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SORTIE 6.07 User Manual - sortie-nd

1. 27 512 580 478 575 656 387 528 638 32 586 706 816 469 644 773 899 514 706 852 992 1836 1 014 1 185 1 404 1 537 1 670 1 808 1 945 2 094 2 244 2 384 2 525 2 694 2 862 3 031 3 logs 4 logs 5 logs Bo 654 904 1 096 1 284 1 453 396 424 ra Bra Baal rane ral A aol rare Form Class 81 DBH inches 1 log 10 40 50 a 115 gt p ae Se S gt S poe o 378 a 706 758 814 870 930 989 1 055 1 121 1 188 1 256 1 330 65 1 403 2 logs 82 100 122 144 170 197 226 256 290 323 360 398 439 480 528 575 624 726 1977 1 184 1 394 1 050 1 272 1 503 1 132 1 376 1 618 11 213 1 480 1 733 11 298 1 586 1 858 1 383 1 691 1 984 1 477 1 806 2 124 1 571 1 922 2 264 1 672 2 044 2 416 1 772 2 167 2 568 1 874 2 300 2 714 1 588 1 723 1 862 2 001 2 152 2 304 2 458 2 612 2 783 2 954 3 127 11 977 2 432 12 860 3 logs 4 logs 5 logs i82 l 100 130 150 160 1186 loo 221 L 170 228 268 265 316 306 366 a39 527 598 492 592 676 544 656754 439 602 724 838 480 659 791 923 3 300 6 logs 933 1 131 1 327 1 006 1 220 1 438 435 466 agi al Bon ral mae awl eel Foal Form Class 84 DBH inches 10
2. i Nil ol wo ol wv olal iR NO S Bi Wi Wl wl w o o nan A N eelle rE EE aj 22 iafe fia 2s ns 22 5 za 9 295 2s 19 25 16 as 2 fsfi aa 2 fear 2s 2127 18 2s 21 28 18 29 2a 28 19 o 2s 222819 22 2s I e2 fee JEJE pee zs e2 l l IE 26 33 09 14 21 Bura Dara ba ia 22 339 11s 22 31 39 14 15 23 32 a 121s 24 Volume board feet by number of usable 16 foot logs Form Class 78 DBH inches 1 log 2 logs 3 logs 4 logs 5 logs 6 logs 10 ge lso 73 IH Je JE 11 las lre los I Ee Je 12 56 92 120 f37 e 13 jo7 112 147 fies J 14 78 132 i74 200 f 15 jo2 156 208 242 16 106 1180 241 285 17 f121 206 278 330 18 136 233 314 B74 W 19 1154 264 358 427 J 20 171 296 401 480 542 21 191 332 450 542 616 22 211 368 500 603 691 23 231 404 552 663 714 b 24 251 441 605 723 782 25 275 484 665 foo ps 26 299 528 725 877 1 021 323 27 28 347 29 1375 30 403 31 1432 32 462 33 492 34 521 35 555 36 1589 37 1622 38 1656 39 694 40 m31 Form Class 79 DBH inches 1 log 10 38 48 58 70 82 A eval aa rere real roma el aa Fel eal oar 788 952 11 111 572 616 667 18 772 826 880 850 1 027 1 201 920 11 112 1 308 991 1 198 1 415 1 070 1 299 1 526 1 149 1 400 1 637
3. Last updated 23 Oct 2006 11 33 AM Light behaviors In this document Snags in light calculations Light parameters 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 Light is the key resource for trees in the SORTIE model A tree s growth and therefore its probability of mortality and reproductive ability is a function of the amount of light it receives Consequently great care is taken in SORTIE to calculate the amount of light that each tree 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 In order to calculate the amount of light a tree gets SORTIE simulates taking a fisheye photograph over each tree to determine which parts of the sky are blocked by taller trees
4. Model menu Run Runs the model with the currently loaded parameter file 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 there are unsaved changes to the current file a temporary file is written so that the model runs with those changes included Keep an eye on the status bar at the bottom of the SORTIE screen It will display the status messages from the running model Run Batch Allows you to select a batch file and then run the batch You can read more about batch runs here You create batch setup files using the batch file setup window You can run batch files without having a parameter file loaded Pause If there is a run in progress you can pause it with this option You can resume the run by choosing Run again This does not apply to batch runs They cannot be paused only stopped Stop run If there is a run in progress this will stop it Last updated 01 Apr 2005 01 45 PM Help menu Contents Accesses the SORTIE help Trees In this document Tree background Tree life history stage transitioning growth and death Tree parameters The basic unit of data in the model is the tree Each tree is a discrete individual with a location in space and attributes which describe its size and shape More information about how tree size is measured and ho
5. Pn a es 16 Ma ASIT raie paa W Wese e e fee i fae w a rera MaNi paa h es a e M e ee 20 21 11 7119 1 41 8 2 4 1 1 111 6 12 2 2 9 I I 22 i22 182 Iial 12 5 1 111 712 3129 i i a OS 1822 i5 222e 147 r8 2a aa ha e sel oe 26 24 11 9123 1 5 12 3 2 7 1 1 11 9 2 5 13 2 I I 28 25 1 92 5 1 6 24 28 1 2 11 9 2 6 13 3 09 1 4 21 3 2 4 4 30 2 6 2 2 6 1 7 2 513 1 2 12 2 7 3 5 0 9 1 4 2 1 13 2 14 5 32 2 7 2 2 7 1 7 2 5 13 1 1 2 2 1 2 9 3 7 1 1 4 2 1 3 2 4 6 34 2 8 2 1 2 7 1 8 2 5 3 3 1 3 2 1 1 3 3 8 1 1 4 2 2 3 3 4 7 36 2 8 2 1 2 8 1 8 2 6 3 4 1 3 2 2 3 3 9 1 1 1 5 2 2 3 3 4 9 38 2 9 2 1 2 8 1 9 2 6 3 4 1 3 2 2 3 1 3 9 1 1 1 5 2 3 3 4 5 1 40 2 9 2 2 2 8 1 9 2 7 3 4 1 4 2 3 3 2 4 1 2 1 5 2 4 3 5 5 3 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 ou
6. Beer s law light filter How it works This behavior simulates a filter that reduces light according to Beer s Law 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 to 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
