero light function Response S term S below Double resource Influence of Resource C The parameter governing the influence of the second resource on t
296. nction used This behavior can be used to simulate the suckering of stumps Apply this behavior to tree type stump of your chosen species Stumps reproduce like other parent trees They use the same probability distribution function and parameters as live members of their species but they get their own J and STR values so that they can produce different numbers of seeds Gap spatial disperse Gap spatial disperse takes forest cover into account when determining the number and placement of seeds The two possible forest covers are gap and closed canopy A gap is defined as a cell in the Dispersed Seeds grid with no more adults than the value of the Maximum adults allowed in gap cell parameter above Parameters for this behavior Parameter name Beta for Stumps Canopy Function Used Gap Function Used Lognormal Canopy Annual STR Lognormal Canopy Beta Lognormal Canopy Xo Lognormal Canopy Xp Lognormal Gap Annual STR Lognormal Gap Beta Lognormal Gap Xo Lognormal Gap Xp Description The value for stumps Stumps use the same probability distribution function as the live members of their species Only required if a behavior is being applied to stumps The probability distribution function to be used to distribute seeds in canopy conditions For the behaviors Non gap spatial disperse and Masting spatial disperse these PDFs are always the ones used The probability distribution function to be used to
297. nd to the probability of fall for a five year timestep The behavior will re scale the probability of fall for other timestep lengths if necessary Basal area amounts are tracked in the Snag Decay Class Dynamics Basal Area grid Each timestep the amount of basal area in square meters per hectare is totaled across all species for live trees live adults and adults that died in the current timestep and harvested trees The size of the grid cells is approximately 400 square meters A tree s neighborhood basal area is the value in the grid cell where the tree is located How to apply it This behavior can be applied to adults and snags of any species It should be executed after mortality and dead tree remover behaviors have been applied in each timestep Disperse behaviors Disperse behaviors create and distribute tree seeds around the plot Dispersal is the first step in seedling recruitment Seed totals for different species are stored in the Dispersed Seeds grid Each of the disperse behaviors adds seeds to this grid The Establishment behaviors decide which seeds in the grid turn into new seedlings For these behaviors parent trees refers to trees over the minimum reproductive DBH for a species These are the only trees which can contribute new seeds to the plot While there is support in the model for seeds to act as individuals see Tree life history stages these seeds are not individuals but merely numbers in a grid You could
298. ne the number of snags of a certain age left standing at a given time The equation is i ee h cr 7 av l Pe iai where e Sis proportion of snags still standing between 0 and 1 e aand bare Weibull parameters Weibull Annual a Parameter for Snag Size Class X Mortality parameter and Weibull Annual b Parameter for Snag Size Class X Mortality parameter e Tis the snag age in years Different sizes of snags fall at different rates This behavior allows you to define three snag size classes and enter different a and b parameters for each A random number is used against this equation for a given tree to determine if it falls in the current timestep How to apply it This behavior can be applied to snags of any species Substrate behaviors Substrate is what seedlings germinate in soil rock and the organic layers on top The quality of the substrate can make a big difference in a seedling s ability to survive and establish The substrate composition in any one place is constantly shifting and changing as new substrate is added to the forest floor and as existing substrate decays These behaviors keep track of the substrate conditions at different locations through time Behavior Description Substrate Keeps track of six kinds of substrate forest floor litter forest floor moss behavior scarified soil tip up mounds decayed logs and fresh logs Detailed oe eee 5 AEN Baa This behavior is a modification of the Substra
299. ng from decay class 1 to decay class 3 Probability of a snag that did not fall moving from decay class 1 to decay class 4 Probability of a snag that did not fall moving from decay class 1 to decay class 5 Probability of a snag that did not fall remaining in decay class 2 Probability of a snag that did not fall moving from decay class 2 to decay class 3 Probability of a snag that did not fall moving from decay class 2 to decay class 4 Probability of a snag that did not fall moving from decay class 2 to decay Dynamics Class 2 To Class 5 Prob 0 1 Snag Decay Class Dynamics Class 3 To Class 3 Prob 0 1 Snag Decay Class Dynamics Class 3 To Class 4 Prob 0 1 Snag Decay Class Dynamics Class 3 To Class 5 Prob 0 1 Snag Decay Class Dynamics Class 4 To Class 4 Prob 0 1 Snag Decay Class Dynamics Class 4 To Class 5 Prob 0 1 Snag Decay Class Dynamics Class 5 To Class 5 Prob 0 1 Snag Decay Class Dynamics Maximum Snag Break Height Snag Decay Class Dynamics Minimum Snag Break Height How it works class 5 Probability of a snag that did not fall remaining in decay class 3 Probability of a snag that did not fall moving from decay class 3 to decay class 4 Probability of a snag that did not fall moving from decay class 3 to decay class 5 Probability of a snag that did not fall remaining in decay class 4 Probability of a snag that did not fall moving from decay class 4 to decay class 5
300. nges Tree map A tree map is available when you have saved the X Y and either the DBH or crown radius of trees in a detailed output file The tree map does not display seedlings XY DBH Tree Map This map displays a circle for each tree that corresponds to the size of its DBH The color matches the species in the legend The DBH Scale Factor controls the size of the circles being displayed The size of the tree circles is this value is multiplied by the DBHs When the value is 1 the circles are approximately life size in relation to each other Use this value to adjust the display for exceptionally large or small trees but if the value is not one remember that the display will not accurately show how close together trees are The Minimum DBH to display setting controls the smallest trees shown on the map This value is in meters Crown Radius Tree Map This map displays a circle for each tree that corresponds to the size of its crown radius The circles are true to size with respect to the plot and each other The color matches the species in the legend The Minimum Crown Radius to Display setting controls the smallest trees shown on the map This value is in meters Click the Update Map button after you have adjusted either display setting Clicking and dragging on the tree map zooms in Once you have zoomed you can restore the original scale by clicking the button marked Restore Original View If you are zoomed you can s
301. nly if planned mortality episode events have already been created or with the Edit Episodic Events Window Data in the grid There is no user accessible data in the grid Mortality Episode Results Grid This grid is created by the Episodic Mortality behavior This is where data on planned mortality episode results is stored The data is stored raw no conversion to per hectare amounts The grid cell resolution is always set to match the Mortality Episode Master Cuts grid Any changes you make to the grid cell resolution will be ignored Data in the grid Data member name Description Cut Density species x cut Number of trees killed in the current timestep for the given species range y and cut range Cut Basal Area species x Total basal area killed in the current timestep for the given species cut range y and cut range Seedlings killed as part of a planned mortality episode in the Cut Seedlings species x i ae current timestep for the given species Neighborhood Seed Predation Grid This grid is created by the Neighborhood Seed Predation and Neighborhood Seed Predation linked behaviors This grid stores the seed rain before predation and the amount of seeds eaten The grid resolution must match the Dispersed Seeds grid All data is stored raw no conversion to per hectare amounts Data in the grid Data member Pav Description name Pre predation Number of seeds of species x in the grid cell before pr
302. nnual probability and X is the number of years per timestep Once a tree s timestep survival probability has been calculated it is compared to a random number to determine whether the tree lives or dies How to apply it This behavior can be applied to seedlings saplings and adults of any species Any tree species type combination to which it is applied must also have a growth behavior applied You must also enter a map of second resource values into the Resource grid GMF mortality GMF mortality is a growth based mortality behavior Trees killed by this behavior will have a mortality reason code of natural Parameters for this behavior Parameter name Description Light Dependent Mortality Light dependent mortality Mortality at Zero Mortality rate at zero growth Growth y 8 How it works The GMF mortality model evaluates the following function to determine the probability of a tree s mortality m G m m Ko m where e mis the probability of mortality e mis the Mortality at Zero Growth parameter for mortality over 2 5 years see Kobe et al 1995 e mis the Light Dependent Mortality parameter for mortality over 2 5 years see Kobe et al 1995 e Gis amount of radial growth in mm yr added to the tree s diameter this timestep The GMF mortality equation is for a5 year timestep The mortality parameters are for a 2 5 year probability of mortality To calculate the 5 year probability of mortality SORTIE uses p
303. not for instance create a list of individual seed positions Seed randomization The numbers of seeds added by the disperse behaviors can be randomized You choose how randomization will be applied If the seed distribution is deterministic no randomization is done Otherwise you can choose a probability distribution function and the number of seeds is treated as the mean of that function You may need to supply additional parameters depending on the probability distribution function you choose This randomization applies to the seeds from all disperse behaviors that you have chosen There are four choices for probability distribution functions the normal the lognormal the Poisson and the negative binomial The forms for these functions can be found here Behavior Description Non spatial disperse behavior Masting non spatial disperse behavior Spatial disperse behaviors Non gap spatial disperse behavior Gap spatial disperse behavior Masting spatial disperse behavior Temperature dependent neighborhood disperse behavior Scatters seeds uniformly across the plot Non spatial disperse has two components basal area dependent seed rain and non density dependent bath seed rain the two of which are independent and can be used together or separately Adds stochasticity to basic seed rain by simulating masting and basic inter year variation in seed production General information on the s
304. nstead of the minimum DBH for reproduction For each tree greater than the reproductive age the number of seeds produced is calculated as seeds STR DBH 30 using the higher of gap or canopy STR along with its matching Each seed is given a random azimuth angle It is then given a random distance that conforms to the probability distribution function of the current forest cover of the parent see more about spatial disperse behavior seed distribution here Once the seed has an azimuth and a distance the function determines which grid cell it should drop in Once the seed has a target grid cell that cell s cover is checked Then the seed s survival is evaluated If the seed is in the cover type with the higher STR it automatically survives Otherwise a random number is compared to the ratio of the lower STR to the higher STR to determine if it survives If the seed survives it may need to be repositioned If both parent and seed are under closed canopy the seed is dropped where it is If the parent is in gap and seedling is in canopy a new distance is calculated as though the parent was also in canopy The shortest of the two distances is used to determine where the seed lands If the seed lands in a gap cell the behavior walks out the line of the seed s path from parent to target landing cell checking each intermediate grid cell s cover along the way If any of the grid cells in the line are under canopy cover the seed drops in
305. number of seedling recruits produced by a 30 cm DBH parent tree the Weibull Canopy Annual STR or Weibull Gap Annual STR parameters e DBH is the DBH in cm of the k T parent trees within a specified radius of location i e Disa species specific dispersal parameter the Weibull Canopy Dispersal or Weibull Gap Dispersal parameters e mix is the distance in meters from point i to the kth parent tree e and f are disperse parameters the Weibull Canopy Theta or Weibull Gap Theta and Weibull Gap Beta or Weibull Canopy Beta parameters The lognormal function is as follows fae Fa E i a nfm Ag erp Tf npg P 05 p ZHAN N eid i 2 l B g Res siJ n ia StL oy ir NS c mime An E F lh where oo A n p i and where e Riis the density m2 of seedlings at a given point i e STR the standardized total recruits is the number of seedling recruits produced by a 30 cm DBH parent tree the Lognormal Canopy Annual STR or Lognormal Gap Annual STR parameters e DBH is the DBH in cm of the k T parent trees within a specified radius of location i e mix is the distance in meters from point i to the kth parent tree e Xo is the mean of the function the Lognormal Canopy Xo or Lognormal Gap Xo parameters e Xz is the standard deviation of the function the Lognormal Canopy X or Lognormal Gap Xp parameters e fis a disperse parameter the Lognormal Canopy Beta or Lognormal Gap Beta
306. number of surviving seeds has been determined the behavior assigns that number back to the Dispersed Seeds grid cell How to apply it Apply this behavior to seeds of your desired species Any species to which it is applied must also have any disperse behavior applied Density Dependent Seed Survival This behavior assesses seed survival as a function of the local density of conspecific seeds Parameters for this behavior Parameter name Description Slope of Density The slope of the density dependence function for determining how many Dependence seedlings establish per square meter c in the equations below Steepness of Density The steepness of the density dependence function for determining how Dependence many seedlings establish per square meter 6 in the equations below How it works This behavior takes the seeds that have been dispersed to each grid cell of the Dispersed Seeds grid and calculates how many will survive The number of seeds that survives is calculated as Rsp Ssp exp c Dens where e Rs is the number of surviving seeds of a given species in the seed grid cell e Sy is the original number of seeds of that species in that grid cell e Dens is the density of seeds number per square meter of that species in that grid cell e cis the Slope of Density Dependence parameter e ois the Steepness of Density Dependence parameter Once the number of surviving seeds has been determined the behavior assigns
307. o get their effective height which is what will be applied when determining the thickness of the filter overhead Again this behavior does not set this height but will use it if another behavior sets it This behavior DOES NOT ACTUALLY CALCULATE LIGHT LEVELS Any tree species and types to which this filter is applied must also have one of the other light behaviors assigned to it This behavior assumes the value is a GLI value using Sail Light will probably not produce good results This behavior only affects tree types and species to which it is applied in the behavior list of the parameter file It will ignore all other trees even if they are short enough to be beneath the filter level How to apply it This behavior may be applied to seedlings saplings and adults of any species Constant GLI Parameters for this behavior Parameter name Description Constant GLI Constant GLI Value The GLI value assigned to all trees 0 100 How it works This assigns a constant GLI value to all trees to which it is assigned This value is set in the Constant GLI Constant GLI Value 0 100 parameter How to apply it This behavior may be applied to seedlings saplings and adults of any species Gap Light behavior This behavior shortcuts the light calculation process by considering GLI to be binary either full light 100 or no light 0 This simulates a simplified version of gap light dynamics How it works This behavior uses
308. o reproduce conditions from another run There are two ways to add grid initial conditions to a parameter file the first is the Grid setup window This allows you to work with grid values directly in a spreadsheet like format The other way is to add a grid map from a detailed output file Grid list Complete list of all grids Average Light grid Basal Area Light grid Carbon Value grid Competition Harvest Results grid Detailed Substrate grid Detailed Substrate calcs grid Dispersed Seeds grid Foliar Chemistry grid Gap Light grid GLI Map grid Harvest Master Cuts grid Harvest Storm Damage grid Storm Killed Partitioned Biomass grid Storm Light grid Storm Susceptibility grid Substrate grid Substrate calcs grid Substrate Favorability grid Temperature Dependent Neighborhood Survival grid Weibull Climate Quadrat Growth grid Windstorm Results grid Years Since Last Harvest grid Average Light Grid Average Light This grid is created by the Average Light behavior It contains the averages of the values of the GLI Map grid It is important to set the cell sizes of the two grids exactly as you want them The default grid cell resolution is set to 8 m X 8 m Data in the grid Data member name Description GLI Average GLI value Basal Area Light Grid This grid is created by the Basal Area Light behavior Each grid cell holds tree basal area data and a light le
309. o text format This tool uses a wizard format to set up batch extraction You reach this tool from the Tools menu from the main SORTIE window Step 1 Choose detailed output files to extract from In the first window of the wizard you choose which output files to extract from These files do not have to be in the same directory nor do they have to be from the same run Use the file chooser on the left to select files then use the Add files to batch to add them to the batch list If you change your mind select files on the batch list on the right then use the Remove files from batch button Once you have your list of batch files click Next The wizard will examine your list of detailed output files to determine what data are available for extraction This may take awhile for a very long list of files Once the analysis step is done the wizard will take you to step 2 Step 2 Choose extraction options The next window in the wizard offers you the available list of charts to extract data for by chart type This is the same set of options that would be offered if you were using data visualization interactively as usual The options listed is the set of options available in all of the files in your batch Some files may be missing some of the options You can still choose any option that option will be skipped for any files that do not support it When you choose an option you will be prompted for a file name root This root will b
310. of neighborhood trees Calculates the amount of diameter change from a constant basal area increment Simulates herbivory by allowing trees to grow at different rates when browsed versus unbrowsed Calculates the amount of diameter change from a constant radial increment Uses a double Michaelis Menton function to calculate relative growth based on two resources light and a second resource Uses multiple effects including neighbor competitiveness to calculate growth rates for juvenile trees Increments growth as a function of DBH and neighboring basal area and incorporates a lag period after harvesting during which trees acclimate to their post harvest growing conditions Does either diameter or height growth as a linear function of GLI Increments growth according to a simple linear equation with the possibility of two sets of parameters for each species one for high light conditions and one for low light conditions Linear growth w exponential shade reduction Logistic growth Logistic growth w size dependent asymptote Lognormal bi level growth height only Lognormal with exponential shade reduction Michaelis Menton with negative growth height only Michaelis Menton with photoinhibition height only NCI growth Power growth height only Puerto Rico semi stochastic diam only Puerto Rico storm bi level growth diam with auto Calculates either diameter or heigh
311. ogistic Bi Level Low Light a parameter e b inhigh light conditions this is the Logistic Bi Level High Light b parameter in low light conditions this is the Logistic Bi Level Low Light b parameter e D tree diam in cm diamjo for seedlings DBH for others If the timestep length is not one year the actual probability of survival for the timestep is calculated as p p where p is the annual probability of survival p is the timestep probability of survival and T is the number of years per timestep Once the survival probability for the timestep is known for a tree then a random number is compared to this probability to determine if the tree lives or dies Light levels come from the Storm Light grid produced by the Storm Light behavior The threshold between the use of high light and low light parameters is set in the Logistic Bi Level High Light Mortality Threshold 0 100 parameter This behavior can also be used without Storm Light In this case only the low light mortality parameters are used How to apply it This behavior can be applied to seedlings saplings and adults of any species If you wish to use the light level parameter switch also use the Storm Light behavior NCI mortality This behavior uses the effects of neighbor competitiveness to influence tree survival NCI stands for neighborhood competition index A tree s maximum potential probability of survival is reduced due to competitiveness and sev
312. olume Form Class 60 100 Bole Volume Parameter b0 The bO parameter for the bole volume equation Bole Volume Paramet OI The b parameter for the bole volume equation Bole Volume Parameter 2 The b2 parameter for the bole volume equation Bole Volume Parameter D3 The b3 parameter for the bole volume equation Bole Volume Parmeter 4 The b4 parameter for the bole volume equation Bole Volume The b5 parameter for the bole volume equation Parameter b5 How it works Tree volume is calculated as follows V b0 b1 DBH b3 DBH Height where e V gross volume in cubic feet e Height bole length in feet as a multiple of 16 for usable 16 foot logs e DBH DBH in inches e b0 5 are the following parameters Bole Volume Parameter b0 Bole Volume Parameter b1 Bole Volume Parameter b2 Bole Volume Parameter b3 Bole Volume Parameter b4 and Bole Volume Parameter b5 The bole length is the number of 16 foot logs the tree can provide in feet i e 3 logs bole length of 48 feet The base of the bole is the top of the cut stump the top of the bole is the merchantable height This behavior defines the merchantable height as the height at which the trunk diameter inside the bark tapers to 60 of DBH To determine at what bole length the merchantable height occurs the behavior tries fitting in as many 16 foot logs as possible before the 60 taper occurs The amount of taper
313. on Precipitation Change B B in the function for varying precipitation through time Precipitation Change C C in the function for varying precipitation through time Precipitation Change Precip Lower The lower bound for allowed precipitation values Bound Precipitation Change Precip Upper The upper bound for allowed precipitation values Bound How it works The value for plot precipitation is a function of time elapsed since the start of the run as follows Pappas where e P is the mean annual precipitation in mm at time t e P is the mean annual precipitation value at the start of the run as assigned in the Plot parameters e Bis the Precipitation Change B parameter e Cis the Precipitation Change C parameter e tis the time elapsed in years since the start of the run This value is then given to the Plot object which makes it available to other behaviors in the run You can set bounds on the possible precipitation values using the Precipitation Change Precip Lower Bound and Precipitation Change Precip Upper Bound parameters Values are not allowed to go outside these limits How to apply it Add this behavior to the run You can use it alone or in addition to the Temperature Climate Change behavior You do not need to assign this behavior to trees Temperature Climate Change This behavior changes the value of the Mean Annual Temperature parameter of the SORTIE plot This can be used to simulate
314. on Factor parameter This value is multiplied by the final biomass value How to apply it Apply this behavior to saplings adults or snags of any species and enter parameters in the Parameter edit window This behavior does not automatically create output Once you have added this behavior to your run the Detailed output setup window for trees will have a tree data member called Tree Biomass Add this to your detailed output file to output biomass in metric tons Mg You can then view charts and graphs with the resulting volume data using data visualization on your detailed output file Foliar Chemistry This behavior calculates chemistry components as a function of DBH The components calculated are N P specific leaf area SLA percent acid detergent fiber percent acid detergent cellulose percent acid detergent lignin percent condensed tannins and total phenolics Parameters for this behavior Parameter name Description lt th Foliar Chemistry Cellulose The proportion of foliar dry weight 0 1 that is acid detergent cellulose Concentration Foliar Chemistry Ee oa aaa The proportion of foliar dry weight 0 1 that is acid detergent fiber Foliar Chemistry fk Rohan welun The a parameter in the equation for foliar dry weight Foliar Chemistry ane a D The b parameter in the equation for foliar dry weight Foliar Chemistry ME COENE The proportion of foliar dry weight 0 1 that is acid detergent
315. on infested e is the Insect Infestation Initial Rate parameter as a value between 0 and 1 This is the function intercept or the infestation rate at the first timestep of infestation e Max is the Insect Infestation Max Rate parameter as a value between 0 and 1 This is the maximum infestation rate that will occur regardless of how long the infestation lasts e Tis the time in years since the start of the infestation e Xo is the Insect Infestation X0 parameter This is the time at which half of the maximum infestation rate is reached e X is the Insect Infestation Xb parameter This controls the steepness of the rise of the curve You choose when an infestation begins with the Insect Infestation First Timestep parameter The only way that an infestation ends is if there are no more infested trees in the plot You can set a minimum DBH of infestation using the Insect Infestation Min DBH parameter The proportion of trees infested at time T does not depend on additions to or subtractions from the pool of eligible trees Each timestep the number of infested trees of each species is counted and additional trees are randomly selected for new infestation until approximately the right number are infested If for some reason there are more trees infested than there should be at that time no additional trees are infested When selecting trees for infestation the location of the trees is not considered It is assumed that all trees have an equ
316. oot logs 2 log 3 log DBH tree tree in 24 2a 3d 2d 3d 4th 2d 3d 4th Sth 2d 3d 4th Sth 6th log log log log log log log log log log log log log log log ao fia i2 fis l l l fe fe fe fe fe fe l l 4 log tree 5 log tree 6 log tree a p fur fi hapa a aw P mp2 sp b ps upp po amp peste pa fis a pe fu fis pe far z pa fis faa fos fs fo fia fio fas faa a ps as as foo faa fas x2 xo ne os foo fra faa a2 ow o ps p espr psf fiz gt er os foo fra fax a2 as Volume board feet by number of usable 16 foot logs Form Class 78 DBH inches 6 logs es ie fe fee se fon ae o p ios a pe o a ccc aefa a ra aw a e ie asa so J ist at ose fer JE Form Class 79 DBH inches 6 logs aa fr feo a fe foe a ofits ne fas faa e efi ose rote oe re a ae a rao ise mw oa ma fes as ne eo f os fie fr 1932 22u Form Class 80 DBH inches 6 logs ele be e ste t spe ta ae mpa e e a fa he fae a pa a a aE ra fae se iat ae co ie test at os fie fares Form Class 81 DBH inches 6 logs 7 we fe i fee ioe a feo fifo a pa ha p fia o ar io fro a is for ue 52 as fos foes ras ss fs s f is fo f fers f a fse fiona iao fias fra s feo roe fisie 19598 25 Form Class 84 o fe fn e e eee m fe fi fes pe E mo fo hs rs e E u fe fo po p E s fio fies oso
317. ope of the curve for the crowding effect equation The steepness of the curve for the crowding effect equation The sensitivity of a tree s growth rate to its DBH Set this to 0 to remove the DBH term altogether The mode of the size effect curve The variance of the size effect curve The value by which to divide neighbor basal area Whether to use all neighbors larger than the minimum DBH false or only neighbors larger than the target tree true For a tree the amount of growth per year is calculated as Growth Max Growth Size Effect Crowding Effect Max Growth is the maximum diameter growth the tree can attain in cm yr entered in the NCI Maximum Potential Growth cm yr parameter Size Effect and Crowding Effect are factors which act to reduce the maximum growth rate and will vary depending on the conditions a tree is in Each of these effects is a value between 0 and 1 Size Effect is calculated as In DBH z Xb 0 5 SE e where e DBH is of the target tree in cm e Xois the NCI Size Effect Mode in cm X0 parameter e Xis the NCI Size Effect Variance in cm Xb Crowding Effect is calculated as CE exp C DBH BA BADiv where e Cis the NCI Crowding Effect Slope C parameter e DBH 1s of the target tree in cm e yis the NCI Size Sensitivity to NCI gamma parameter for the target tree s species e Dis the NCI Crowding Effect Steepness D parameter e BA is the su
318. opy probability distribution function is lognormal Lognormal Canopy The standard deviation of the lognormal function under canopy Xp Masting Disperse Masting Beta Masting Disperse Masting CDF a Masting Disperse Masting CDF b Masting Disperse Masting Group Masting Disperse Masting Lognormal Xo Masting Disperse Masting Lognormal Xp Masting Disperse Masting STR Mean Masting Disperse Masting STR Standard Deviation Masting Disperse Mast Proportion Participating 0 1 Masting Disperse Non Masting Beta Masting Disperse Non Masting STR Mean Masting Disperse Non Masting STR Standard Deviation Masting Disperse conditions or under non masting conditions in the case of Masting spatial disperse see equation below This is only required if the canopy probability distribution function is lognormal The B value under masting conditions The a value in the cumulative density function that is used to decide when masting events occur The b value in the cumulative density function that is used to decide when masting events occur Species in the same group always mast together If all the group numbers are different then each species masts separately The actual numbers do not matter just whether species have identical numbers The mean of the lognormal function under masting conditions This is only required for a species if the canopy probability distribution functio
319. or defines the merchantable height as the height at which the trunk diameter inside the bark tapers to 60 of DBH The behavior tries fitting in as many 16 foot logs as possible before the 60 taper occurs The amount of taper at the top of the first 16 foot log is established by the tree s form class A species s form class is the percentage of DBH to which the bole has tapered at the top of the first 16 foot log Then the behavior determines how many more logs the tree contains The amount of taper at the top of the first 16 foot log is subtracted from the DBH to see how much taper is left before the 60 merchantable height diameter is reached There is no formula that establishes clearly how many logs will fit the behavior uses a trial and error approach taken from Messavage and Girard 1956 This paper includes the table below for upper log taper for trees of various DBH and bole heights The behavior uses this table to determine the maximum number of logs it can fit into the taper available Trees below 10 inches of DBH contain no merchantable timber and have a value of zero Trees greater than 40 inches of DBH are treated like 40 inch trees Once the behavior figures out how many 16 foot logs a tree contains it uses another set of tables based on form class to determine how many board feet of timber the tree contains These tables are also from Messavage and Girard 1956 and are shown below Average upper log taper inches in 16 f
320. or diameter growth Phaded Posar Intercept of the size dependent growth potential in cm yr for height Height Intercept in growth cm yr a Shaded Linear Height Shade Effect of shading for height growth Exponent c Shaded Linear Helen lore Slope of the size dependent annual growth potential for height growth How it works This behavior calculates an amount of diameter or height growth as Y a b diam GLI 100 T where e Y amount of diameter increase in mm or the amount of height increase in cm e a Shaded Linear Diam Intercept in mm yr a parameter for diameter growth or the Shaded Linear Height Intercept in cm yr a parameter for height growth e b Shaded Linear Diam Slope b parameter for diameter growth or the Shaded Linear Height Slope b parameter for height growth e c Shaded Linear Diam Shade Exponent c parameter for diameter growth or the Shaded Linear Height Shade Exponent c parameter for height growth e diam diameter diameter at 10 cm for seedlings and saplings DBH for adults e GLI global light index as a percentage between 0 and 100 calculated by a light behavior e T number of years per timestep If calculating height growth In order to find the total amount of height increase for a timestep the behavior takes as an input the amount of diameter growth increase Assume that the number of years per timestep is X The amount of diameter increase is
321. or the different distributions using the appropriate parameters You do not need to set values for distributions that a species does not use Once the number of seeds per square meter has been established for a species that quantity of seed is distributed evenly across the plot The presence or absence of parent trees of that species makes no difference to the number of seeds To simulate synchrony in masting species can be collected into masting groups The decision to mast or not to mast using the binomial distribution is performed once for each group using the first species in the group s p value The number of seeds per square meter is established as for a single species but those seeds are divided amongst the group s species according to the relative basal area of adults of each species in the plot If there are no trees of any of the group s species the seeds are divided equally amongst the species How to apply it Apply this behavior to adults of the species you wish to use Spatial disperse behaviors Spatial disperse behaviors rely on the location and size of parent trees to determine the number and placement of seeds The placement of the seeds is controlled by a probability distribution function You can choose between the Weibull and lognormal functions The Weibull function is as follows where and where e Riis the density m2 of seedlings at a given point i e STR the standardized total recruits is the
322. ortality behaviors do not actually remove dead trees from memory They set a flag which marks trees as dead This is because some other behaviors such as the Substrate group have specific interest in dead trees Dead trees are eventually removed from memory by the Dead tree remover behavior You may notice this behavior in your behavior list It is included automatically It is important to include this behavior in your run to avoid incorrect results in behaviors that use dead trees and unacceptably slow model run times Behavior Description Aggregated Kills trees randomly to match a predetermined mortality rate clumping together Mortality the deaths in both time and space BC Mortality Kills trees as a function of growth rate a Simulates the effects of herbivory by allowing different background mortality Stochastic rates for browsed and unbrowsed trees Mortality Competition Meet Kills trees as a function of growth Uses the results of the NCI growth behavior Density Self Thinning Mortality Exponential Growth and Resource Based Mortality GMF Mortality Gompertz Density Self Thinning Growth and Resource Based Mortality Height GLI Weibull Mortality with Browse Insect Infestation Mortality Logistic Bi Level Mortality NCI Mortality Post Harvest Skidding Mortality Self Thinning Senescence Stochastic Bi Level Calculates the probability of mortality of an individua
323. output file SORTIE can display data from both kinds of output files summary files and detailed output files SORTIE analyzes the contents of files that it is given and lets you know what it is capable of displaying from that data Load an output file by choosing the menu option File gt Open output file Choose the file you want to view either a summary output file with a out extension or a detailed output file with a gz tar extension The file name will appear at the top of the main SORTIE window in the list that says Open output files You can have as many files open as you wish To display a chart choose a file in the list marked Open output files at the top of the main SORTIE window SORTIE will analyze the contents of the file and show you what it can display in the list marked Chart choices for this file The chart choices are broken apart by type There may not be a choice for every type of chart Choose the chart you want to display and click the Draw Chart button The chart will appear in the main SORTIE window You can open as many charts as you wish A legend also opens for each file that applies to all its chart windows The main SORTIE window acts as a desktop for the chart windows displayed They can be minimized maximized moved and resized within the window You can close them using the X button in the top right You will notice that the legends have check boxes next to each species name along with a color bo
324. output files The summary output file contains basic plotwide summary data for each timestep in the run You choose what data you want SORTIE to save using Edit gt Output options You can use the summary output file to save data for both live and dead trees The dead tree data for a given timestep is only for trees that died in that timestep The dead trees are coded by mortality reason You choose which mortality reasons you want to see data for Not all mortality reasons are available for every run Check the documentation for your chosen disturbance behaviors and mortality behaviors for more information on which codes will apply to your run Your choices for what to save are e Adult tree relative basal area Adult Rel BA e Adult tree absolute basal area Adult Abs BA e Adult tree relative density Adult Rel Den e Adult tree absolute density Adult Abs Den e Sapling relative basal area Sapl Rel BA e Sapling absolute basal area Sapl Abs BA e Sapling relative density Sapl Rel Den e Sapling absolute density Sapl Abs Den e Seedling absolute density Sdl Abs Den e Snag tree relative basal area Snag Rel BA e Snag tree absolute basal area Snag Abs BA e Snag tree relative density Snag Rel Den e Snag tree absolute density Snag Abs Den Basal area is in square meters per hectare and density is in numbers per hectare Relative values are in proportions Each data type is calculated separately for each species an
325. ow the defined suppression threshold before it is considered to be suppressed Absolute growth is calculated with the equation where e Y logl0 radial growth 1 e SF is the suppression factor e Ais the Asymptotic Diameter Growth A parameter e Sis the Slope of Growth Response S parameter e GLI is the global light index calculated by a light behavior Amount of diameter growth per timestep is calculated as growth 10 1 2 10 T where T is the number of years per timestep The absolute growth behaviors also take into account suppression status A tree is considered suppressed if its growth rate for the previous timestep falls below a certain threshold That threshold is the rate of growth at which X of juveniles die where X is a user settable parameter The threshold is calculated for each species by solving the BC mortality equation for G growth where m is the threshold growth rate A tree s suppression state is a multiplicative factor in its growth rate If a tree is not suppressed the suppression factor in the growth equation is set to 1 no effect on growth If the tree is suppressed the suppression factor is calculated as follows SF el 8 YLR d YLS where e SF is the suppression factor e gis the Length of Current Release Factor parameter e YLR is the length of the last or current period of release in years e dis the Length of Last Suppression Factor parameter e YLS is the length of
326. p mound substrate that survive to become seedlings Expressed as a value between 0 and 1 The proportion of plot area that is mound area as opposed to ground area Expressed as a value between 0 and 1 The area of the plot that is mound and the area that is ground are in fixed relative proportion to each other This fixed proportion is entered in the Proportion of Plot Area that is Mound parameter Each grid cell in the Substrate grid has been divided by the Substrate behavior into six substrate types each of those types is further divided into mound and ground according to the fixed proportion making twelve total substrate types For example if 20 of a grid cell s area is forest floor litter and 60 of the plot area is mound then the area of the grid cell that is forest floor litter mound substrate is 12 and the area of grid cell that is forest floor litter ground substrate is 8 The behavior takes the substrate composition of each grid cell in the Substrate grid calculates the amount of the twelve substrate types and converts it into a single number for each species called the substrate favorability index The favorability index is the sum of the proportions of each substrate multiplied by the proportion of seeds that germinate on that substrate This index represents the proportion of total seeds of that species that are expected to survive in that area of the plot This index is stored in the grid Substrate Favorability
327. paired with any height only growth behavior and the allometric height growth behavior can be paired with any diam only growth behavior How to apply it These behaviors can be applied to seedlings saplings and adults of any species Any tree species type combination to which it is applied must also have a growth behavior applied that grows the opposite tree dimension Basal area NCI growth This behavior uses the effects of neighbor competitiveness to influence growth rates NCI stands for neighborhood competition index In this case the NCI is based on the basal area of neighboring trees A tree s maximum potential growth rate is reduced due to competitiveness and several other possible factors Parameters for this behavior Parameter name NCI Maximum Crowding Distance in meters NCI Maximum Potential Growth cm yr NCI Minimum Neighbor DBH in cm NCI Crowding Effect Slope C NCI Crowding Effect Steepness D NCI Size Sensitivity to NCI gamma NCI Size Effect Mode in cm X0 NCI Size Effect Variance in cm Xb Basal Area NCI BA Divisor Basal Area NCI Use Only Larger Neighbors How it works Description The maximum distance in m at which a neighboring tree has competitive effects on a target tree Maximum potential diameter growth for a tree in cm yr The minimum DBH for trees of that species to compete as neighbors Used for all species not just those using NCI growth The sl
328. parameters The maximum distance that seeds are allowed to disperse is the length of the grid in the longest direction up to a maximum of 1000 meters Because of the torus shape of the plot a seed deposited at the very limit of the distance could end up back underneath the parent tree For this reason if you are using a very flat dispersal kernel you may wish to consider a non spatial disperse method The normalizer Equation 3 of Ribbens et al 1994 serves two functions It reduces parameter correlation between STR and the dispersion parameter D and scales the distance dependent dispersion term so that STR is in meaningful units i e the total of seedlings produced in the entire seedling shadow of a 30 cm DBH parent tree Non gap spatial disperse f Non gap spatial disperse is called non gap to distinguish it from gap disperse The non gap means that forest cover is ignored Parameters for this behavior Parameter name Description The B value for stumps Stumps use the same probability distribution Beta for Stumps function as the live members of their species Only required if a behavior is being applied to stumps The probability distribution function to be used to distribute seeds in canopy conditions For the behaviors Non gap spatial disperse and Masting spatial disperse these PDFs are always the ones used Canopy Function Used The annual STR value Standardized Total Recruits or all seeds Lognormal Canop
329. patial disperse algorithm Disperses seeds in a spatial way ignoring forest cover Gap spatial disperse takes forest cover into account when determining the number and placement of seeds Variant of the Non gap spatial disperse behavior that adds masting and more stochasticity in seed production Calculates seed density based on annual mean temperature and the basal area of neighborhood adults Non spatial disperse The non spatial in non spatial disperse refers to the fact that this behavior ignores the location of parent trees and scatters seeds uniformly across the plot Non spatial disperse has two components basal area dependent seed rain and non density dependent bath seed rain the two of which are independent and can be used together or separately For basal area dependent seed rain the number of seeds added is in direct proportion to the amount of basal area of parent trees of a given species Bath seed rain adds a constant number of seeds each timestep even if there are no parent trees of that species in the plot Parameters for this behavior Parameter name Intercept of Mean Non Spatial Seed Rain seeds m yr Slope Mean Non Spatial Seed Rain seeds m ha of BA yr Minimum DBH for Reproduction in cm Seed Distribution Seed Dist Clumping Parameter Neg Binomial Seed Dist Std Deviation Normal or Lognormal How it works Description The intercept of the non spatial seed rain function Thi