7. 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 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 function 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 f 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 How it works The behavior starts each timestep by updating the forest cover of each cell gap or canopy It co
8. 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 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 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 How it works 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 factors which act to reduce the maximum survival probability and will vary depending on the conditions a tree is in All values are bounded between 0 and 1 Size Effect is calculated as 2 DEH sH vf Vx a 2 Xb SH g where e DBH is of
9. ha You intend to specify cut amounts as an amount of basal area to remove in square meters per hectare SORTIE will calculate the actual amount of basal area to remove by multiplying the cut amount by the area to which the harvest is applied SORTIE will work its way down the trees in the cut area in size order removing each one that brings the amount of basal area removed closer to the target amount without going over If the size class range and the cut area are both large the amount of basal area removed is likely to be very close to the target Diameter Range s to cut Enter the size class ranges you are cutting You must enter at least one but in order to enter more than one you must specify Partial cut under Cut type For each size class enter the minimum and maximum DBH and the amount to cut in that range The units of amount to cut will depend on what you have entered in Cut amount type Cut ranges may not overlap Choosing the area to which to apply the harvest To specify the plot area to which to apply the harvest select the appropriate cells on the map Cells are each 8 meters by 8 meters Selected cells will show up in color and unselected cells will be white You can click and drag to mark out an area or click on individual cells Clicking or dragging on selected colored cells causes them to become unselected white 07 Dec 2004 10 27 AM Edit Mortality Episode Window This window is reached from the Edit E
10. Any species not using that function can omit this value Crown Height Exponent The exponent in the standard equation for calculating crown height Any species not using that function can omit this value Crown Radius Exponent The exponent in the standard equation for determining the crown radius Any species not using that function can omit this value 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 Maximum Tree Height in meters 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 Power Function a The a parameter in the power function for the height diameter relationship Any species not using that function can omit this value Power Function Exponent b The exponent or b parameter in the power function for the height diameter relationship Any species not using that function can omit this value Sapling Crown Height Height Function The allometric relationship used to relate tree height in m and height or length of the crown in m for saplings Each of the choices is described in detail below Sapling Crown Radius Diameter Function The allometric relationship used to relate DBH in cm and crown radius in m for saplings Each of the choices is described in detail below Sapling
11. Forest models defined by field measurements II Estimation error analysis and dynamics Ecological Monographs 66 1 43 Papaik M J 1998 Effects of windstorm in northern temperate forests Master s Thesis Bard College 1998 Ribbens E Pacala S W and Silander J A 1994 Recruitment in forests calibrating models to predict patterns of seedling dispersal Ecology 75 1794 1806 Scott C T 1979 Northeastern forest survey revised cubic foot volume equations Northeastern Forest Experiment Station Research Note NE 304 Wright E F C D Canham and K D Coates 2000 Effects of suppression and release on sapling growth for eleven tree species of Northern interior British Columbia Canadian Journal of Forest Research 30 1571 1580 Wright E F Coates K D and Bartemucci P 1998 Regeneration from seed of 6 tree species in the interior cedar hemlock forests of British Columbia as affected by substrate and canopy gap position Can J For Res 28 1352 1364 Wright E F Coates K D Canham C D and Bartemucci P 1998 Species variability in growth response to light across a climatic gradient in northwestern British Columbia Can J For Res 28 871 886 Last updated 29 Aug 2005 08 49 AM Glossary Adult tree A tree whose DBH is at least the minimum DBH for adulthood See the trees topic for more Allometry The relationships between various aspects of a tree s size and shape See the allometry topic for more Ba
12. 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 _ expla e s DBH 1 expla e s DBH 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 Winds
13. e Zis the Competition Mortality Shape Parameter Z parameter e max is the Competition Mortality Maximum Parameter max parameter which indicates the maximum relative increment subject 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 How it works The probability of mortality is calculated with a double Michaelis Menton function A C Xdiam N x density A CX diam 5 Pm densify 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 is 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 Eff