330. pe of the line describing the drop off in seedling survival as a function of GLI above the optimum GLI Slope of Dropoff The slope of the line describing the dropoff in seedling survival as a Below Optimum GLI function of GLI below the optimum GLI How it works The effects of light levels on seed survival is graphed as Light Effect Proportion Established Lope 0 GLI 100 To assess the effects of light level on the number of seeds that survive this behavior retrieves the light level from the Storm Light grid that corresponds to the point in the center of each Dispersed Seeds grid cell The proportion of seeds that survive for a given species is calculated as e If GLI lt GLlop LE 1 Sig GLIop GLD If GLI GLlo p LE 1 e If GLI gt GLI LE 1 Spi GLI GLlopi e GLI is the light level at the center of the Dispersed Seeds grid cell e GLI is the GLI of Optimum Establishment 0 100 parameter e Sj is the Slope of Dropoff Below Optimum GLI parameter e Sj is the Slope of Dropoff Above the Optimum GLI parameter Once the proportion of seeds that survive at the given light level has been calculated this value is multiplied by the number of seeds to reduce them by the proper amount The new reduced number of seeds is put back in the Dispersed Seeds grid How to apply it Apply this behavior to seeds of your desired species Any species to which it is applied must also have a Disperse behavio
331. pe of the line describing the drop off in seedling survival as a function of GLI above the optimum GLI The slope of the line describing the dropoff in seedling survival as a function of GLI below the optimum GLI Fraction of light transmitted through the snag tree crown for each species Applies to those snags whose age is less than or equal to Upper age yrs of snag light extinction class 1 Expressed as a fraction Snag Age Class 2 Light Extinction Coefficient 0 1 Snag Age Class 3 Light Extinction Coefficient 0 1 Upper Age Yrs of Snag Light Extinction Class 1 Upper Age Yrs of Snag Light Extinction Class 2 How it works between 0 and 1 If your run does not work with snags you can ignore this Otherwise a value must be provided for all species Fraction of light transmitted through the snag tree crown for each species Applies to those snags whose age is greater than Upper age yrs of snag light extinction class 1 but is less than or equal to Upper age yrs of snag light extinction class 2 Expressed as a fraction between 0 and 1 If your run does not work with snags you can ignore this Otherwise a value must be provided for all species Fraction of light transmitted through the snag tree crown for each species Applies to those snags whose age is greater than Upper age yrs of snag light extinction class 2 Expressed as a fraction between 0 and 1 If your run does not work with snags you can ignore this
332. pen for a run you can use the menu command File gt Close run output file to close each of the run s output files Once all output files are closed the run will switch back to the more efficient mode Line graphs You can produce several kinds of line graphs Four kinds of line graphs absolute density relative density absolute basal area and relative basal area can be produced from either summary output files or detailed output output files If you know you want to look at these graphs you should save a summary output file The graphing performance will be significantly better Another set of line graphs absolute volume and relative volume can be created via the detailed output file If you are saving a summary output file and have defined subplot areas the line graphs will also be available for each subplot in addition to the whole plot Subplots are not available in detailed output files In order to view basal area and density graphs from a summary output file save data for each kind of graph you want to see in the Summary output setup window To view these graphs from a detailed output output file save the DBH tree data member for saplings adults or snags or the Diam 10 tree data member for seedlings For more on how to save these tree data members see the Setup tree save options window To view volume graphs in the detailed output file save the Tree Volume tree data member for your chosen tree types To access t
333. plies to radial increment limited growth behaviors Asymptote of the Michaelis Menton growth function at high light Diameter Growth A Slope of Growth Response S Length of Current Release Factor Length of Last Suppression Factor Mortality Threshold for Suppression Years Exceeding Threshold Before a Tree is Suppressed function term A below Slope of the Michaelis Menton growth function at zero light function term S below Controls the magnitude of the effects of release Controls the magnitude of the effects of suppression Defines the growth rate for suppressed status in terms of tree mortality The value is expressed as the proportion of trees which die at the growth rate which defines suppressed status expressed as a fraction between 0 and 1 For instance if this value is 0 1 the growth rate for suppressed status is one at which 10 of trees die with that growth The number of years for which a tree s growth must be below the defined suppression threshold before it is considered to be suppressed Absolute growth is calculated with the equation where e Y logl0 radial growth 1 e SF is the suppression factor e Ais the Asymptotic Diameter Growth A parameter e Sis the Slope of Growth Response S parameter e GLI is the global light index calculated by a light behavior Amount of diameter growth per timestep is calculated as growth 10 1 2 10 T where T is the number of y
334. proportions of each kind of substrate are tracked in the Substrate grid You can change this grid s cell resolution Within each cell the grid keeps track of each substrate s area as a proportion of the total area Each timestep Substrate looks for harvest events and tree death It finds harvest events by looking in the Harvest grid it finds dead trees by looking for the flag set by the Mortality behaviors Harvest events completely replace existing substrate with their substrate signatures Each dead tree rolls the dice with a random number to determine if it falls and if it falls if it exposes tip up mounds substrate All the new substrate created by harvest and tree fall is then totaled up When there is new substrate in a grid cell Substrate reduces the other substrate amounts in the cell to make way for the amount of new substrate Then Substrate creates a record of the substrate change called a cohort The substrates in a cohort decay as the cohort ages Cohorts have a set lifetime of a certain number of years which you set in the parameters After this they are deleted This means that the effects of a substrate change event linger with decreasing intensity for a number of years after the event occurs The final proportions of scarified soil tip up mounds and fresh logs are found by adding up the decayed values in the cohorts The final proportion of decayed logs is found by adding up the amount by which fresh logs have decayed i
335. ps DBH diameter at 10cm relationship The standard diameter Height is a function of DBH or diameter at 10 cm These are called standard height because they were the original SORTIE functions relationships Calculates crown dimensions as a function of tree size and local crowding DBH is a linear function of diameter at 10 cm The linear diameter height relationship Height is a linear function of diameter The reverse linear diameter Diameter is a linear function of height height relationship The power diameter height relationship Height is a power function of diameter at 10 cm The standard crown depth and radius relationships Parameters Parameter name Description Crown Height Exponent Crown Radius Exponent Slope of Asymptotic Crown Height Slope of Asymptotic Crown Radius The exponent in the standard equation for calculating crown depth The exponent in the standard equation for determining the crown radius Slope of the standard equation for determining crown depth Slope of the standard equation for determining crown radius Crown radius is calculated as where rad C DBH e radis the crown radius in meters e Cis the Slope of Asymptotic Crown Radius parameter e ais the Crown Radius Exponent parameter e DBH is the tree s DBH in cm Crown radius is limited to a maximum of 10 meters Crown depth is calculated as where ch C2 height e
336. quation Ignored for conifers B3 in the quality probability equation Ignored for conifers Quality Vigor Classifier Species Type Quality Vigor Classifier Vigor Beta 0 Quality Vigor Classifier Vigor Beta 1 Class 1 Quality Vigor Classifier Vigor Beta 1 Class 2 Quality Vigor Classifier Vigor Beta 1 Class 3 Quality Vigor Classifier Vigor Beta 1 Class 4 Quality Vigor Classifier Vigor Beta 1 Class 5 Quality Vigor Classifier Vigor Beta 1 Class 6 Quality Vigor Classifier Vigor Beta 2 Quality Vigor Classifier Vigor Beta 3 How it works Whether a species is deciduous or coniferous Bo in the vigor probability equation Biclass in the vigor probability equation for trees with a current tree class of 1 Biciass in the vigor probability equation for trees with a current tree class of 2 Biciass in the vigor probability equation for trees with a current tree class of 3 Biclass in the vigor probability equation for trees with a current tree class of 4 Biclass in the vigor probability equation for trees with a current tree class of 5 Biciass in the vigor probability equation for trees with a current tree class of 6 B2 in the vigor probability equation B3 in the vigor probability equation Tree classification is as follows Species Type Quality DBH Range Class Species are defined as deciduous or coniferous using the Quality Vigor Classifier Species Type pa
337. quired if the gap probability distribution function is lognormal The standard deviation of the lognormal function under gap conditions Maximum Parent Trees Allowed in Gap Cell Seed Distribution Seed Dist Clumping Parameter Neg Binomial Seed Dist Std Deviation Normal or Lognormal STR for Stumps Weibull Canopy Annual STR Weibull Canopy Beta see equation below This is only required if the gap probability distribution function is lognormal Maximum number of trees above the minimum DBH for reproduction that are allowed in a grid cell for that cell to still have gap status as opposed to closed canopy The distribution method to be applied to seeds randomization The forms for these functions can be found here Choices are e Deterministic no randomization e Poisson use the number of seeds as the mean in a Poisson probability distribution function e Normal use the number of seeds as the mean in a normal probability distribution function You must then supply a standard deviation for the function e Lognormal use the number of seeds as the mean in a lognormal probability distribution function You must then supply a standard deviation for the function e Negative binomial use the number of seeds as the mean in a negative binomial probability distribution function You must then supply a clumping parameter If you have chosen the negative binomial probability distribution function for See
338. r Cannot be equal to zero Gamma parameter Phi parameter Standard deviation of growth stochasticity cm yr Use zero if growth should have no stochasticity Probability of autocorrelation from year to year as a value from 0 to 1 Use 0 if there should be no autocorrelation The amount of height growth is calculated as where aGLi Y oP H y GLI B e Yis the amount of height growth for one year in cm e GLI is the light level e ais the Michaelis Menton Neg Growth Alpha parameter e fis the Michaelis Menton Neg Growth Beta parameter e yis the Michaelis Menton Neg Growth Gamma parameter e is the Michaelis Menton Neg Growth Phi parameter e His the tree s height in cm Optionally the value of Y can be randomized by adding to it a stochastic factor SF which is a random draw on a normal distribution with mean zero and standard deviation set using the Michaelis Menton Neg Growth Growth Standard Deviation parameter SF can be positive or negative and is in units of centimeters of height growth If you do not want to add SF set the value of this parameter to zero If you are using the stochastic factor SF you can also introduce autocorrelation in the growth stochasticity Each year for each tree a random number is compared to the value in the Michaelis Menton Neg Growth Autocorrelation Prob 0 1 parameter for that tree s species to determine if the stochastic factor will be autocorrelated for that year
339. r Bi Level Intercept for Low Light Growth a parameter e b growth slope in high light conditions this is the Linear Bi Level Slope for High Light Growth b parameter in low light conditions this is the Linear Bi Level Slope for Low Light Growth b parameter e diam diameter diameter at 10 cm for seedlings and saplings DBH for adults e T number of years per timestep Light levels come from the Storm Light grid produced by the Storm Light behavior The threshold between the use of high light and low light parameters is set in the Linear Bi Level Threshold for High Light Growth 0 100 parameter This behavior can also be used without Storm Light In this case only the low light growth parameters are used How to apply it This behavior can be applied to seedlings saplings and adults of any species If you wish to use the light level parameter switch also use the Storm Light behavior You can use either the diam with auto height or diam only version Linear growth w exponential shade reduction This behavior does either diameter or height growth as a function of GLI Parameters for this behavior Parameter name Description ped ringar x Intercept of the size dependent growth potential in mm yr for diameter Diam Intercept in ent mm yr a 8 Shaded Linear Diam Shade Effect of shading for diameter growth Exponent c Shaded Linear f pa o O Slope of the size dependent annual growth potential f
340. r and the Storm Light behavior applied Substrate Based Seed Survival With Microtopography This behavior assesses seed survival based on substrate conditions allowing for site microtopography to influence seed survival In this scenario the plot is divided into small scale mounds The portion of the plot that is slightly elevated is mound The portion of the plot between the mounds at lower elevation is ground The size of the mounds and their height is not important Parameters for this behavior Parameter name Fraction Seeds Germinating on Ground Decayed Logs Fraction Seeds Germinating on Ground Forest Floor Litter Fraction Seeds Germinating on Ground Forest Floor Moss Fraction Seeds Germinating on Ground Fresh Logs Fraction Seeds Germinating on Ground Scarified Soil Fraction Seeds Germinating on Ground Tip Up Fraction Seeds Germinating on Mound Decayed Logs Description The proportion of those seeds that land on decayed logs ground substrate that survive to become seedlings Expressed as a value between 0 and 1 The proportion of those seeds that land on forest floor litter ground substrate that survive to become seedlings Expressed as a value between 0 and 1 The proportion of those seeds that land on forest floor moss ground substrate that survive to become seedlings Expressed as a value between 0 and 1 The proportion of those seeds that land on fresh logs ground substrate that su
341. r for the species of individual i e y is the Gen Harvest Regime Cut Preference Gamma parameter for the species of individual i e 4 1s the Gen Harvest Regime Cut Preference Mu parameter for the species of individual i e BAR is the percent of total adult basal area to remove between 0 and 100 e DBH is the individual s DBH The term o is o at bh BAR where e ais the Gen Harvest Regime Cut Preference A parameter e bis the Gen Harvest Regime Cut Preference B parameter e cis the Gen Harvest Regime Cut Preference C parameter e BAR is the percent of total adult basal area to remove between 0 and 100 An individual s probability of removal is compared with a random number to determine if that individual is cut The preference function takes into account the target basal area removal rate of the plot However the function shape does not necessarily produce a mean removal probability equal to that of the target removal rate particularly near 0 and 100 If you wish the behavior can refine the probabilities on a second pass to get closer to the target You can set a tolerance using the Gen Harvest Acceptable Deviation From Cut Target parameter This is expressed as a proportion of the removal rate between 0 and 1 So a value of 0 1 allows first pass acceptable deviation of 10 percent from the target If the actual removal rate falls outside this limit the function adjusts all preferences by a correction factor and re evaluates ind
342. r hectare of adult trees within the entire plot e BAPH is the basal area in m per hectare of adult trees within the entire plot e BAL is the sum of the basal area of all trees taller than the height of the target tree in m per hectare The instrumental equation for calculating rad is as follows radi a b DBH c Height d DBH e Height f DBH g STPH h BAPH i BAL j Height DBH where e ais the Non Spatial Density Dep Inst Crown Radius a parameter e bis the Non Spatial Density Dep Inst Crown Radius b parameter e cis the Non Spatial Density Dep Inst Crown Radius c parameter e dis the Non Spatial Density Dep Inst Crown Radius d parameter e eis the Non Spatial Density Dep Inst Crown Radius e parameter e fis the Non Spatial Density Dep Inst Crown Radius f parameter e gis the Non Spatial Density Dep Inst Crown Radius g parameter e his the Non Spatial Density Dep Inst Crown Radius h parameter e iis the Non Spatial Density Dep Inst Crown Radius i parameter e jis the Non Spatial Density Dep Inst Crown Radius j parameter e DBH is the DBH of the tree in cm e Height is the tree height in meters e STPH is number of stems per hectare of adult trees within the entire plot e BAPH is the basal area in m per hectare of adult trees within the entire plot e BAL is the sum of the basal area of all trees taller than the height of the target tree in m per hectare The NCI crown
343. r name Description Proportion of scarified soil The proportion of the grid cell area that is scarified soil Proportion of forest floor The proportion of the grid cell area that is forest floor Proportion of tip up mounds The proportion of the grid cell area that is tip up mounds Proportion of fresh logs The proportion of the grid cell area that is fresh logs Proportion of decayed logs The proportion of the grid cell area that is decayed logs Packages Data member name Description Substrate cohort age The age of the substrate cohort in timesteps Substrate cohort new scarified soil The proportion of cell area that is scarified soil added in substrate this cohort Substrate cohort new tip up The proportion of cell area that is tip up mounds substrate mounds substrate added in this cohort The proportion of cell area that is fresh logs added in this t h fresh 1 Substrate cohort new fresh logs ee Substrate calcs Grid This grid is called substratecalcs and is created by the Substrate behavior This grid is used for intermediate calculations when calculating the values in the Substrate grid The grid cell resolution must match Substrate s Data in the grid Data member Description name Amount of new tip up mounds New tip up mounds area by grid cell in square meters Fresh logs added X timesteps ago up to the value in the Substrate parameter Maximum number of years that decay occurs converted to timesteps as a proportion of
344. r name Description lt th Partitioned Height Biomass Leaf The slope in the linear biomass equation for leaves Slope a Partitioned Height Biomass Leaf The intercept in the linear biomass equation for leaves Intercept b Partitioned Height Biomass Bole The slope in the linear biomass equation for boles Slope a Partitioned Height The intercept in the linear biomass equation for boles Biomass Bole Intercept b How it works Biomass is calculated in exactly the same way and using the same parameters as for the Partitioned Height Biomass behavior except it only calculates the biomass of those trees killed by the Storm damage killer behavior How to apply it Apply this behavior to saplings adults or snags of any species This behavior does not automatically create output Once you have added this behavior to your run the Detailed output grid setup window will list the Storm Killed Partitioned Biomass grid You can then view the contents of this grid as a table using SORTIE s data visualization system Tree Bole Volume Calculator This behavior calculates merchantable tree volume Make sure to distinguish between this behavior and the other tree volume behavior Parameters for this behavior Parameter name Description lt th Calculates the amount of taper to the top of the first 16 foot log in a tree This is the diameter at the top of that log as a percentage of DBH between 60 and 100 Bole V
345. r that it should remove enough basal area to bring each range back down to its target basal area Since Harvest actually does the tree removal see that behavior s documentation for the method used If the amount of basal area in any given range is less than the target no trees are cut in that range How to apply it Add this behavior to your run Harvest is also needed in the run and should be placed after Selection Harvest in the behavior order Windstorm Windstorm kills trees due to storm events Trees removed by this behavior will have a mortality reason code of storm Parameters for this behavior Parameter name Description Windstorm DBH The b value in the equation used to determine the mortality of an Exponent b individual tree as a result of a storm Windstorm Minimum DBH for The minimum DBH for trees to be killed in storm events Windstorm Mortality Windstorm Mortality Intercept a Windstorm Sea Surface Temperature Cyclicity Period Years Windstorm Severity for 1 Year Return Interval Storm Windstorm Severity for 5 Year Return Interval Storm Windstorm Severity for 10 Year Return Interval Storm Windstorm Severity for 20 Year Return Interval Storm Windstorm Severity for 40 Year Return Interval Storm Windstorm Severity for 80 Year Return Interval Storm Windstorm Severity for 160 Year Return Interval Storm Windstorm Severity for 320 The a valu
346. r year Effect C Weibull Climate Growth Temp Effect A Weibull Climate Growth Temp Effect B Weibull Climate Growth Temp Effect C Weibull Climate Growth Max Neighbor Search Radius m Weibull Climate Growth Max Potential Growth cm yr Weibull Climate Growth Minimum Neighbor DBH cm Weibull Climate Growth Size Effect X0 Weibull Climate Growth Size Effect Xb Weibull Climate Growth Size Effect Minimum DBH How it works The A parameter for the temperature effect The effect is based on mean annual temperature in degrees Celsius The B parameter for the temperature effect The effect is based on mean annual temperature in degrees Celsius The C parameter for the temperature effect The effect is based on mean annual temperature in degrees Celsius The maximum distance in m at which a neighboring tree has competitive effects on a target tree Maximum potential diameter growth for a tree in cm yr The minimum DBH for trees of that species to compete as neighbors Used for all species not just those using Weibull Climate growth The mode of the size effect curve The variance of the size effect curve The minimum possible DBH for size effect Trees with a DBH less than this value will use this value in the size effect calculation instead For a tree the amount of diameter growth per year is calculated as Growth Max Growth Size Effect Precipita
347. rameter Trees that do not have vigor and quality designations such as new adult trees or initial conditions trees that were not specifically assigned these values are randomly given vigor and quality according to defined probabilities that these trees are vigorous or of sawlog quality These probabilities are defined as values between 0 and 1 in the Quality Vigor Classifier Prob New Adults Vigorous and Quality Vigor Classifier Prob New Adults Sawlog parameters Coniferous species are not assigned a quality value and values entered for those species are ignored Vigor and quality for a tree may change through time The probability of transition between states is a function of previous class and size and is evaluated for each tree each timestep The probability of a tree being vigorous in the current timestep 1s e Px Pi efx where Px Bo Bictass B2 DBH p3 In DBH where e ois the Quality Vigor Classifier Vigor Beta 0 parameter e P ictass is one of the following depending on the current class designation of the tree o Quality Vigor Classifier Vigor Beta 1 Class 1 Quality Vigor Classifier Vigor Beta 1 Class 2 Quality Vigor Classifier Vigor Beta 1 Class 3 Quality Vigor Classifier Vigor Beta 1 Class 4 Quality Vigor Classifier Vigor Beta 1 Class 5 o Quality Vigor Classifier Vigor Beta 1 Class 6 e 21s the Quality Vigor Classifier Vigor Beta 2 parameter e 31s the Quality Vigor Classifier Vigor Beta 3 paramet
348. rameters for those behaviors To edit the behavior parameters use the Edit gt Parameters menu option You may want to work with one set of parameters at a time when you are first entering them because the window will validate your entries before accepting them and it will be easier troubleshoot one section at a time When editing the parameters if you are not sure what a parameter is or what value you should enter you can check the parameters page for that behavior functional group It lists all parameters for all behaviors in that group in alphabetical order with a short description of each and tells you what behavior they belong to Once the parameters are entered you can view them all at once and save a copy of a text version as a record State change behaviors State change behaviors act on the basic properties of the virtual plot being modeled Behavior Description Precipitation Climate Changes the value of the Mean Annual Precipitation parameter of the SORTIE Change plot behavior Temperature Climate Changes the value of the Mean Annual Temperature parameter of the SORTIE Change plot behavior Precipitation Climate Change This behavior changes the value of the Mean Annual Precipitation parameter of the SORTIE plot This can be used to simulate the effects of climate change If the run does not have a behavior that uses precipitation this will have no effect Parameters for this behavior Parameter name Descripti
349. rate fallen logs are assumed to be cone shaped Since they land on their sides the area of the cone is approximated to a triangle Thus each new fresh log contributes the following amount of new fresh log area FL DBH h 2 where e FL is new fresh log area in square meters e DBH is the DBH of the fallen tree in m e his the height of the fallen tree in m A dead adult or sapling as a certain probability of contributing fresh log substrate this probability is specified in the Proportion of Dead that Fall parameter Snags always add fresh log substrate upon their death How new fresh log area is distributed depends on the value in the Use Directional Tree Fall parameter If false a dead tree contributes all of its fresh log area into the grid cell where it was rooted In other words it doesn t fall over so much as vertically collapse If true a trees is allowed to fall in a random direction The amount of new fresh log area is distributed over the grid cells that the log overlays Relationship 5 governs the amount of newly exposed tip up mounds created by fallen dead trees For each fallen tree the amount of new tip up mounds area is calculated as OA x r F where e OA is the new tip up mounds area in square meters e ris the tree trunk radius in meters e Fis the Uprooted Tree Radius Increase Factor for Root Rip Out parameter which accounts for the effects of root disturbance A tree contributes all of its new tip up
350. rched for neighbors Neighbors m Basal Area Light Whether each species is a conifer or an angiosperm for the purposes of Species Type light calculations How it works This behavior uses a grid called Basal Area Light to manage light levels Light levels are calculated for each cell in the grid trees to which this behavior are assigned receive the light level of the cell in which they are located The behavior begins by calculating the total basal area and angiosperm basal area in the neighborhood of each Basal Area Light grid cell The neighborhood is a circle with its center on the center of the grid cell and a radius given in the Basal Area Light Search Radius for Neighbors m parameter Whether a neighborhood tree counts as angiosperm or conifer depends on what its species is set to in the Basal Area Light Species Type parameter Seedlings and snags are never included in these basal area totals Other trees are only included if their DBH is equal to or greater than the value set in the Basal Area Light Minimum DBH for Trees parameter Once the basal areas are calculated the behavior adds them together to create a total basal area and compares this value to the previous timestep s total basal area If the value has not changed by more than the amount set in the Basal Area Light Minimum BA Change for New GLI m2 parameter no further action is taken The previous timestep s GLI and basal area values are kept For each g
351. re needed Once those steps are complete you can enter your parameter values by choosing the menu option Edit gt Parameters which will open the Parameters window You may want to only display and edit one category of parameter at a time since all values in the parameter window must be valid before you can save your changes Output A basic parameter file creates no output by default You can perform a run with it but there will be no results There are two kinds of output files summary output files and detailed output files You can set up either or both of these using the Edit gt Output options menu command from the main SORTIE ND window Initial conditions Set initial conditions for trees and grids to define the model state at the beginning of the run Initial conditions can have a big effect on run outcome Replicating a point in another run You can replicate a point in another run in your parameter file in order to have it as the starting point in a new run You might do this to create a branch point where you determine what might have happened if the parameters in the first run had been a little different or perhaps you did a run solely to create mature forest initial conditions for a new run The first run should have saved a detailed output file with as much data as possible The new parameter file should be compatible with the first it should have a common species set and most of the same behaviors You can then
352. redator population instantaneous rate of change in season 2 Season 2 Func Resp nies The predator population foraging efficiency for each seed species Foraging Efficiency Func Resp Keep If true this means that the final predator density at the end of the Predator Densities behavior mini model run is the initial density for the next mini model Between Timesteps run If false every time the behavior mini model runs it is re initialized Func Resp Max Decline Rate Season 1 predators week Func Resp Max Decline Rate Season 2 predators week Func Resp Max Intake Rate seeds per predator per day Func Resp Number of Weeks in Which Seedfall Occurs Func Resp Predator Initial Density num sq m Func Resp Proportion of Seeds Germinating Each Week Func Resp Seed Predation Output Filename If Desired Func Resp Week Germination Begins Func Resp Week Season 2 Begins Func Resp Weeks to Run Seed Predation Model 1 52 How it works with the value of the Predator initial density num sq m parameter The maximum rate of decline in the predator population in the absence of any food in predators per week for season 1 The maximum rate of decline in the predator population in the absence of any food in predators per week for season 2 The maximum number of seeds of each species that can be eaten by one predator in one day The number of weeks at the beginning of the behavior mini
353. requency Parameter that controls the cyclicity of storm frequency This value is part of the sine curve term and controls where on the sine curve storms start occurring Parameter that controls the trend of cyclicity of storm frequency This value is part of the trend term and is the intercept of the function controlling the increase or decrease of overall frequency cycling For no cyclicity at all set this term to 1 For no trend in cyclicity set this term to 0 Parameter that controls the trend of cyclicity of storm frequency This value is part of the trend term and is the slope at which frequency cycling increases or decreases For no cyclicity or no trend in cyclicity set this term to 0 There are two ways storms can occur randomly according to a storm regime of your choosing or scheduled at certain timesteps Both methods can be used together Random storms according to a storm regime Storm severity is assessed on a scale from 0 no damage to 1 total damage This interval of storm severity values is subdivided into ten storm severity classes You assign each storm severity class a return interval The reciprocal of the return interval gives the annual probability of each type of storm The overall frequency of storms can remain constant or it can change through time It has been reported in Goldenburg et al 2001 that storm activity in the North Atlantic cycles along with sea surface temperature This behavior can thus chang
354. required if the canopy probability distribution function is Weibull The for the Weibull function under canopy conditions see equation ae ea below This is only required if the canopy probability distribution oe function is Weibull The dispersal value for the Weibull function under canopy conditions or Weibull Canopy under non masting conditions in the case of Masting spatial disperse see Dispersal equation below This is only required if the canopy probability distribution function is Weibull The 0 for the Weibull function under canopy conditions or under non Weibull Canopy masting conditions in the case of Masting spatial disperse see equation Theta below This is only required if the canopy probability distribution function is Weibull How it works For each tree greater than reproductive age the number of seeds produced is calculated as seeds STR DBH 30 These seeds are cast in random azimuth directions from the tree and at random distances that conform to the chosen probability distribution function see more about spatial disperse behavior seed distribution here How to apply it Apply this behavior to all trees of at least the minimum reproductive age for your chosen species If the minimum reproductive age is less than the Minimum adult DBH be sure to apply this behavior to saplings as well as adults In the parameters choose the appropriate probability distribution function for each species under Canopy fu
355. reshold growth rate A tree s suppression state is a multiplicative factor in its growth rate If a tree is not suppressed the suppression factor in the growth equation is set to 1 no effect on growth If the tree is suppressed the suppression factor is calculated as follows SF el S VER 4 LS where e SF is the suppression factor e gis the Length of Current Release Factor parameter e YLR is the length of the last or current period of release in years e dis the Length of Last Suppression Factor parameter e YLS is the length of the last or current period of suppression in years Details of this model are published in Wright et al 2000 Absolute growth limited to radial increment How it works This behavior calculates an amount of diameter growth according to the absolute growth equation Growth is limited to a maximum of the constant radial increment for the species of tree to which it is being applied The increment is calculated as described in the Constant radial growth behavior Note that the increment parameter specifies radial growth the behavior makes all necessary conversions How to apply it This behavior can be applied to seedlings saplings and adults of any species Any tree species type combination to which it is applied must also have a light behavior applied You can use either the diam with auto height or diam only version Absolute growth limited to basal area increment How it works This
356. ric height growth and allometric diameter growth behaviors were developed to help bridge this gap When used with a behavior that only increments diameter or height they will preserve height or diameter differences that have developed across individuals in a species Behavior Description Absolute Calculates an amount of diameter growth according to the Michaelis Menton growth limited absolute growth equation Growth is limited to a maximum of a constant radial to radial increment Absolute growth limited to basal area increment Non limited absolute growth Allometric diameter growth diam only Allometric height growth Basal area NCI growth Constant basal area growth Browsed relative growth Constant radial growth Double resource relative growth Juvenile NCI growth Lagged post harvest growth Linear growth Linear bi level growth increment Calculates an amount of diameter growth according to the Michaelis Menton absolute growth equation Growth is limited to a maximum of a constant basal area increment Calculates an amount of diameter growth according to the Michaelis Menton absolute growth equation If you have a behavior that primarily updates tree height this behavior updates diameter to ensure even growth If you have a behavior that primarily updates tree diameter this behavior updates height to ensure even growth Calculates growth rate based on the basal area
357. rid cell in which a new GLI is to be calculated a mean GLI value is calculated as follows where e GLI is the mean GLI value as a value between 0 and 100 e ais the Basal Area Light Mean GLI a Parameter e b is the Basal Area Light Angiosperm b Parameter e cais the Basal Area Light Angiosperm c Parameter e BA is the angiosperm basal area for that grid cell in square meters e b is the Basal Area Light Conifer b Parameter e cis the Basal Area Light Conifer c Parameter e BA is the conifer basal area for that grid cell in square meters This mean GLI is translated into a value for the lognormal random draw as follows In GLIn 6 7 2 where GLI is the mean GLI value calculated above and is the Basal Area Light Lognormal PDF Sigma parameter This value is then used to produce a random lognormally distributed number from the following distribution J fing x j 1 J52 3 E AX where is the value calculated above and is the Basal Area Light Lognormal PDF Sigma parameter This number is the GLI value between 0 and 100 Once each Basal Area Light grid cell has gotten a GLI value trees to which this behavior applies get the value of GLI from the grid cell in which they are located How to apply it This behavior may be applied to seedlings saplings and adults of any species Beer s law light filter How it works This behavior simulates a filter that reduces light a
358. rnal SORTIE name of the data member which is what is displayed to you when you choose new data members You cannot change the first six default columns The executable writes a file in response with the trees that it wishes to harvest Tree harvest file that the executable will write on the Edit Harvest Interface window If you have set up new tree data members the executable also writes a second file with a list of live trees to update Tree update file that the executable will write on the Edit Harvest Interface window All trees in both of these files must come from the tree list that SORTIE wrote for that timestep No tree may appear in both files The file format of the user response files is identical to that of the SORTIE file with the same columns in the same order Each harvest timestep all these files are overwritten If there are no trees eligible for harvesting SORTIE still writes a file with only the first two header lines no individual tree lines It expects the executable to do the same if it does not want trees harvested or updated Adding new variables You can request that SORTIE create new data members under the executable s control for the trees to which this behavior applies Set this up in the New tree data members to add section of the Edit Harvest Interface window You can create as many as you want You can give them any name up to 9 characters long They each hold a float value The values are uninit
359. rols the magnitude of the effects of release Controls the magnitude of the effects of suppression Defines the growth rate for suppressed status in terms of tree mortality The value is expressed as the proportion of trees which die at the growth rate which defines suppressed status expressed as a fraction between 0 and 1 For instance if this value is 0 1 the growth rate for suppressed status 1s one at which 10 of trees die with that growth The number of years for which a tree s growth must be below the defined suppression threshold before it is considered to be suppressed Absolute growth is calculated with the equation Ate rnar AFGI F rd cyrrr A iri where e Y logl0 radial growth 1 e SF is the suppression factor e Ais the Asymptotic Diameter Growth A parameter e Sis the Slope of Growth Response S parameter e GLI is the global light index calculated by a light behavior Amount of diameter growth per timestep is calculated as growth 10 1 2 10 T where T is the number of years per timestep The absolute growth behaviors also take into account suppression status A tree is considered suppressed if its growth rate for the previous timestep falls below a certain threshold That threshold is the rate of growth at which X of juveniles die where X is a user settable parameter The threshold is calculated for each species by solving the BC mortality equation for G growth where m is the th
360. rs It holds the number of seeds of each species that have been created by dispersal This grid defaults to a cell resolution of 8 m X 8 m which you can change Data in the grid Data member name Description Number of seeds for Spades The number of seeds in each grid cell belonging to Species X Whether the cell is in gap true or under closed canopy false Only Gap status 3 7 P used if there are behaviors which use forest cover The count of adult trees for determining gap status Only used if there Adult tree count j i are behaviors which use forest cover Foliar Chemistry Grid This grid is created by the Foliar Chemistry behavior This is where the amount of different foliar chemistry components is stored All data is stored raw no conversion to per hectare amounts The grid cell resolution is set to 8 m X 8 m You can change this to whatever you wish Data in the grid Data member name Description Kg N for species X Amount of N for species X in kg Kg P for species X Amount of P for species X in kg Kg SLA for species X Amount of SLA for species X in kg Kg Lignin for species X Amount of lignin for species X in kg Kg Fiber for species X Amount of fiber for species X in kg Kg Cellulose for species X Amount of cellulose for species X in kg Kg Tannins for species X Amount of tannins for species X in kg Kg Phenolics for species X Amount of phenolics for species X in kg Gap Light Grid
361. rs a behavior to calculate light levels for trees one to determine the amount of tree growth as a result of the amount of light and one to select trees to die if they grow too slowly Behaviors are placed in a certain order to correctly structure their interactions The simulation Forests tend to operate on annual cycles and so does SORTIE The unit of time in SORTIE is the timestep It represents a set of one or more years A single timestep consists of each behavior acting once in their defined order The process is repeated for the number of timesteps that you set and that s a single simulation or run The basic structure of the SORTIE system is very simple Its power lies in its incredible flexibility Almost every aspect of the model is under direct user control The parameter file When you start the SORTIE software you are using a tool that helps you to define the state data and behaviors that will make up a simulation Once you have done this you have created a parameter file The parameter file completely defines a run You can load and run your parameter file any time Setting up SORTIE ND for your site The major research projects involving SORTIE all began with multi year field studies to gather data and analyze tree life cycle processes in the location being studied This resulted in SORTIE simulations that reflect as accurately as possible local conditions in the real world This means that there is no standard setup
362. rs since storms started and Sr is the Windstorm Sea Surface Temperature Cyclicity Period Years parameter e dis the Windstorm Storm Cyclicity Sine Curve d parameter which controls the sine curve s amplitude e fis the Windstorm Storm Cyclicity Sine Curve f parameter which controls the sine curve s frequency e gis the Windstorm Storm Cyclicity Sine Curve g parameter which controls where on the sine curve storms start occurring e mis the Windstorm Storm Cyclicity Trend Function Slope m parameter e iis the Windstorm Storm Cyclicity Trend Function Intercept i parameter To turn off all cyclicity and use constant storm probabilities set Windstorm Storm Cyclicity Sine Curve d to 0 Windstorm Storm Cyclicity Trend Function Slope m to 0 and Windstorm Storm Cyclicity Trend Function Intercept i to 1 The other values are unimportant To use only the sine portion with no trend line set both Windstorm Storm Cyclicity Trend Function Slope m and Windstorm Storm Cyclicity Trend Function Intercept i to 0 To use only the trend portion set Windstorm Storm Cyclicity Sine Curve d to 0 For each storm that occurs Windstorm decides what trees will die as a result A tree s probability of mortality is calculated as follows where e pis the tree s probability of mortality e ais the Windstorm Mortality Intercept a parameter e cis the Windstorm Storm Intensity Coefficient c parameter e bis the Windstorm
363. rvive to become seedlings Expressed as a value between 0 and 1 The proportion of those seeds that land on scarified soil ground substrate that survive to become seedlings Expressed as a value between 0 and 1 The proportion of those seeds that land on tip up ground substrate that survive to become seedlings Expressed as a value between 0 and 1 The proportion of those seeds that land on decayed logs mound substrate that survive to become seedlings Expressed as a value between 0 and 1 Fraction Seeds Germinating on Mound Forest Floor Litter Fraction Seeds Germinating on Mound Forest Floor Moss Fraction Seeds Germinating on Mound Fresh Logs Fraction Seeds Germinating on Mound Scarified Soil Fraction Seeds Germinating on Mound Tip Up Proportion of Plot Area that is Mound How it works The proportion of those seeds that land on forest floor litter mound substrate that survive to become seedlings Expressed as a value between 0 and 1 The proportion of those seeds that land on forest floor moss mound substrate that survive to become seedlings Expressed as a value between 0 and 1 The proportion of those seeds that land on fresh logs mound substrate that survive to become seedlings Expressed as a value between 0 and 1 The proportion of those seeds that land on scarified soil mound substrate that survive to become seedlings Expressed as a value between 0 and 1 The proportion of those seeds that land on tip u
364. s How trees are organized the tree population Trees are organized by location and size in what is called the tree population The tree population divides up the plot into 8 m by 8 m grid cells and tracks the trees in each cell by height The tree population is where the list of tree species is defined It tracks all of the allometry relationships for each of these species and manages life history stage transitions and attribute updates for individual trees Tree life history stages and transitions Tree life history stage also referred to as tree type along with species is the basic way to classify trees When you set up behaviors for a run you tell each behavior which trees to act on by species and type There is support for seven tree life history stages in the model e Seed e Seedling Seedlings are defined as trees less than the height set in the parameter Max Seedling Height meters normally 1 35 meters thus seedlings have no DBH Their primary size measurement is the diameter at 10 cm height diamjo e Sapling Saplings are defined as having a DBH greater than 0 and less than the Minimum adult DBH defined in the tree parameters Seedlings and saplings are sometimes referred to collectively as juveniles e Adult Adults are defined as having a DBH equal to or greater than the Minimum adult DBH defined in the tree parameters e Stump Stumps are saplings or adults that have been cut by the Harvest behavior e Snag S