14. for randomizing storm severity across the plot This parameter is ignored if the Storm Damage Application parameter is not set to Stochastic Used by the Storm disturbance behavior Storm Damage Application 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 Used by the Storm disturbance behavior Storm Damage Intercept a for Medium Damage The storm damage intercept parameter a for the equation calculating the probability of medium damage Used by the Storm damage applier behavior Storm Damage Intercept a for Heavy Damage The storm damage intercept parameter a for the equation calculating the probability of heavy damage Used by the Storm damage applier behavior Storm DBH Coefficient d The storm DBH coefficient d for the equations calculating the probability of damage Used by the Storm damage applier behavior Storm Heavy Damage Survival Prob Intercept a The a value in the probability of survival logit function for trees with heavy damage Used by the Storm killer behavior Storm Heavy Damage Survival Prob DBH Coeff b The b value in the probability of survival logit function for trees with heavy damage Used by the Storm killer behavior Storm Intensity Coefficient b The storm intensity coefficient
15. hvr A harvest regime file is a specification for harvest and planting for a run A harvest regime file can be read in once a parameter file has been loaded The parameter file must have the same species and in the same order as the file originally used to create the harvest regime file In addition the loaded parameter file must have a number of timesteps at least as large as the timestep of the last harvest or planting event The old versions of SORTIE relied upon a hard wired grid cell area for the harvest and planting specifications while the new version may have a different resolution SORTIE will make the conversion but the areas of harvest and or planting may be slightly different afterwards To read a harvest regime file use File gt Open file e Output files out Old output files can be viewed in the data visualization functions of the model Parameter files par SORTIE ND versions up to 6 04 support these parameter files Later versions including this one do NOT support par files You can download and install a version of SORTIE ND up to 6 04 and read this topic in its user manual for instructions on how to import your file You can then save it into a SORTIE ND parameter file which can be opened by later SORTIE ND versions Tree map files stmf The format for tree map files from older versions of SORTIE is no longer supported However SORTIE ND does support a different tab delimited tree map file format It is e
16. in cm parameter Seedlings and snags never contribute to BAg 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 The final total growth amount is added to the tree s DBH Height is calculated according to the appropriate allometric equation How to apply it This behavior can be applied to saplings and adults of any species It cannot be applied to seedlings Basal area NCI growth diam only This behavior works exactly like the Basal area NCI growth diam with auto height behavior to calculate an amount of diameter increase How to apply it This behavior can be applied to saplings and adults of any species It cannot be applied to seedlings Allometric height incrementer How it works This behavior calculates an amount of height growth The amount of height increase is the difference between the results of the allometry equation for the diameter before and after the growth increment is applied It can be paired with any behavior that increments diameter only This behavior takes as inputs the diameters of a tree before and after its amount of diameter growth increase has been applied by whatever behavior has calculated this amount of increase It then uses the diameter height a
17. is set to Random This is the total number of seedlings to plant as a value per hectare SORTIE determines the actual number to plant by multiplying this value by the planting area Spacing m You enter this value if the Plant spacing is set to Gridded This is the distance in meters between newly planted seedlings in an 8 meter by 8 meter plot grid cell If this distance is larger than 4 only one seedling per grid cell will be planted Choosing the area to which to apply the planting To specify the plot area to which to apply the planting select the appropriate cells on the map Cells are each 8 meters by 8 meters Selected cells will show up in color and unselected cells will be white You can click and drag to mark out an area or click on individual cells Clicking or dragging on selected colored cells causes them to become unselected white 07 Dec 2004 10 26 AM 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 filena