365. s The complete file is validated every time you save it You can save a file that does not pass validation but you cannot run it Making a human readable copy of the parameter file The parameter file is in the XML data format and is not easily readable by humans SORTIE will create tab delimited text versions of data that you can open in any text editor or spreadsheet program To save your parameter values use the Edit gt Parameters window To save grid map values use the Edit gt Grid layer setup window Files you save in this way are for your reference only They cannot be used as input Detailed output files The model saves its detailed output in a detailed output file A simulation s detailed output file is in fact a collection of individual files packaged together Within the detailed output package are two types of files a copy of the parameter file originally used to perform the run and individual timestep files which hold the saved data for each timestep All the files are written in plain text in the XML data format Contents of a detailed output file Detailed output timestep files are collections of map files that you set up using the Edit gt Output setup window They are identified by having _x added to the filename where x is the timestep number The parameter file copy is given the detailed output package s filename Each file produced is then compressed using the GZIP program and all the files for a single run are
366. s a table using SORTIE s data visualization system Merchantable Timber Value This behavior calculates the value of merchantable timber Parameters for this behavior Parameter name Description lt th Merchantable Timber Value Form The form class of the species Valid values are 78 79 80 81 84 and 85 Class Bie panai The price per thousand board feet for each species The currency used Timber Value Price er ate 1000 Board Feet l How it works The value for each tree is calculated by finding out its volume in board feet and multiplying that by the price for its species The price is held in the Merchantable Timber Value Price 1000 Board Feet parameter The currency used doesn t matter The tree s final value is placed in a tree data member called Merchantable Value The total value for each species is saved in a grid called Merchantable Timber Value You can save these values in a detailed output file for analysis The volume of merchantable timber in a tree depends on its size and form class These control how many 16 foot logs there are in a tree and how many board feet of timber assuming 0 25 inch thickness those logs can create The form class is entered in the Merchantable Timber Value Form Class parameter The behavior begins by finding out how many 16 foot logs the tree can provide in its bole The base of the bole is the top of the cut stump the top of the bole is the merchantable height This behavi
367. s always used Normal means that each timestep for each species a new probability is drawn from a normal distribution Random Browse Probability PDF Random Browse If the probability is being varied each timestep according to a normal Browse Probability distribution this is the standard deviation of that distribution This value Standard Deviation is ignored if the probability is not being varied How it works The trees eligible for browsing are those trees to which this behavior is applied Each species has a probability of browse that is the same for all members of that species Each timestep for each eligible tree a random number is used against its species probability to decide whether the tree is browsed The probability of browse for a species can be constant or it can vary each timestep If it is constant the probability of browse is always the value in the Random Browse Annual Browse Probability 0 1 parameter If the probability is to vary a new value is drawn from a random distribution using the value in Random Browse Annual Browse Probability 0 1 parameter as the mean and the value in Random Browse Browse Probability Standard Deviation as the standard deviation This draw happens once per species per timestep all individuals of a species always face the same probability of browse in a given timestep If the timestep length is more than one year the annual probability of browse is turned into a timestep probab
368. s and k 1 N neighbors of each species of at least a DBH of NCI Crown Radius Minimum Neighbor DBH or NCI Crown Depth Minimum Neighbor DBH in cm out to a distance of NCI Crown Radius Max Search Distance for Neighbors m or NCI Crown Radius Max Search Distance for Neighbors m a is the NCI Crown Radius Alpha parameter or the NCI Crown Depth Alpha parameter is the NCI Crown Radius Beta parameter or the NCI Crown Depth Beta parameter y is the NCI Crown Radius Gamma parameter or the NCI Crown Depth Gamma parameter Aiz is the NCI Crown Radius Lambda for Species X Neighbors parameter or the NCI Crown Depth Lambda for Species X Neighbors for the target species relative to the kth neighbor s species DBH is the DBH of the kth neighbor in cm DBH is the DBH of the target tree for which to calculate crown dimensions in cm distance g is distance from target to neighbor in m DBH diameter at 10 cm relationship Seedlings use the diameter at 10 cm as their primary indicator of size and have no DBH Saplings use both DBH and diamjo The use of both measurements by saplings helps to maintain continuity between the seedling and adult life history stages Adults use only DBH Parameters Parameter name Description Intercept of DBH to Diameter at 10 cm Relationship The intercept of the linear relationsip between the DBH in cm and the diameter at 10 cm height in cm in small trees Used by all species Slope of DBH
369. s in each run once per timestep However at the end of the run for parameter file A 100 virtual years will have passed while for parameter file B 500 years will have passed The forests at the end of each of the two runs would probably look quite different There is of course a tradeoff When a timestep is more than one year long behaviors do their best to approximate what happens in those successive years They can only do that based on the model state at the beginning of the timestep without knowing how things might change from year to year because of other behaviors Depending on the simulation this approximation might create results that are very different from the results that would have come from a single year timestep simulation Choosing a timestep length A one year timestep is the default choice because it makes sure that SORTIE can model short term interactions directly instead of approximating them There are two main reasons for choosing a multi year timestep shortening processing time for runs that are otherwise unreasonably long and using parameters that have been estimated for multiple years and cannot easily be rescaled That second reason can only apply in rare situations since most behaviors require parameters scaled to one year even when a multi year timestep is being used Study the documentation for each behavior you want to use In some cases behaviors insist on a particular timestep length to ensure proper f
370. s is the bath seed rain term Set this value to zero to turn off bath non spatial seed rain The slope of the non spatial seed rain function This is the basal area dependent seed rain term Set this value to zero to turn off basal area dependent non spatial seed rain The minimum DBH at which a tree can reproduce This value does not have to match the Minimum adult DBH The distribution method to be applied to seeds randomization The forms for these functions can be found here Choices are e Deterministic no randomization e Poisson use the number of seeds as the mean in a Poisson probability distribution function e Normal use the number of seeds as the mean in a normal probability distribution function You must then supply a standard deviation for the function e Lognormal use the number of seeds as the mean in a lognormal probability distribution function You must then supply a standard deviation for the function e Negative binomial use the number of seeds as the mean in a negative binomial probability distribution function You must then supply a clumping parameter If you have chosen the negative binomial probability distribution function for Seed distribution this is the clumping parameter of the function in seeds per m If you have not chosen that PDFs then this parameter is not required If you have chosen the normal or lognormal probability distribution functions for Seed distribution this is
371. s the annual post harvest risk of windthrow e py is the Post Harvest Skid Mort Windthrow Harvest Basic Prob parameter e oy is the Post Harvest Skid Mort Windthrow Size Effect parameter e DBH is the tree s DBH in cm e Ky 1s the Post Harvest Skid Mort Windthrow Intensity Effect parameter e mis the harvest intensity from the tree s HarvInten data member from the HARP external harvesting program available for download from the SORTIE web site e is the Post Harvest Skid Mort Windthrow Crowding Effect parameter e BA is the neighborhood basal area in sq m per ha within a radius set by the Post Harvest Skid Mort Crowding Effect Radius parameter e ty is the Post Harvest Skid Mort Windthrow Harvest Rate Param parameter e His the number of timesteps since the last harvest in this tree s grid cell e tis the number of years per timestep e is the Post Harvest Skid Mort Windthrow Background Prob parameter and Si Ps tks m o s BA exp ts H t i where e Siis the annual postharvest risk of standing death e sis the Post Harvest Skid Mort Snag Recruitment Basic Prob parameter e x is the Post Harvest Skid Mort Snag Recruitment Skidding Effect parameter e mis the harvest intensity from the tree s HarvInten data member from the HARP external harvesting program available for download from the SORTIE web site e sis the Post Harvest Skid Mort Snag Recruitment Crowding Effect parameter e BA is the neighborhood
372. scription lt th Partitioned DBH Biomass Bole The slope in the linear biomass equation for boles Slope a Partitioned DBH Biomass Bole The intercept in the linear biomass equation for boles Intercept b Partitioned DBH Biomass Branch The slope in the linear biomass equation for branches Slope a Partitioned DBH The intercept in the linear biomass equation for branches Biomass Branch Intercept b Partitioned DBH Biomass Leaf The slope in the linear biomass equation for leaves Slope a Partitioned DBH Biomass Leaf The intercept in the linear biomass equation for leaves Intercept b How it works Biomass is calculated in exactly the same way and using the same parameters as for the Partitioned DBH Biomass behavior except it only calculates the biomass of those trees killed by the Storm damage killer behavior How to apply it Apply this behavior to saplings adults or snags of any species This behavior does not automatically create output Once you have added this behavior to your run the Detailed output grid setup window will list the Storm Killed Partitioned Biomass grid You can then view the contents of this grid as a table using SORTIE s data visualization system Storm Killed Partitioned Height Biomass This behavior calculates biomass of trees killed in storms as a linear function of tree height partitioned into leaf and bole biomass Parameters for this behavior Paramete
373. ses the accuracy of the calculations Setting this to a larger value increases the speed at which the calculations are made The total tree s volume is the sum of the volumes of each of the segments Any segments whose beginning or ending diameter is less than the value in the Minimum Trunk Diameter for Volume Calculations in cm parameter are not included in the volume total The volume of a tree trunk segment is found as follows V A Az2 2 1 where e A is the cross sectional area at the bottom of the trunk segment in square meters e Ap is the cross sectional area at the top of the trunk segment in square meters e Vis the volume of the trunk segment in cubic meters e Lis the length of the trunk segment value in the Trunk Segment Length for Volume Calculations in m parameter The cross sectional area of a tree trunk at a particular point above the ground such as at the beginning or end of a trunk segment is calculated as A n d 2 where A is the cross sectional area in square meters and d is the diameter of the tree inside the bark at that height in meters To find the diameter of the tree trunk inside the bark at a particular height above the ground the taper equation is used This equation comes from Kozak 2004 Forest Chronicle 80 507 515 it s the 2002 model The equation is rl d aq D ay H ay Y h Zz h 1 ga i hA thy 1 i D t H th A a to i p where X 1 hi H
374. set to either Normal or Lognormal this is the standard deviation used when randomizing Stochastic Pattern Damage Distribution Storm Damage Application Storm Storm Cyclicity Sine Curve d Storm Storm Cyclicity Sine Curve f Storm Storm Cyclicity Sine Curve 8 Storm Storm Cyclicity Trend Function Intercept i Storm Storm Cyclicity Trend Function Slope m How it works storm severity across the plot This parameter is ignored if the Storm Damage Application parameter is not set to Stochastic and the Stochastic Pattern Damage Distribution is not set to either Normal or Lognormal If the Storm Damage Application parameter is set to Stochastic this is the probability distribution function to use for randomizing storm severity across the plot This parameter is ignored if the Storm Damage Application parameter is not set to Stochastic How storm damage is applied to different locations across the plot If Deterministic the storm s severity is applied equally to all locations If Stochastic the storm s severity is randomized across the plot according to your chosen probability distribution function Parameter that controls the cyclicity of storm frequency For no cyclicity set this value to 0 This value is part of the sine curve term and controls the sine amplitude Parameter that controls the cyclicity of storm frequency This value is part of the sine curve term and controls the sine f
375. sion Class 1 but is less than or equal to Light Transmission Upper Age Yrs of Snag Light Transmission Class 2 Expressed as a 0 1 fraction between 0 and 1 If your run does not work with snags you can ignore this Otherwise a value must be provided for all species Fraction of light transmitted through the snag tree crown for each AS species Applies to those snags whose age is greater than Upper Age Amount Canopy oe S Yrs of Snag Light Transmission Class 2 Expressed as a fraction Light Transmission 0 1 between 0 and 1 If your run does not work with snags you can ignore this Otherwise a value must be provided for all species Uprae ecnan cl The upper age limit in years eae the first o can of ee fae Shes ide transmission Snags with an age less than or equal to this age have a light transmission coefficient matching Snag Age Class 1 Light Transmission T issi lass 1 i See eae Coefficient If your run does not work with snags you can ignore this The upper age limit in years defining the second age class of snag light transmission Snags with an age greater than the upper limit for size class 1 but less than or equal to this age have a light transmission coefficient matching Snag Age Class 2 Light Transmission Coefficient Snags with an age greater than this value are in age class three If your run does not work with snags you can ignore this Upper Age Yrs of Snag Light Transmission
376. sions How to apply it This behavior can be applied to seedlings saplings and adults of any species Any tree species type combination to which it is applied must also have a light behavior applied You can use either the diam with auto height or diam only version Relative growth limited to basal area increment How it works This behavior calculates an amount of diameter growth according to the relative growth equation Growth is limited to a maximum of a constant basal area increment The amount of diameter increase is calculated by dividing the annual basal area increment of the tree s species by the diameter of the tree The increment is calculated as described in the Constant basal area growth behavior How to apply it This behavior can be applied to seedlings saplings and adults of any species Any tree species type combination to which it is applied must also have a light behavior applied You can use either the diam with auto height or diam only version Non limited relative growth How it works The amount of increase returned by the relative growth equation is applied to the tree How to apply it This behavior can be applied to seedlings saplings and adults of any species Any tree species type combination to which it is applied must also have a light behavior applied Relative growth height only This behavior uses the Michaelis Menton function to do height growth How it works After the Michaelis Menton func
377. sity Dep Inst Crown Height b Non Spatial Density Dep Inst Crown Height c Non Spatial Density Dep Inst Crown Height d Description The a term in the instrumental crown depth equation used to calculate crown radius The b term in the instrumental crown depth equation used to calculate crown radius The c term in the instrumental crown depth equation used to calculate crown radius The d term in the instrumental crown depth equation used to calculate crown radius Non Spatial Density Dep Inst Crown Height e Non Spatial Density Dep Inst Crown Height f Non Spatial Density Dep Inst Crown Height g Non Spatial Density Dep Inst Crown Height h Non Spatial Density Dep Inst Crown Height i Non Spatial Density Dep Inst Crown Height j Non Spatial Exp Density Dep Crown Radius D1 Non Spatial Exp Density Dep Crown Radius a Non Spatial Exp Density Dep Crown Radius b Non Spatial Exp Density Dep Crown Radius c Non Spatial Exp Density Dep Crown Radius d Non Spatial Exp Density Dep Crown Radius e Non Spatial Exp The e term in the instrumental crown depth equation used to calculate crown radius The f term in the instrumental crown depth equation used to calculate crown radius The g term in the instrumental crown depth equation used to calculate crown radius The h term in the instrumental crown depth equation used
378. sperse behavior applied as well as the Functional response seed predation behavior linked This behavior should be placed after that behavior in the ordered list of model behaviors In order to make results more verifiable Neighborhood Seed Predation produces a grid called Neighborhood Seed Predation This grid stores the pre predation seed rain and amount of seeds eaten for each cell in the Dispersed Seeds grid This grid has no effect on calculations but can be saved in the output file for review Establishment behaviors Establishment behaviors assess seed survival and create new seedlings from seeds Establishment behaviors do not create or distribute the seeds The Disperse behaviors perform that function The seed survival behaviors act to reduce the number of seeds based on various environmental effects They can be used alone or in combination Once they have completed their work the number of surviving seeds can be turned into seedlings by either the Seed Establishment or Establishment with Microtopography behaviors Behavior Description Conspecific Tree Density Dependent Seed Survival Assesses seed survival as a function of the local density of conspecific trees Density Dependent Seed Assesses seed survival as a function of the local density of conspecific seeds Survival Establishment with Microtopography Simulates microtopography in the plot and assigns new seedlings a rooting height as a funct
379. ss Scheduled storms You can also schedule storms to occur at certain timesteps Use the Edit Scheduled Storms window to do this You specify the year NOT the timestep you want the storm to occur and a minimum and maximum severity for each The actual storm severity will be a random number between the maximum and minimum You can schedule as many as you want including multiple storms per timestep If there is also a storm regime present non zero values for the return intervals those storms can also occur The storm regime storms can also happen between scheduled storms If a storm occurs the behavior calculates the amount of damage that occurs A storm s damage index severity is randomly chosen within the boundaries of its severity class The damage is stored in a grid called Storm Damage The final output of the behavior is a map of storm damage severity across the plot as an index between 0 and 1 If multiple storms occur each storm s severity is recorded separately The way storm damage is calculated depends on two things the pattern of storm susceptibility across the plot entered in the Plot Storm Susceptibility Pattern parameter and the method of storm damage application entered in the Storm Damage Application parameter Storm susceptibility is measured on a scale from 0 not susceptible to damage to gt 1 highly susceptible to damage The pattern of storm susceptibility can be either Uniform meaning all locations w
380. st Day of Growing Season Amount Canopy Light Transmission 0 1 Snag Age Class 1 Amount Canopy Light Transmission 0 1 Snag Age Class 2 Amount Canopy Light Transmission 0 1 Snag Age Class 3 Amount Canopy Light Transmission 0 1 Upper Age Yrs of Snag Light Transmission Class 1 Upper Age Yrs of Snag Light Transmission Class 2 Description The fraction of total solar radiation that is direct beam radiation as opposed to diffuse Expressed as a value between 0 and 1 Used to determine the amount of solar radiation seen at the plot location The first day of the growing season as a Julian day number between 1 and 365 Trees only get light during the growing season The last day of the growing season as a Julian day number between 1 and 365 Trees only get light during the growing season Fraction of light transmitted through the tree crown for each species Expressed as a fraction between 0 and 1 A value must be provided for all species even if they don t all use light Fraction of light transmitted through the snag tree crown for each species Applies to those snags whose age is less than or equal to Upper Age Yrs of Snag Light Transmission Class 1 Expressed as a fraction between 0 and 1 If your run does not work with snags you can ignore this Otherwise a value must be provided for all species Fraction of light transmitted through the snag tree crown for each species Applies to t
381. st Harvest Skid Mort Windthrow Harvest Basic Prob Post Harvest Skid Mort Windthrow Harvest Rate Param Post Harvest Skid Mort Windthrow Intensity Effect Post Harvest Skid Mort Windthrow Size Effect How it works The effect of neighborhood basal area on standing death probability Determines how quickly the effects of harvesting on standing death probability taper off Effect of harvest intensity on postharvest probability of standing death Annual postharvest risk of windthrow after harvest effects have completely tapered off The effect of neighborhood basal area on windthrow probability Basic annual probability for windthrow after a harvest Determines how quickly the effects of harvesting on windthrow probability taper off Intensity effect parameter used for determining risk of windthrow Size effect term when determining risk of windthrow If no harvest has occurred yet in this run the probability of dying in a timestep is Prob 1 1 B where e Prob is the probability of dying before the end of the timestep e fis the Post Harvest Skid Mort Pre Harvest Background Mort Rate parameter e tis the number of years per timestep If a harvest has occurred in the tree s cell during the run the probability of mortality is Prob 1 1 W S i multiplying over years i 1 t number of years per timestep Wi p w w DBH ky m ny BA exp ty H t i where e Wii
382. t or b parameter in the power function for the height Exponent b diameter relationship The power diam height function is height a dio 4 where height is tree height in m ais the Power Function a parameter b is the Power Function Exponent b parameter djo is diameter at 10 cm in cm Setting up trees parameters Here is the complete list of parameters for the tree population and allometry Not all of them are required Tree parameters Parameters dealing with tree initial conditions none of these are required Initial Densities The density of trees in number per hectare for that size class Initial Density ha Seedling Height Class 1 Number of seedlings per hectare to create in the first seedling height class The lower bound of this class is 0 cm and the upper bound is the value in the Seedling Height Class 1 Upper Bound in cm parameter Initial Density ha Seedling Height Class 2 Number of seedlings per hectare to create in the second seedling height class The lower bound of this class is the value in the Seedling Height Class 1 Upper Bound in cm parameter and the upper bound is the value in the Seedling Height Class 2 Upper Bound in cm parameter Initial Density ha Seedling Height Class 3 Number of seedlings per hectare to create in the third seedling height class The lower bound of this class is the value in the Seedling Height Class 2 Upper Bound in cm parameter and the upper bound
383. t event as a value between 0 and 1 This is not required if the Harvest behavior is not used The proportion of substrate that is tip up mounds substrate in areas that had a partial cut harvest event as a value between 0 and 1 This is not required if the Harvest behavior is not used The proportion of substrate that is scarified soil in areas that had a partial cut harvest event as a value between 0 and 1 This is not required if the Harvest behavior is not used The proportion of substrate that is tip up mounds substrate in areas that had a partial cut harvest event as a value between 0 and 1 This is not required if the Harvest behavior is not used The proportion of the total number of newly dead trees that fall each year as a value between 0 and 1 This does not apply to snags The proportion of fallen trees that uproot to create new tip up mound substrate as a value between 0 and 1 The fixed proportion of the forest floor litter moss pool that is moss Expressed as a value between 0 and 1 Proportion of Snags that Uproot Proportion of Fallen that Uproot Proportion of Forest Floor Litter Moss Pool that is Moss Proportion of Snags that Uproot Scarified Soil Annual Decay Alpha Scarified Soil Annual Decay Beta Tip Up Mounds Annual Decay Alpha Tip Up Mounds Annual Decay Beta Uprooted Tree Radius Increase Factor for Root Rip Out Use Directional Tree Fall How it works The proportion o
384. t growth as a function of GLI Calculates either diameter or height growth as a logistic function of GLI Calculates either diameter or height growth as a function of tree size and GLI Increments growth according to a lognormal equation with the possibility of two sets of parameters for each species one for high light conditions and one for low light conditions Calculates either diameter or height growth as a function of tree size and GLI Uses a modified Michaelis Menton function to do height growth You can optionally add autocorrelation and a degree of stochasticity to the growth Uses a modified Michaelis Menton function to do height growth Uses multiple effects including neighbor competitiveness to calculate growth rates Uses a power function to do height growth Combines a deterministic growth function for small trees with completely stochastic growth for larger trees It s meant to be used when a species uses a height growth behavior as the primary growth method Increments growth according to two possible growth equations one to be used in low light conditions and the other to be used in high light conditions This behavior was originally created for the Puerto Rico model height Relative growth limited to radial increment Relative growth limited to basal area increment Non limited relative growth Relative growth height only Stochastic gap growth Weibull climate growth Weibull cl
385. t to mortality All trees with a relative increment greater than or equal to max will live How to apply it This behavior can be applied to saplings and adults of any species It cannot be applied to seedlings Any tree species type combination to which it is applied must also have NCI growth This behavior can only be applied with a one year timestep Density Self Thinning Mortality This behavior calculates the probability of mortality of an individual juvenile tree as a function of the density and mean diameter of the neighborhood trees Only neighborhood seedlings and saplings are taken into account in this behavior Trees killed by this behavior will have a mortality reason code of natural Parameters for this behavior Parameter name Description Density Self Thinning Asymptote The asymptote of the density self thinning function A Density Self Thinning Density Effect S The parameter controlling the density effect of the density self thinning function Density Self Ta The parameter controlling the effect of neighbor mean diameter of the density self thinning function Effect C Density Bele The minimum density of neighbors in stems ha for density self thinning Thinning Minimum 4 f mortality A tree with a lower density of neighbors than this value will Density for Mortality ee ha l Density Self Thinning The maximum radius in m within which to search for neighbors to Neighborhood calc
386. tailed Substrate behavior Tip up mounds Scarified soil Decay class 5 logs l i 10 Forest floor Like in Substrate decay among the log decay classes and for tip up mounds and scarified soil relationships 1 5 7 and 9 is a function of substrate age according to the equation where t is time in years since the last decay transition Decay calculations for the 5 log decay classes are performed on an annual basis so it is possible to advance by more than one decay class in a single multi year timestep At the end of each timestep the age of all logs is rounded to the nearest multiple of the timestep duration This is necessary to keep memory requirements manageable Log substrate is created by the processes of tree fall and breakage along the bole relationship 6 Detailed Substrate looks at flags set by mortality and snag dynamics behaviors to determine whether a sapling adult tree or snag has either fallen or broken to a certain height in the current timestep If so it adds the appropriate area to the log substrate pool Like in Substrate tree boles are modeled as cones The projected horizontal area is therefore a triangle if the top of the tree is included or a trapezoid if only considering the lower section of a tree New log substrate does not need to enter in decay class 1 the Prop Live Trees Entering Decay Class X 0 1 and Prop Snags Entering Decay Class X 0 1 parameters determine the probabilit
387. tailed output file for analysis Tree Volume Calculator This behavior calculates the volume of tree trunks It can be used to find both merchantable volume and total volume Make sure to distinguish between this behavior and the other tree volume behavior Parameters for this behavior Parameter name Description Taper Equation HRAell Suen CO The ay parameter in the taper equation below Taper Equation DBH Exponent al The a parameter in the taper equation below Taper Equation Height Exponent The az parameter in the taper equation below a2 Se rae The b parameter in the taper equation below eee see The bz parameter in the taper equation below paneer 5 ree The b3 parameter in the taper equation below eee ie The b4 parameter in the taper equation below Taper Equation X SGT SOS The bs parameter in the taper equation below Taper Equation X Exponent 6 b6 Diameter Outside Bark Constant al Diameter Outside Bark First Degree Parameter a2 Diameter Outside Bark Second Degree Parameter a3 Height to Begin Calculating Trunk Volume in cm Minimum Trunk Diameter for Volume Calculations in cm Trunk Segment Length for Volume Calculations in m How it works The be parameter in the taper equation below The a parameter in the equation for calculating tree diameter outside bark below The az parameter in the equation for calculating tree diameter outside bark below The a3 par
388. te behavior that primarily E incorporates greater detail in tracking log cover Substrate This behavior keeps track of six kinds of substrate forest floor litter forest floor moss scarified soil tip up mounds decayed logs and fresh logs Forest floor litter and forest floor moss form a common pool in fixed relative proportion to each other These six substrates form a cycle Fresh logs decay into decayed logs Decayed logs scarified soil and tip up mounds decay into forest floor litter and moss If no new substrate were created eventually the whole forest would be uniformly covered in forest floor substrate The creation of new substrate decreases the amount of forest floor litter and moss and starts the process over again There are two ways in which new substrate is added harvest treatments and tree fall Each kind of harvest treatment partial cut gap cut and clear cut has its own substrate signature which you set in the parameters The existing substrate proportions after a harvest are erased and replaced with this signature The other type of substrate change event tree fall allows SORTIE to account for small scale dynamics by allowing some dead trees to fall and create tip up mounds When a live tree dies there is a certain probability that the tree will fall at death to create new fresh log substrate Snags marked as dead always contribute new fresh log substrate For both dead snags and live trees there is a certain prob
389. ter c of the Chapman Richards crown radius equation The Chapman Richards equation for calculating crown radius is where rad i a 1 e PBR e radis the crown radius in meters e DBH is the tree s DBH in cm e iis the Chapman Richards Crown Radius Intercept parameter which represents the crown radius of the smallest possible sapling e ais the Chapman Richards Asymptotic Crown Radius parameter e bis the Chapman Richards Crown Radius Shape 1 b parameter e cis the Chapman Richards Crown Radius Shape 2 c parameter The Chapman Richards equation for calculating crown depth is where cheiva l e y e chis the distance from the top to the bottom of the crown cylinder in meters e His the tree s height in m e iis the Chapman Richards Crown Height Intercept parameter which represents the crown depth of the smallest possible sapling e ais the Chapman Richards Asymptotic Crown Height parameter e bis the Chapman Richards Crown Height Shape 1 b parameter e cis the Chapman Richards Crown Height Shape 2 c parameter The non spatial density dependent crown depth and radius relationships The density dependent equations for crown radius and crown depth use non spatial measures of density to influence crown radius and crown depth Density is measured across the plot as a whole not locally thus non spatial Crown Radius Parameters Parameter name Non Spatial Density Dep Inst Crown Height a Non Spatial Den
390. ter e bis the Masting Disperse Masting CDF b parameter When the run starts it is assumed a masting last event took place in timestep 1 A random number is used to determine whether a mast occurs in the current timestep Disperse happens the same way in mast and non mast timesteps but the parameters used are different Species may be organized into groups to create synchrony in masting The Masting Disperse Masting Group parameter allows you to assign group numbers to species The actual value of the group number is not important It only matters if more than one species has the same number If one species in a group masts all species in that group do Each group s mast decision is made separately so sometimes more than one group may mast at a time If all species have a different group number then they all mast independently of one another Which trees disperse Of the group of trees eligible to disperse those with DBHs above the value in the Minimum DBH for Reproduction in cm parameter some can be randomly selected to participate in disperse The proportion dispersing is set in Masting Disperse Mast Proportion Participating 0 1 for mast timesteps and Masting Disperse Non Mast Proportion Participating 0 1 for non mast timesteps The group of trees participating is chosen again each timestep No adjustment is made to the number of seeds produced per tree Fewer trees participating in disperse means fewer total seeds will be pro
391. th approaches Time Since Harvest the potential growth after a harvest Rate Param How it works A tree s potential growth is calculated by PARG a exp DBH exp n BA exp w DBH where e PARG is potential annual radial growth mm y e DBH isin cm e PA is the basal area in sq m of adult trees within the distance given in the Post Harvest Growth NCI Distance m parameter e ais the Post Harvest Growth Max Growth Constant parameter the maximum radial growth in millimeters per year e ois the Post Harvest Growth DBH Growth Effect parameter e 7 is the Post Harvest Growth NCI Constant parameter e q is the Post Harvest Growth DBH NCI Effect parameter If no harvest has occurred yet in this run then the tree s actual growth ARG equals PARG If a harvest has occurred at some point during this run then ARG is calculated by ARG ARGpre PARG ARGpre 1 exp t H t where e ARG is annual radial growth mm y for the current timestep e ARGpre is annual radial growth for the last timestep prior to harvest e His the number of timesteps since the last harvest e tis the number of years per timestep e tis the Post Harvest Growth Time Since Harvest Rate Param parameter Annual radial growth ARG is used to calculate timestep diameter growth using DG ARG t 2 10 where is the number of years per timestep Model forms are based on those in Thorpe et al 2010 How to apply it This beh
392. than or equal to 1 This is not required if the Harvest behavior is not used For the initial conditions the proportion of substrate area that is large logs of species group X decay class Y All initial conditions values added together must be less than or equal to 1 For the initial conditions the proportion of substrate area that is small logs of species group X decay class Y All initial conditions values added together must be less than or equal to 1 The a exponent in the decay equation as applied to large logs of species group X decay class Y This value must be a negative number The a exponent in the decay equation as applied to small logs of species Small Class Y Log Decay Alpha Species Group X Large Class Y Log Decay Beta Species Group X Small Class Y Log Decay Beta Species Group X Large Class Y Partial Cut Log 0 1 Species Group X Small Class Y Partial Cut Log 0 1 Tip Up Mounds Annual Decay Alpha Tip Up Mounds Annual Decay Beta Uprooted Tree Radius Increase Factor for Root Rip Out Use Directional Tree Fall How it works group X decay class Y This value must be a negative number The B exponent in the decay equation as applied to large logs of species group X decay class Y The B exponent in the decay equation as applied to small logs of species group X decay class Y After a partial cut harvest the proportion of substrate area that is large logs of species group X decay
393. the Harvest behavior is not used The proportion of substrate that is tip up mounds substrate in areas that had a clear cut harvest event as a value between 0 and 1 This is not required if the Harvest behavior is not used hea ras The a exponent in the decay equation logs Note that this is annual decay as applied to decayed 2 ras The B exponent in the decay equation logs Note that this is annual decay as applied to decayed ras The a exponent in the decay equation logs Note that this is annual decay as applied to fresh Th ay ee P xp Be le e B exponent in the decay equation logs Note that this is annual decay as applied to fresh The proportion of substrate that is decayed logs in areas that had a gap cut harvest event as a value between 0 and 1 This is not required if the Harvest behavior is not used The proportion of substrate that is fresh logs in areas that had a gap cut harvest event as a value between 0 and 1 This is not required if the Harvest behavior is not used The proportion of substrate that is scarified soil in areas that had a gap cut harvest event as a value between 0 and 1 This is not required if the Harvest behavior is not used The proportion of substrate that is tip up mounds substrate in areas that had a gap cut harvest event as a value between 0 and 1 This is not required if the Harvest behavior is not used The proportion of
394. the detailed output file e The Plot dimensions must be the same e Each map that you want to use must make sense as a complete dataset For instance you cannot do a run with a tree map in which you have saved the X coordinates of trees but not the Y coordinates e If any behavior specific data was saved for trees those same behaviors must be enabled for the current run For more see the tree data member list topic The detailed output file can be used to completely save the state of the model If your detailed output file saves everything you could start a new analysis using any timestep of a previous analysis as the starting point In order to save a complete detailed output file use the Save Everything button on the Setup detailed output file window To load a detailed output file as initial conditions first load the parameter file Then using File gt Open File choose the detailed output file A window will open showing the sub files within the detailed output file one per timestep Double click the timestep you want to load You can either replace existing data or add to it If you choose to add data if an existing tree map is loaded those trees will be combined with the new tree map Grid values will be overwritten either way If you don t want to use all the maps you can erase those for individual grids and trees using the Edit menu options Grid layer setup and Manage tree maps Loading and displaying data from an
395. the current timestep for the given species Cut Basal Area species x Total basal area cut in the current timestep for the given species DetailedSubstrate Grid This grid is created by the Detailed Substrate behavior The grid holds the relative proportions of the various substrate types If the Harvest behavior is present for the run then this grid s resolution must match the Harvest Results grid Otherwise it defaults to a cell resolution of 8 m X 8 m which you can change This grid holds packages with a different data structure from the main grid to track Substrate cohorts Data in the grid Data member name Description Proportion of scarified soil The proportion of the grid cell area that is scarified soil Proportion of forest floor The proportion of the grid cell area that is forest floor Propor on o BPP The proportion of the grid cell area that is tip up mounds mounds Teel Lay Total logs expressed as a proportion between 0 and 1 The sum of all log proportions Total Log Volume Total log volume in m3 per ha The sum of all log volumes Prop Sp Group X Small Species group X decay class Y small logs as a proportion Decay Y between 0 and 1 Prop Sp Group X Large Species group X decay class Y large logs as a proportion between Decay Y O and 1 Vol Sp Group X Small Decay Y Vol Sp Group X Large Decay Y Packages Data member name Substrate cohort age Species group X decay class Y small log volume in m3 per ha
396. the number of seeds as the mean in a negative binomial probability distribution function You must then supply a clumping parameter If you have chosen the negative binomial probability distribution function for Seed distribution this is the clumping parameter of the function in seeds per m If you have not chosen that PDFs then this parameter is not required If you have chosen the normal or lognormal probability distribution functions for Seed distribution this is the standard deviation of the function in seeds per m If you have not chosen these PDFs then this parameter is not required The dispersal value for the Weibull function under canopy conditions or Weibull Canopy under non masting conditions in the case of Masting spatial disperse see Dispersal equation below This is only required if the canopy probability distribution function is Weibull The 9 for the Weibull function under canopy conditions or under non Weibull Canopy masting conditions in the case of Masting spatial disperse see equation Theta below This is only required if the canopy probability distribution function is Weibull How it works Deciding when to mast For each timestep the probability of masting for each species is calculated from the following cumulative distribution function l De E 1 A a where e yis the probability of masting e Xis the number of years since last mast e ais the Masting Disperse Masting CDF a parame
397. the probability of a seedling rooting in that location e Height is the height of the dead substrate tree in m e GLI is the light level 0 100 taken at the trunk of the substrate tree halfway between the ground and the bottom of the crown e ais the Tree Fern Establishment Seedling Prob a parameter e bis the Tree Fern Establishment Seedling Prob b parameter eae e cis the Tree Fern Establishment Seedling Prob c parameter The GLI is calculated from the forest as it is at the tree s death this may be different from any GLI value calculated at the beginning of the timestep since growth will have occurred The substrate tree itself is not yet a snag if snags are used in the run so it will cast shade as a living tree would SORTIE uses a random number to decide whether a new seedling will root based on this probability If a seedling does root its height is HS m n Height where e HSis the seedling height in cm e Height is the height of the dead substrate tree in m e mis the Tree Fern Establishment Seedling Height m parameter ee e nis the Tree Fern Establishment Seedling Height n parameter The seedling s location is exactly the same as that of the dead substrate tree Its diameter is calculated from its height using the appropriate allometric function It is not forced to be a seedling if its height is tall enough to become a sapling this is allowed This behavior does nothing further to the dead substrate tr
398. ther medium or heavy e a is the storm damage intercept for that tree s species for that damage category either the Storm Damage Intercept a for Medium Damage parameter or the Storm Damage Intercept a for Heavy Damage parameter e bis the Storm Intensity Coefficient b parameter for that tree s species e cis the storm s severity at the tree s location between 0 and 1 as calculated by the Storm disturbance behavior e dis the Storm DBH Coefficient d parameter for that tree s species This behavior uses a random number to determine what damage category a tree falls in If the random number is less than the probability for medium damage the tree is undamaged If the random number is greater than the probability for medium damage but less than the probability for heavy damage the tree gets medium damage If the random number is greater than the probability for heavy damage the tree gets heavy damage If a tree is damaged a counter is set for time since damage This behavior checks this counter every timestep When the amount of time specified in the Number of Years Damaged Trees Take to Heal has passed the tree is considered healed and no longer has a record of storm damage If a damaged tree is damaged again in a new storm it gets the most severe damage category that can apply to it and must go through the maximum healing time again in order to become undamaged How to apply it Apply this behavior to the trees that can receive stor