18. nearby SORTIE determines how much light comes from different parts of the sky and takes this into account so shading neighbors in different directions will have different impacts on the total amount of light a tree gets The fisheye photo can be taken at one of two positions either at the top of the crown or at mid crown The major difference between the two is that when the photograph is taken at mid crown trees near the same height as the target tree will be included in the shading effects This can make a big difference in even age stands Sky Simulation At the beginning of a run if light behaviors are being used the amount of light coming from each part of the sky for the plot s location is calculated The sun s position in the sky is tracked throughout the growing season Diffuse radiation assumed to be isotropic coming equally from all directions is then added to the direct beam radiation Below the minimum solar angle it is assumed that no light comes from those portions of the sky because of the density of the surrounding forest It is wise not to set this angle too low otherwise SORTIE must look very far away for shading neighbors To determine the amount of sun coming from each portion of the sky the sky is first divided into a hemispheric grid For GLI calculations the grid cells are equal area segments of a user settable resolution For Sail Light calculations the sky is divided into one degree sized grid cells For
19. 1 Since SORTIE data visualization can only display the contents of output files the first step in using this feature is to set up some output files to view You can see more on individual chart types here so you can save the appropriate data for the charts you re interested in seeing For more on the output file types and how to set them up see either the summary files or the detailed output files topics 2 Once you have completed a parameter file for your run and have set up your output the next step is to create some output for SORTIE to analyze 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 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 To view the output of the current run it is recommended that you first pause the run 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 Then 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 4 Open the charts you wish to view see Displaying the data from a file If a chart
20. 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 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 is a basic sine wave Curve 2 has an increased frequency plus an upwards trend The actual probability of an individual storm that takes place in a storm regime with a cyclical frequency is P F P Fi Ld 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 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 years since storms started and Sr is the
21. 11 226 1 495 1 750 1 304 1 590 1 864 1 394 1 702 12 000 934 998 1 063 1 124 1 186 1 258 61 1 329 2 logs 78 96 117 138 160 183 212 240 272 305 342 378 418 458 499 540 588 11 868 2 294 12 693 10 o6 W24 ha 153 176 182 211 214 252 l 414 406 561 342 464 558 636 378 514 621 T10 418 571 687 792 458 628 1753 875 499 685 826 960 1742 899 i810 980 1 144 1 046 1 358 1 488 1 619 1 754 1 888 2 026 2 163 2 312 2 461 2 616 2 771 2 937 3 logs 4 logs 5 logs 77 te 1357 28 29 385 30 413 31 444 32 474 33 1506 34 538 35 1570 36 602 37 638 38 674 39 712 40 750 Form Class 80 DBH inches 1 log 10 39 49 83 112 a eo Sr 244 sr ae 877 1 061 1 242 635 686 737 792 848 907 966 1 026 1 087 1 154 1 220 1 292 163 1 365 2 logs 80 98 120 141 166 190 219 248 281 314 350 387 428 469 514 558 606 654 948 11 148 1 350 1 020 1 235 1 458 1 100 1 338 1 572 1 181 1 440 1 685 11 265 1 544 1 808 11 349 1 647 1 932 11 435 1 754 2 000 1 521 1 860 2 189 1 620 1 980 2 338 1 720 2 101 2 488 1 822 2 232 2 632 11 923 2 362 12 775 og W127 146 156 i81 186 216 221 260 256 hos
22. 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 A parameter file is as long as it needs to be depending on how you want to set up your run At the least the parameter file must specify the length of the run see Run Setup describe the plot define the tree species and their attributes list the behaviors in the order in which they will run and provide whatever data the behaviors need In addition parameter files can contain very detailed initial conditions in the form of maps of tree and grid data This data is normally produced in detailed output files For more on how to add this data to a parameter file see Adding to a parameter file Editing a parameter file The SORTIE ND model interface is designed to give you all the tools you need to create and modify your parameter files You are welcome to view and modify the new parameter files directly if you wish They can be opened in any text editor Be warned however that with the XML data format this is an extremely daunting task and you will never actually need to do it 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 Tree Setup to set up the basics of
23. AGREED TO IN WRITING WILL ANY COPYRIGHT HOLDER OR ANY OTHER PARTY WHO MAY MODIFY AND OR REDISTRIBUTE THE PROGRAM AS PERMITTED ABOVE BE LIABLE TO YOU FOR DAMAGES INCLUDING ANY GENERAL SPECIAL INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE USE OR INABILITY TO USE THE PROGRAM INCLUDING BUT NOT LIMITED TO LOSS OF DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGES END OF TERMS AND CONDITIONS www gnu org
24. Crowding Distance in meters The maximum distance in m at which a neighboring tree has competitive effects on a target tree Used in the NCI growth behavior diam with auto height and NCI growth behavior diam only behaviors NCI Maximum Potential Growth cm yr Maximum potential diameter growth for a tree in cm yr Used in the NCI growth behavior diam with auto height and NCI growth behavior diam only behaviors NCI Minimum Neighbor DBH in cm The minimum DBH for trees of that species to compete as neighbors Used for all species not just those using NCI growth Used in the NCI growth behavior diam with auto height and NCI growth behavior diam only behaviors NCI DBH Divisor q The value by which neighbor DBHs are divided when calculating NCI Set this value to something greater than if necessary to decrease the competitive effects of neighbors Used in the NCI growth behavior diam with auto height and NCI growth behavior diam only behaviors NCI Neighbor Storm Damage eta Complete 0 1 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 Used in the NCI growth behavior diam with auto height and NCI growth behavior diam only behaviors NCI Neighbor Storm Damage eta Medium 0 1 The fraction to which a neighbor s competitive effect is reduced when the ne
25. E W Direction in meters The length of the plot in the east west direction in meters e Plot Length in the Y N S Direction in meters The length of the plot in the north south direction in meters e Plot Latitude in decimal degrees The plot latitude expressed in degrees and partial degrees i e 39 10 15 Aug 2004 10 01 PM Creating 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 In this document Setting up the tree population Setting up the behavior list Setting parameter values Other options 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 Tree setup window At a minimum you must create a list of tree species If you want to define the initial conditions of your tree population using densities in size classes and you know what you want your size classes to be you can set them up at this point Otherwise you can always come back to this window by choosing Edit gt Tree setup Setting up the behavior list After your tree population is defined the wizard will take you to the Edit simulation flow window so you can set up the list of
26. Enter your output file name here You can use the Browse button to help you enter a path If you don t use a path your file may be hard to find Detailed output files end up with a gz tar extension Save everything This saves all possible data The resulting detailed output file will probably be quite large This option is handy when you are still tweaking your parameter file You can save everything run for a few timesteps and review the data using the data visualization tools This option is also a good one when you wish to have the complete state of the model at every timestep perhaps to use as input to new runs This option takes effect right away and cannot be canceled Clear everything Erases all detailed output settings This option takes effect right away and cannot be canceled Trees Sets options for saving trees by opening the Setup tree save options window The text just below this button will tell you if there are currently any tree save settings You are not required to save tree data Grid data layers Sets options for saving grids by opening the Setup grid save options window The text just below this button will tell you if there are currently any grid save settings You are not required to save grid data Set up subplots Sets up subplots for tree data by opening the Edit subplots window Subplots are regions within the plot as a whole that will have data saved separately You can find more information in the d
27. 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 extinction 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 GLhp LE 1 Sto GLIop GLI If GLI GLI LE 1 If GLI gt GLlo p LE 1 Sni GLI GLIp 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 Spi 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 gr
28. 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 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 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 number of trees heavily damaged in recent storms This behavior calculates the light levels at th
29. Growth in sq cm yr parameter e diamis the tree s diameter in cm e Tis the number of years per timestep Tree height is allowed to update automatically according to the allometry equations 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 Constant basal area growth diam only How it works The amount of diameter increase is calculated from a constant basal area increment The increase 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 and a height incrementing growth behavior applied Constant radial growth diam with auto height 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 Tree height is allowed to update automatically according to the all