399. ther the diam with auto height or diam only version Relative growth limited to basal area increment How it works This behavior calculates an amount of diameter growth according to the relative growth equation Growth is limited to a maximum of a constant basal area increment The amount of diameter increase is calculated by dividing the annual basal area increment of the tree s species by the diameter of the tree The increment is calculated as described in the Constant basal area growth behavior How to apply it This behavior can be applied to seedlings saplings and adults of any species Any tree species type combination to which it is applied must also have a light behavior applied You can use either the diam with auto height or diam only version Non limited relative growth How it works The amount of increase returned by the relative growth equation is applied to the tree How to apply it This behavior can be applied to seedlings saplings and adults of any species Any tree species type combination to which it is applied must also have a light behavior applied Relative growth height only This behavior uses the Michaelis Menton function to do height growth How it works After the Michaelis Menton function is used to calculate Y as described in the section above the amount of height growth is calculated as G Y Height where e Gis the amount of height growth for one year in cm e Height is the height of th
400. there is a message bar that will keep you updated on the number of timesteps completed If you would like to know what is happening in the run you can open output files while the run is still in progress Interrupting and restarting a run You can pause or stop a run that is in progress Either use the buttons or the menu options in the Run menu When either option is chosen SORTIE will finish the current timestep before stopping or pausing This ensures that output files will be complete and valid Closing the SORTIE window will force a quit but the output may be unrecoverable in that case The difference between pausing and stopping is that a paused run can be restarted using the run command but a stopped run cannot Batch runs SORTIE ND can do simulations one at a time or in groups A group of simulations is a batch run A batch run consists of simulations performed on one or more parameter files with each parameter file running one or more times Setting up a batch run A batch run is defined using a batch file You work with batch files using the Batch file setup window A batch file is an XML file which lists a set of parameter files to run and the number of times to run each file Before you begin a batch run prepare all of your parameter files Save them all to an appropriate place If you are saving output in your parameter files make sure that the directory ies that the output will be written to already exist It doesn
401. they survive it this behavior will not try to kill them again even if they are still damaged A certain proportion of heavily damaged trees that die create tip ups The probability of this is in the parameter Storm Prop Heavy Damage Dead Trees that Tip Up If snags are used in this run those trees that die in either damage category except for tip ups become snags A time since damage counter is set for each of these snags After the amount of time specified in the Number of Years Storm Damaged Snags Last has passed this behavior will remove those snags killing them They are not available for later processes such as substrate This behavior will not do anything to any snag that it did not kill If snags are not used in this run trees that die have a flag set indicating that they are dead They are available during the timestep in which they die to substrate and other processes in exactly the same manner as trees that die due to natural mortality They will be subject to the same cleanup and removal processes as well If a heavily damaged dead tree tips up and snags are used in the run the tip up becomes a snag that has its dead flag set to true It is available during the timestep in which it dies to substrate and other processes in exactly the same manner as other snags that die due to natural mortality It is subject to the same cleanup and removal processes as well If snags are not used in the run then tip ups are treated like all ot
402. thod to be applied to seeds randomization The forms for these functions can be found here Choices are e Deterministic no randomization Seed Distribution e Poisson use the number of seeds as the mean in a Poisson probability distribution function e Normal use the number of seeds as the mean in a normal probability distribution function You must then supply a standard deviation for the function Seed Dist Clumping Parameter Neg Binomial Seed Dist Std Deviation Normal or Lognormal Temp Dep Neigh Disperse A Temp Dep Neigh Disperse B Temp Dep Neigh Disperse M Temp Dep Neigh Disperse N Temp Dep Neigh Disperse Max Distance for Conspecific Adults m Temp Dep Neigh Disperse Presence B Temp Dep Neigh Disperse Presence M Temp Dep Neigh Disperse Presence Threshold 0 1 e Lognormal use the number of seeds as the mean in a lognormal probability distribution function You must then supply a standard deviation for the function e Negative binomial use the number of seeds as the mean in a negative binomial probability distribution function You must then supply a clumping parameter If you have chosen the negative binomial probability distribution function for Seed distribution this is the clumping parameter of the function in seeds per m If you have not chosen that PDFs then this parameter is not required If you have chosen the normal or lognormal probability distr
403. ting a parameter file This topic covers creating a parameter file from scratch To make a basic parameter file you need to define the tree population choose the list of behaviors that will run and enter parameter values for your file You can save your work at any point in the process and come back to it later Setting up the tree population You can use the File menu and choose the option New parameter file for a short wizard that will get you started First you will see the Edit species list window Enter a list of tree species You can always come back to this window to edit the list later by choosing Edit gt Tree setup Setting up the behavior list After you have entered a species list the wizard will take you to the Edit simulation flow window so you can set up the list of behaviors for your run You can approach this from either the tree perspective by setting up the list of behaviors for each tree type or from the behavior perspective by starting with a list of behaviors and assigning each to specific groups of trees See the link above for detailed instructions on choosing behaviors Again you can always come back to this window to make changes by choosing the menu option Edit gt Model flow At this point the new parameter file wizard ends Setting parameter values You must complete the steps above before you can edit parameters because it is the tree population and the list of behaviors that defines what parameters a
404. ting snags Fall probability is a function of tree size decay class neighborhood basal area and recent harvest activity Trees and snags that do not fall are run through a snag decay class transition matrix Model forms are based on those in Vanderwel et al 2006 Parameters for this behavior Parameter name Description Snag Decay Class Dynamics Snag Fall Snag fall alpha parameter Alpha Snag Decay Class Dynamics Snag Fall Snag fall beta parameter Beta Snag Decay Class Dynamics Snag Fall Snag fall eta parameter Eta Snag Decay Class Pon Snes Fell Snag fall gamma 2 parameter Gamma 2 Snag Decay Class Dynamics Snag Fall Gamma 3 Snag Decay Class Dynamics Snag Fall Gamma 4 Snag Decay Class Dynamics Snag Fall Gamma 5 Snag Decay Class Dynamics Snag Fall Kappa Snag Decay Class Dynamics Snag Fall Zeta Snag Decay Class Dynamics Tree Fall Alpha Snag Decay Class Dynamics Tree Fall Beta Snag Decay Class Dynamics Tree Fall Delta Snag Decay Class Dynamics Tree Fall Iota Snag Decay Class Dynamics Tree Fall Lambda Snag Decay Class Dynamics Tree Fall Theta Snag Decay Class Dynamics Live To Class 1 Prob 0 1 Snag fall gamma 3 parameter Snag fall gamma 4 parameter Snag fall gamma 5 parameter Snag fall kappa parameter Snag fall zeta parameter Tree fall alpha parameter Tree fall beta parameter Tree fall delta parameter Tree fall iota parameter Tree fall lamb
405. tion General light parameters used by this behavior Parameter name Beam Fraction of Global Radiation Clear Sky Transmission Coefficient First Day of Growing Season Last Day of Growing Season Amount Canopy Description The fraction of total solar radiation that is direct beam radiation as opposed to diffuse Expressed as a value between 0 and 1 Used to determine the amount of solar radiation seen at the plot location The first day of the growing season as a Julian day number between 1 and 365 Trees only get light during the growing season The last day of the growing season as a Julian day number between 1 and 365 Trees only get light during the growing season Fraction of light transmitted through the tree crown for each species Light Transmission 0 1 Snag Age Class 1 Amount Canopy Light Transmission 0 1 Snag Age Class 2 Amount Canopy Light Transmission 0 1 Snag Age Class 3 Amount Canopy Light Transmission 0 1 Upper Age Yrs of Snag Light Transmission Class 1 Upper Age Yrs of Snag Light Transmission Class 2 How it works Expressed as a fraction between 0 and 1 A value must be provided for all species even if they don t all use light Fraction of light transmitted through the snag tree crown for each species Applies to those snags whose age is less than or equal to Upper Age Yrs of Snag Light Transmission Class 1 Expressed as a fraction between 0 and 1
406. tion in millimeters as entered for the Plot Temperature Effect is calculated as we ee oy where e Ais the Weib Clim Quad Growth Temp Effect A parameter e Bis the Weib Clim Quad Growth Temp Effect B parameter e Cis the Weib Clim Quad Growth Temp Effect C parameter e Tis the plot s annual mean temperature in degrees Celsius as entered for the Plot Crowding Effect is calculated as CE exp C ND where e Cis the Weib Clim Quad Growth Competition Effect C parameter e Dis the Weib Clim Quad Growth Competition Effect D parameter e ND is the number of neighbors The ND value is a count of all neighbors with a DBH at least that of the Weib Clim Quad Growth Minimum Neighbor DBH cm parameter out to a maximum distance from the center of the grid cell set in the Weib Clim Quad Growth Max Neighbor Search Radius m parameter The value is a straight count it is not scaled or relativized in any way Seedlings never compete The amount of growth is in cm year For multi year timesteps the annual growth rate is multiplied by the number of years per timestep How to apply it This behavior can be applied to seedlings saplings and adults of any species You can use either the diam with auto height or diam only version Mortality behaviors The mortality behaviors cause tree death due to natural life cycle causes and competition Tree death due to disturbance is covered by other behaviors M
407. tion Effect Crowding Effect Temperature Effect Max Growth is the maximum diameter growth the tree can attain in cm yr entered in the Weibull Climate Growth Max Potential Growth cm yr parameter Size Effect Precipitation Effect Crowding Effect and Temperature Effect are all factors which act to reduce the maximum growth rate and will vary depending on the conditions a tree is in Each of these effects is a value between 0 and 1 Size Effect is calculated with a lognormal function as follows In DBH i a Xb 0 5 SE e where e DBH is of the target tree in cm e Xois the Weibull Climate Growth Size Effect X0 parameter this is the mode of the function expressed in cm e X is the Weibull Climate Growth Size Effect Xb parameter this is the variance of the function expressed in cm You can set a minimum DBH for the size effect in the Weibull Climate Growth Size Effect Minimum DBH parameter Any target tree whose DBH is less than this value will get a size effect based on the minimum DBH instead This allows you to avoid problems with very small trees that can occur because of the shape of the lognormal function Precipitation Effect is calculated as ee ese aay where e Ais the Weibull Climate Growth Precip Effect A parameter e Bis the Weibull Climate Growth Precip Effect B parameter e Cis the Weibull Climate Growth Precip Effect C parameter e Ps the plot s annual precipitat
408. tion is used to calculate Y as described in the section above the amount of height growth is calculated as G Y Height where e Gis the amount of height growth for one year in cm e Height is the height of the tree in cm e Xis the Relative Michaelis Menton Growth Height Exponent parameter If the timestep is more than one year long growth is recalculated for each year of the timestep increasing the height each time How to apply it This behavior can be applied to seedlings saplings and adults of any species Any tree species type combination to which it is applied must also have a light behavior and a diameter growth behavior applied Relative growth behaviors Several behaviors apply a relative growth version of the Michaelis Menton function Parameters for these behaviors Parameter name Adult Constant Area Growth in sq cm yr Adult Constant Radial Growth in mm yr Asymptotic Diameter Growth A Asymptotic Height Growth A Slope of Growth Response S Relative Michaelis Menton Growth Diameter Exponent Description The constant amount of basal area by which to increase a tree s basal area Applies to basal area increment limited behaviors The constant value by which to increase a tree s radius at breast height Applies to radial increment limited growth behaviors Asymptote of the Michaelis Menton growth function at high light function term A below for diameter growth Asymptote of
409. to calculate crown radius The i term in the instrumental crown depth equation used to calculate crown radius The j term in the instrumental crown depth equation used to calculate crown radius The D1 term The a term The b term The c term The d term The e term The f term Density Dep Crown Radius f Crown Depth Parameters Parameter name Non Spatial Density Dep Inst Crown Radius a Non Spatial Density Dep Inst Crown Radius b Non Spatial Density Dep Inst Crown Radius c Non Spatial Density Dep Inst Crown Radius d Non Spatial Density Dep Inst Crown Radius e Non Spatial Density Dep Inst Crown Radius f Non Spatial Density Dep Inst Crown Radius g Non Spatial Density Dep Inst Crown Radius h Non Spatial Density Dep Inst Crown Radius i Non Spatial Density Dep Inst Crown Radius j Description The a term in the instrumental crown radius equation used to calculate crown depth The b term in the instrumental crown radius equation used to calculate crown depth The c term in the instrumental crown radius equation used to calculate crown depth The d term in the instrumental crown radius equation used to calculate crown depth The e term in the instrumental crown radius equation used to calculate crown depth The f term in the instrumental crown radius equation used to calculate crown depth The g term i
410. trees are included in calculations The resulting values are stored in the Relative Neighborhood Density grid How to apply it Add this behavior to your run There is no need to apply it to specific tree species or types Indeed any such specifications will be ignored This behavior does not automatically create output Once you have added this behavior to your run the Detailed output grid setup window will list the Relative Neighborhood Density grid Save all the data members of this grid You can then view the Q values as a line graph and use the graph to save the values as a text file State Reporter This behavior reports the values of state variables How it works Each timestep this behavior retrieves the values of various variables capturing the current base state of SORTIE and stores them in the grid State Variables Currently the only state variables captured are for climate How to apply it Add this behavior to your run This behavior does not automatically create output Once you have added this behavior to your run the Detailed output grid setup window will list the State Variables grid You can then view the contents of this grid as a table using SORTIE s data visualization system Storm Killed Partitioned DBH Biomass This behavior calculates biomass of trees killed in storms as a linear function of DBH partitioned into leaf branch and bole biomass Parameters for this behavior Parameter name De
411. tribution save only DBH for saplings and adults If you want to keep tabs on a type of data but you don t need a lot of detail consider saving this data less often than every timestep Use a summary file to get plotwide information instead of a detailed output file where possible When you are interested in spatial variation such as when you are working with harvest treatments you might wish to get statistics on just one area within the plot You can create subplots in either summary output or detailed output files This is also helpful if you have an extremely large plot but you want a lot of detail In that case the detailed output file can become too large to work with A representative subplot may give you the information you need To study an interesting effect that you wish to be able to reproduce you may want to save a detailed output file that you can use as initial conditions in a subsequent run In this case you would use the Save everything button in the Setup detailed output file window This file is likely to be extremely large but can be very useful As an example you find that around timestep 15 the curve of sapling density curves up sharply in a very unexpected way You want to be able to experiment with the growth parameters at timestep 15 to see if you can find what conditions that curve is sensitive to You could Save everything for a run of 20 or so timesteps You could create a parameter file with new growth parameters
412. ts easily each time you load an output file e SORTIE ND tracks open chart windows at the top of the screen so you can quickly pull up the one you want e A file history in the File menu keeps track of recently opened parameter and output files What s New archive Basic SORTIE modeling concepts SORTIE is an individual based forest simulator designed to study neighborhood processes This means that the trees in the forest are modeled individually not as averages or spatial aggregates Each individual has a location in space SORTIE specializes in modeling the interactions of trees with their nearest neighbors to study local neighborhood dynamics SORTIE state data The basic SORTIE model state is defined by the plot trees and grids The plot is the underlying location in which the simulation takes place It has a particular size and shape and attributes for climate and geographic location The trees are the individuals making up the forest on the plot Grids hold additional data that varies from place to place such as soil chemistry or light level at the forest floor All of these together define the model state at a particular time Behaviors The processes that act to change the model state are called behaviors Behaviors often correspond to biological processes They are individually contained units but often work together to create a complex interacting system For instance a simulation might consist of three behavio
413. ulate neighbor density for density self thinning Radius in m How it works The probability of mortality is calculated with a double Michaelis Menton function 3 A C x diam a dD lt density aS jj A i E x BAM D cr a density where e Pmis the probability of mortality for an individual tree e density is the density of neighboring seedlings and saplings in stems ha within a radius defined in the Density Self Thinning Neighborhood Radius in m parameter e diam mis the mean diameter of neighbors measured 10 cm above root collar in cm e Ais the Density Self Thinning Asymptote A parameter e Cis the Density Self Thinning Diameter Effect C parameter e Sis the Density Self Thinning Density Effect S parameter If the value of density is less than the value in the Density Self Thinning Minimum Density for Mortality ha parameter the tree does not die How to apply it This behavior can be applied to seedlings and saplings of any species It cannot be applied to adults This behavior can only be applied with a one year timestep Exponential Growth and Resource Based Mortality This behavior calculates probability of mortality as a function of growth and some second resource The identity of the second resource is unimportant and could be anything from exchangeable calcium levels to soil moisture Trees killed by this behavior will have a mortality reason code of natural Parameters for th
414. ully These extreme numbers incredibly large or small numbers will crash SORTIE if they happen and cannot be guarded against ahead of time Be very careful when selecting parameters and test your parameters to ensure they produce sensible results for a wide range of tree sizes If you have problems with SORTIE crashing try verifying that this behavior is the problem by removing it from the run and trying again If you can verify that this behavior is the problem carefully re examine your parameters How to apply it Apply this behavior to saplings adults or snags of any species and enter parameters in the Parameter edit window This behavior does not automatically create output Once you have added this behavior to your run the Detailed output setup window for trees will have a tree data member called Tree Volume Add this to your detailed output file to output volume in cubic meters You can then view charts and graphs with the resulting volume data using data visualization on your detailed output file What is a grid A grid is a structure for holding model data that varies across space It contains cells organized by row and column that cover the entire plot Grids are part of the state data of SORTIE Examples of grids are soil fertility substrate storm damage susceptibility maps and number of seeds dispersed A single grid can be set up to hold more than one value per cell In addition packets of information called pack
415. um Neighbor DBH in cm parameter out to a maximum distance set in the Weibull Climate Survival Max Neighbor Search Radius m parameter The value is a straight count it is not scaled or relativized in any way Seedlings never compete The probability of survival is for a single year For multi year timesteps the timestep survival probability is the annual probability raised to the power of the number of years per timestep Once the probability has been calculated a random number is used to determine whether a tree lives or dies How to apply it This behavior can be applied to saplings and adults of any species It cannot be applied to seedlings Weibull snag mortality behavior This behavior controls snag fall Snags are standing dead trees Obviously they can t die again so the word mortality is a bit of a misnomer We call the behavior a mortality behavior because it functionally fits in this behavior class Snags that are killed by this behavior are considered to have fallen over If Substrate behaviors are enabled then these fallen trees are available to become new fresh log substrate Any that are not picked up by substrate will be dealt with by the Dead tree remover behavior Trees killed by this behavior will have a mortality reason code of natural Parameters for this behavior Parameter name Description Weibull Annual a Parameter for Snag Weibull annual a parameter for those trees whose DBH is less th