30. 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 You must also use the Storm disturbance and Storm Light behaviors Last updated 28 Nov 2006 10 16 AM Mortality behaviors In this document Mortality parameters Adult Self Thinning Adult Stochastic Mortality Aggregated Mortality BC Mortality Competition Mortality Density Self Thinning Mortality Exponential Growth and Resource Based Morta
31. Last updated 17 Dec 2004 01 49 PM Detailed output map files In this document What are maps Maps as output Maps as input Creating your own map analyses What are maps Maps are files listing individual values for trees and grids Tree maps list individual trees and their attributes X and Y coordinates height etc Grid maps list some or all of the values held in each grid cell Usually maps are produced as part of detailed output files These maps are written in the XML data format in plain text They can be opened directly in a text editor but due to the data format it is probably not useful to do so Maps as output The maps represent the model s data in a semi raw state You can feed the maps of a detailed output file directly into the Data visualizer in order to view them graphically Maps as input If you have all of the tree and grid data from the model as maps you have the complete data set upon which the simulation was based This means you can use maps to recreate all or part of the model state and use it as a starting point for a new simulation possibly with different parameter values For more information on how to add map data to a parameter file see Adding to a parameter file If you wish to directly enter values for trees and grids you can do so For grids you can enter or change grid values using the Grid layer setup window Trees have their own tab delimited text file format For detai
32. Mortality Annual Kill Amount 0 1 The annual mortality rate for a mortality episode as a proportion between 0 and 1 Used by the Aggregated Mortality behavior Aggregated Mortality Clump Size Whether the size of a clump of trees to kill is deterministic or chosen from a negative binomial probability distribution Used by the Aggregated Mortality behavior Aggregated Mortality Clumping Parameter If the size of tree clumps to kill is drawn from a negative binomial probability distribution this is the clumping parameter for the distribution This is not required if a deterministic clump size is used Used by the Aggregated Mortality behavior Aggregated Mortality Number of Trees To Aggregate Determines the size of the clumps of trees killed If the clump size is deterministic all clumps will be this size If the size is to be drawn from a negative binomial probability distribution then this is the mean clump size Used by the Aggregated Mortality behavior Aggregated Mortality Return Interval years The return interval for mortality episodes Used by the Aggregated Mortality behavior Competition Mortality Shape Parameter Z Determines the shape of the mortality function Used by the Competition Mortality behavior DBH at Onset of Senescence in cm DBH at which senescence takes effect Used by the Senescence behavior DBH of Maximum Senescence Mortality Rate as an integer in cm The DBH at which maximum mortality occurs Trees w
33. Mortality Episode Results Carbon Value Merchantable Timber Value Windstorm Results e Partitioned Biomass If you wish to view these tables set up your detailed output file to save all the data from your chosen grids Last updated 15 Nov 2006 07 16 AM Further reading This list along with reprints is also available at www sortie nd org Bolker B M S W Pacala F A Bazzaz C D Canham and S A Levin 1995 Species diversity and ecosystem response to carbon dioxide fertilization conclusions from a temperate forest model Global Change Biology 1 373 381 Canham C D LePage P and Coates K D 2004 A neighbourhood analysis of canopy tree competition effects of shading versus crowding Can J For Res 34 778 787 Canham C D M J Papaik and E J Latty 2001 Interspecific variation in susceptibility to windthrow as a function of tree size and storm severity for northern hardwood tree species Canadian Journal of Forest Research 31 1 1 10 Canham C D Coates K D Bartemucci P and Quaglia S 1999 Measurement and Modeling of Spatially explicit Variation in Light Transmission Through Interior Cedar Hemlock Forests of British Columbia Can J For Res 29 1775 1783 Canham C D A C Finzi S W Pacala and D H Burbank 1994 Causes and consequences of resource heterogeneity in forests Interspecific variation in light transmission by canopy trees Canadian Journal of Forest Research 24 33
34. 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 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 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 ente