416. umber of stems per square meter of trees above the height set in the Conspecific Tree Minimum Neighbor Height m parameter within the radius from the target tree s location set in the Conspecific Tree Search Radius m parameter The probability of mortality is calculated as follows Pm G exp exp H I Den where e P is the probability of mortality for an individual tree e Denis the density of conspecific neighbor trees stems m2 e Gis the Gompertz Density Self Thinning G parameter e His the Gompertz Density Self Thinning H parameter e is the Gompertz Density Self Thinning I parameter How to apply it This behavior can be applied to trees of any species Growth and Resource Based Mortality This behavior calculates probability of survival as a function of growth and some second resource The identity of the second resource is unimportant and could be anything from exchangeable calcium levels to soil moisture Trees killed by this behavior will have a mortality reason code of natural Parameters for this behavior Parameter name Description Growth Resoutce Scaling factor to reduce survival at the mode of the survival probability Scaling Factor rho function Growth Resource Determines the mode of the function along a gradient of the resource R Function Mode mu the mode is the optimal niche of a species Growth Resoutce Survival Increase Specifies the increase in survival caused by amount of gro
417. unctioning It is difficult to guess how long a parameter file will take to run so first try running your parameter file with a one year timestep If you re happy with how long it took SORTIE to run your parameter file use one year timesteps If you think you might need a multi year timestep check the behavior documentation again Each behavior will describe how it handles timesteps of different lengths Make sure you think the approach is reasonable Then try running two versions of your parameter file one with one year timesteps and one with multi year timesteps with both files modeling the same amount of total time for instance 100 one year timesteps and 20 five year timesteps Make sure you think the difference is reasonable What is a tree The basic unit of data in the model is the tree A model tree is a collection of attributes describing one individual The attributes include location in the plot species life history stage and size Additional attributes are added as needed for the use of the particular set of behaviors in arun Location and species for a tree never change Life history stage transitions are handled automatically as a tree moves through its lifecycle Tree size and shape are managed according to allometry settings Behavior specific attributes are managed by the appropriate behavior You work with these attributes when you select data for output or work with tree maps when setting up run initial condition
418. ut is less than or equal to Upper Age Yrs of Snag Light Transmission Class 2 Expressed as a fraction between 0 and 1 If your run does not work with snags you can ignore this Otherwise a value must be provided for all species Fraction of light transmitted through the snag tree crown for each species Applies to those snags whose age is greater than Upper Age Yrs of Snag Light Transmission Class 2 Expressed as a fraction between 0 and 1 If your run does not work with snags you can ignore this Otherwise a value must be provided for all species The upper age limit in years defining the first age class of snag light transmission Snags with an age less than or equal to this age have a light transmission coefficient matching Snag Age Class 1 Light Transmission Coefficient If your run does not work with snags you can ignore this The upper age limit in years defining the second age class of snag light transmission Snags with an age greater than the upper limit for size class 1 but less than or equal to this age have a light transmission coefficient matching Snag Age Class 2 Light Transmission Coefficient Snags with an age greater than this value are in age class three If your run does not work with snags you can ignore this This behavior calculates a GLI value for each cell in a grid object called GLI Map The height at which this GLI value is calculated is set by the Height at Which GLI is Calculated for GLI Map in
419. ut setup window It is generally a good idea to finish setting up a parameter file at this point and to run it There is generally troubleshooting to be done on the basic lifecycle behaviors and the fewer behaviors that are in a run the easier it is to identify and fix problems Add external events If you have behaviors you would like to use beyond the basic tree lifecycle add them at this point These include things like disturbance events and climate change Check behavior order The parameter file specifies which behaviors to include in the simulation and in which order they should be run Theoretically it is possible to put behaviors in any order but of course most simulations constructed that way would not make sense When you structure a run the behaviors are placed in functional groups To prevent nonsensical simulations you cannot move a behavior outside of its functional group in the overall run order however you can re order behaviors within the functional groups Sometimes this will have an effect on the overall simulation outcome and sometimes it won t Refer to the documentation for individual behaviors and functional groups to learn how run order might affect a behavior Setting up behaviors parameters Almost all behaviors need values and settings from the user to function These are called the behavior parameters Once you have established the set of behaviors for your run you will need to provide values for all pa
420. vary depending on the conditions a tree is in All values are bounded between 0 and 1 Size Effect is calculated as In DBH Ix F 0 5 Xp SE e where e DBH is of the target tree in cm e Xo is the NCI Size Effect Mode in cm parameter e X is the NCI Size Effect Variance in cm Shading Effect is calculated as ShE em where e mis the NCI Shading Effect Coefficient m parameter e nis the NCI Shading Effect Exponent n parameter e Sis the amount of shade cast by neighbors from 0 no shade to 1 full shade This value should come from the Sail light behavior This effect is not required To omit the Shading Effect set the NCI Shading Effect Coefficient m parameter to 0 Crowding Effect is calculated as CE e C DBHY NCI P where e Cis the NCI Crowding Effect Slope C parameter e Dis the NCI Crowding Effect Steepness D parameter e DBH is of the target tree in cm e yis the NCI Size Sensitivity to NCI gamma parameter for the target tree s species e NCTis this tree s NCI value equation below The NCI value sums up the competitive effect of all neighbors with a DBH at least that of the NCI Minimum Neighbor DBH in cm parameter out to a maximum distance set in the NCI Max Radius of Crowding Neighbors in m parameter The competitiveness of a neighbor increases with the neighbor s size and decreases with distance and storm damage to the neighbor optional The neighbor s species also matters
421. vel The grid cell resolution defaults to 8 m X 8 m You can set whatever new resolution you wish Data in the grid Data member name Description Light The light level as calculated by the Basal Area Light behavior eaa eI The basal area in square meters of conifers that count towards the light calculation Angiosperm Basal The basal area in square meters of angiosperms that count towards the Area light calculation Carbon Value Grid This grid is created by the Carbon Value behavior It holds the amount of carbon and the value of that carbon for each species This grid has one cell for the whole plot It will ignore any changes you make to the resolution If this grid s data is saved in a detailed output file you can view the contents of this grid as a table using SORTIE s data visualization system Data in the grid Data member name Description Mg of Carbon for Species X The amount of carbon in the plot for Species X in metric tons Carbon Value for Species X The value of the carbon for Species X Competition Harvest Results Grid This grid is created by the Competition Harvest behavior This is where data on competition harvest results is stored The data is stored raw no conversion to per hectare amounts The default grid cell resolution is set to one grid cell for the entire plot You can set whatever new resolution you wish Data in the grid Data member name Description Cut Density species x Number of trees cut in
422. vest occurs This value is ignored if the harvest type is Fixed Interval For fixed basal area threshold harvests the value in Competition Harvest Harvest Type is set to Fixed Interval this is the number of years between harvests This value is ignored if the harvest type is Fixed BA or Fixed BA Amt The type of harvest to perform Fixed BA means that there is a harvest every time the plot reaches a fixed basal area threshold and the amount cut is a proportion of the total basal area Fixed BA Amt means that there is a harvest every time the plot reaches a fixed basal area threshold and the amount to cut is a fixed amount of basal area Fixed Interval means that there is a harvest every X years with the plot being harvested until it is cut back to a certain amount of basal area The minimum DBH in cm of trees that can be harvested For fixed basal area threshold harvests the value in Competition Harvest Harvest Type is set to either Fixed BA or Fixed BA Amt this is the minimum number of years that must pass between harvests even if the plot basal area is over the harvesting threshold This value is ignored if the harvest type is Fixed Interval The maximum DBH in cm of trees that can be harvested The maximum radius in meters at which a target tree of that species competitively affects other trees The competitive effect of targets of Species 1 on neighbors of every other species The effect of
423. vicultural treatments and episodic mortality For more details on this option see the Edit Episodic Events Window topic Harvest interface Use this option to set up the Harvest Interface behavior Schedule storms Use this option to schedule storm events For more details on this option see the Edit scheduled storms window topic Tree population set allometry functions window Use this option to set the allometry functions for tree species and life history stage For more details on this option see the Edit allometry functions window topic Tree population edit species list window Use this option to add rename or remove tree species For more details on this option see the Edit species list window topic Tree population edit initial density size classes window Use this to change the size classes for tree initial densities For more details on this option see the Edit size classes window topic Tree population manage tree maps window Use this to add and remove tree maps for tree initial conditions For more details on this option see the Manage tree maps window topic Grid layer setup Use this option to edit the attributes of the currently loaded grids For more details on this option see the Grid setup window topic Model flow Use this option to edit the list of behaviors their order in the run and the trees to which they are assigned For more details on this option see the Edit simulation window topic
424. w where you set the size classes and some other display controls When you click Display the table is generated Since the table displays all timesteps at once the initial data compilation step can be time consuming In addition to density displayed in stems per hectare or basal area displayed in square meters per hectare by size class the table also displays the mean DBH for trees which contributed to the table meaning those which fell outside the size classes would not be included and if you have saved height the average of the 10 tallest trees in the plot not just the 10 tallest trees that have provided data to the table You can choose to include or not live trees and snags You can also display one species at a time Only those trees for which data has been saved can be included If you omit a species or life history stage it will not show up in the table Stock table When you save DBH and tree volume from the Tree volume calculator you can view a stock table with tree volume broken out by DBH size classes that you define In addition the stock table displays the Mean Annual Increment MAI which is calculated as MAI Volume T number of years per timestep T for a given timestep T and the volume per year for each timestep for those trees that contributed to the table and if you have saved height data the average of the 10 tallest trees in the plot not just the 10 tallest trees who have provided data to the tab
425. when masting Standard deviation parameter for the normal distribution for choosing seeds in masting conditions Values are only required for those species using this distribution when masting Mean parameter for the normal distribution for choosing seeds in non masting conditions Values are only required for those species using this distribution when not masting Standard deviation parameter for the normal distribution for choosing seeds in non masting conditions Values are only required for those species using this distribution when not masting Which probability distribution to use to choose number of seeds during masting events Which probability distribution to use to choose number of seeds when not masting The minimum DBH at which a tree can reproduce This value does not have to match the Minimum adult DBH The distribution method to be applied to seeds randomization The forms for these functions can be found here Choices are e Deterministic no randomization e Poisson use the number of seeds as the mean in a Poisson probability distribution function e Normal use the number of seeds as the mean in a normal probability distribution function You must then supply a standard deviation for the function e Lognormal use the number of seeds as the mean in a lognormal probability distribution function You must then supply a standard deviation for the function e Negative binomial use the number of seeds as th
426. wth with Growth delta Growth Resource Low Growth Affects the shape of the survival probability distribution in low growth Survival Parameter conditions sigma How it works The probability of survival for a tree is calculated with the following equation R 5G 0 Prob p e where e Prob is the annual probability of survival as a value between 0 and 1 e Ris the amount of the second resource e Gis the amount of radial growth in mm yr e pis the Growth Resource Scaling Factor rho parameter which is a scaling factor to reduce survival at the mode of the survival probability function e is the Growth Resource Function Mode mu parameter which determines the mode of the function along a gradient of the resource R this corresponds to the optimal niche of a species meaning where it is the top competitor the absolute winner of competition e ois the Growth Resource Survival Increase with Growth delta parameter which specifies the increase in survival caused by amount of growth e ois the Growth Resource Low Growth Survival Parameter sigma parameter which affects the shape of the survival probability distribution in low growth conditions The amount of the second resource is captured in a grid object called Resource Currently it is up to you to enter a map of the values for this resource grid for instructions on how to do this see the Grid Setup Window topic This behavior does not in any w
427. x GLI of the location in which a seed lands Light level calculations can take into account the change in light blocking by snags and trees with storm damage if desired Parameters for this behavior Parameter name Description The fraction of total solar radiation that is direct beam radiation as Baa uO opposed to diffuse Expressed as a value between 0 and 1 See more on Global Badiaon GLI calculations Clear Sky gt er f a Used to determine the amount of solar radiation seen at the plot location Coefficient See more on GLI calculations ee Sion fe The first day of the growing season as a Julian day number between 1 GLILi oa and 365 Seeds only get light during the growing season See more on Chul ae GLI calculations GLI of Optimum The GLI value of optimum survival for seeds as a value between 0 and Establishment 0 100 100 Height in m At Which to Calculate GLI Last Day of Growing Season for GLI Light Calculations Light Extinction Coeff of Complete Damage Trees 0 1 Light Extinction Coeff of Medium Damage Trees 0 1 Light Extinction Coeff of Undamaged Trees 0 1 Minimum Solar Angle for GLI Calculations in rad Number of Altitude Sky Divisions for GLI Light Calculations Number of Azimuth Sky Divisions for GLI Light Calculations Slope of Dropoff Above the Optimum GLI Slope of Dropoff Below Optimum GLI Snag Age Class 1 Light Extinction Coefficient 0 1 The height i
428. x Unchecking the box next to a species removes it from all of that file s charts Clicking on the color next to the species name lets you choose a new color for that species The charts themselves can also be modified by right clicking on them You can reset axis ranges and zoom in and out You can save the graph as a separate image file in PNG format by choosing Save As and you can also send the graph to a printer The legends for detailed output files have an extra set of controls marked Timestep at the bottom Use the arrows to step back and forth through the timesteps As you step through and watch a chart pay attention to axis ranges The data visualizer is meant to analyze each dataset it charts and optimize the chart accordingly It does not attempt to keep the view consistent The data visualizer can only show you what you have saved from the run If you do not save any data for a particular species in a detailed output file for instance that species won t show up in any charts you open even if there were many individuals of that species in the run If your data does not look the way you expect it to start by carefully examining your output settings to make sure you actually saved everything you meant to Have patience when working with detailed output files When you move through timesteps change charts and open new charts the data visualizer often must go back and sift through the detailed output file for the data it needs Wit
429. y and processing time required for a grid is proportional to the number of total values it holds which is the number of values per cell multiplied by the number of cells For most grids you can define the size of the cells by using the Grid setup window You do not have to choose the size of a grid s cells all grids have default values If you choose to adjust a grid s cell size you should pick the largest possible value that adequately captures the resolution of the process being modeled to minimize the model s memory requirements and maximize the speed required to update it If you have a set of behaviors that work together and you are defining cell sizes for multiple grids picking even multiples of a number for different grids such as 2 4 8 will help maximize the efficiency of data transfer between them Setting up grid initial conditions In addition to setting a grid s cell size you can also set its initial values As with trees setting the initial values of a grid can have an impact on the outcome of a run For many grids setting the initial values in the grid cells is not required or in some cases even allowed for instance a grid that is used to report on plot biomass will not accept input The documentation for the behavior that creates the grid will guide you as to whether you can or need to provide initial values If setting the initial values for a grid is optional you choose to set them generally because you want t
430. y of entering the substrate pool in each of the 5 decay classes for both snags and dead saplings adults Detailed Substrate allows new substrate proportions to be specified following clear cut gap and partial harvesting If the total proportion of substrate after harvesting specified by parameters is less than 1 the remainder will be distributed in proportion to pre harvest substrate values In comparison remaining substrate after harvest is assigned to moss and litter pools in the Substrate behavior This change is designed to allow legacy substrates such as logs and tip up mounds to persist after a harvest event In addition to tracking log area Detailed Substrate also stores the volume of each type of log substrate in each grid cell For new inputs log volume is calculated as LV 1 3 x DBH 2 h where e LV is new log volume in m e DBH is the DBH of the fallen tree in m e his the height of the fallen tree in m For initial volume and volume added after harvest LV 1 3 m 100 PLA MDBH 2 where e LV is initial log volume or volume added after harvest in m ha e PLA is the proportional log area in the grid cell from 0 to 1 e MDBH is the mean DBH of logs of that type either initial or added by harvest These are set with parameters A reasonable default is values of 0 5 and 1 5 of the diameter boundary are used for small and large size classes respectively Log volume differs from log area proportions
431. y produced by a 30 cm DBH tree in one year for the lognormal function Annual STR under canopy conditions see equation below This is only required if the canopy probability distribution function is lognormal The for the lognormal function under canopy conditions see equation below This is only required if the canopy probability distribution function is lognormal Lognormal Canopy Beta Lognormal Canopy Xo Lognormal Canopy Xp Minimum DBH for Reproduction in cm Seed Distribution Seed Dist Clumping Parameter Neg Binomial Seed Dist Std Deviation Normal or Lognormal STR for Stumps Weibull Canopy Annual STR The mean of the lognormal function under canopy conditions or under non masting conditions in the case of Masting spatial disperse see equation below This is only required if the canopy probability distribution function is lognormal The standard deviation of the lognormal function under canopy conditions or under non masting conditions in the case of Masting spatial disperse see equation below This is only required if the canopy probability distribution function is lognormal The minimum DBH at which a tree can reproduce This value does not have to match the Minimum adult DBH The distribution method to be applied to seeds randomization The forms for these functions can be found here Choices are e Deterministic no randomization e Poisson use the number of seeds as the
432. your own risk If any storm damage parameters are set to anything other than 1 it is recommended but not required that you have the Storm damage applier behavior applied Post Harvest Skidding Mortality This mortality behavior simulates an increase in mortality after harvesting attributable to skidding damage or other effects The increase in mortality tapers off through time DBH and neighborhood basal area can also affect mortality in this behavior Model forms are based on those in Thorpe et al 2010 Trees killed by this behavior will have a mortality reason code of natural Parameters for this behavior Parameter name Description Post Harvest Skid Mort Crowding Maximum distance in m for neighbors to have a competitive effect Effect Radius Post Harvest Skid Mort Pre Harvest Background Mort Rate Annual mortality rate 0 1 if no harvest has occurred this run Post Harvest Skid Mort Snag Annual postharvest risk of standing death after harvest effects have Recruitment completely tapered off Background Prob Post Harvest Skid Mort Snag Recruitment Basic Prob Basic probability of standing death after harvest Post Harvest Skid Mort Snag Recruitment Crowding Effect Post Harvest Skid Mort Snag Recruitment Rate Param Post Harvest Skid Mort Snag Recruitment Skidding Effect Post Harvest Skid Mort Windthrow Background Prob Post Harvest Skid Mort Windthrow Crowding Effect Po

SORTIE-ND User Manual Version 7.01 Beta

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