35. Neighbor Distance Effect beta The effect of the distance of a neighbor tree on its competitiveness for a target species Used in the NCI mortality behavior NCI Neighbor Storm Damage eta Complete 0 1 The fraction to which a neighbor s competitive effect is reduced when the neighbor has sustained complete storm damage Used in the NCI mortality behavior NCI Neighbor Storm Damage eta Medium 0 1 The fraction to which a neighbor s competitive effect is reduced when the neighbor has sustained medium storm damage Used in the NCI mortality behavior NCI Shading Effect Coefficient m The coefficient in the shading effect equation Set this value to 0 if you do not wish to use shading Used in the NCI mortality behavior NCI Shading Effect Exponent n The exponent in the shading effect equation If you set the NCI Shading Effect Coefficient m parameter to 0 this value is ignored Used in the NCI mortality behavior NCI Size Effect Mode in cm The mode of the size effect curve Used in the NCI mortality behavior NCI Size Effect Variance in cm The variance of the size effect curve Used in the NCI mortality behavior NCI Size Sensitivity to NCI gamma The sensitivity of a tree s survival probability to its DBH Used in the NCI mortality behavior NCI Storm Effect Complete Damage 0 1 The fraction by which a tree s survival probability is reduced when it has sustained complete storm damage Used in the NCI mortality behavior N
36. Storm Class 0 1 0 2 The return interval in years of storms of severity 0 1 0 2 Set this to 0 to turn off storms of this severity Used by the Storm disturbance behavior e Return Interval for Severity Storm Class 0 2 0 3 The return interval in years of storms of severity 0 2 0 3 Set this to 0 to turn off storms of this severity Used by the Storm disturbance behavior e Return Interval for Severity Storm Class 0 3 0 4 The return interval in years of storms of severity 0 3 0 4 Set this to 0 to turn off storms of this severity Used by the Storm disturbance behavior e Return Interval for Severity Storm Class 0 4 0 5 The return interval in years of storms of severity 0 4 0 5 Set this to 0 to turn off storms of this severity Used by the Storm disturbance behavior e Return Interval for Severity Storm Class 0 5 0 6 The return interval in years of storms of severity 0 5 0 6 Set this to 0 to turn off storms of this severity Used by the Storm disturbance behavior e Return Interval for Severity Storm Class 0 6 0 7 The return interval in years of storms of severity 0 6 0 7 Set this to 0 to turn off storms of this severity Used by the Storm disturbance behavior Return Interval for Severity Storm Class 0 7 0 8 The return interval in years of storms of severity 0 7 0 8 Set this to 0 to turn off storms of this severity Used by the Storm disturbance behavior Return Interval for Severity Storm
37. 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 this tree member you must add the Tree volume calculator behavior to your run Histograms The visualizer can produce a histogram for most tree and grid values in a detailed output file 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 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
38. b for the equations calculating probability of damage Used by the Storm damage applier behavior Storm Medium Damage Survival Prob Intercept a The a value in the probability of survival logit function for trees with medium damage Used by the Storm killer behavior Storm Medium Damage Survival Prob DBH Coeff b The b value in the probability of survival logit function for trees with medium damage Used by the Storm killer behavior Storm Prop Heavy Damage Dead Trees that Tip Up The proportion of those heavily damaged trees that are killed in the storm that tip up as a value between 0 and 1 For how a tipped up tree is treated see the behavior description Used by the Storm killer behavior Windstorm DBH Exponent b The b value in the equation used to determine the mortality of an individual tree as a result of a storm Used by the Windstorm behavior Windstorm Minimum DBH for Windstorm Mortality The minimum DBH for trees to be killed in storm events Used by the Windstorm behavior Windstorm Mortality Intercept a The a value in the equation used to determine the mortality of an individual tree as a result of a storm Used by the Windstorm behavior Windstorm Sea Surface Temperature Cyclicity Period Years Parameter that controls the cyclicity of storm frequency This value cannot be 0 Used by the Windstorm behavior Windstorm Severity for 1 Year Return Interval Storm The severity of storms with a y
39. behavior e Height to Begin Calculating Trunk Volume in cm 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 e Minimum Trunk Diameter for Volume Calculations 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 e Trunk Segment Length for Volume Calculations in m 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 Carbon Value This behavior calculates the amount of carbon per species and its value 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 Ap
40. 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 are 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 Other options Once you have completed the three steps above you have created a basic parameter file For more options on adding to a parameter file see the topic Adding to a parameter file Adding to a parameter file This topic covers the additions you can make to a parameter file For more on how to create a basic parameter file from scratch see the topic Creating a parameter file Otherwise you can start with an existing parameter file and modify it A b
41. between 0 and 1 Used by the Substrate Based Seed Survival With Microtopography behavior Slope of Density Dependence The slope of the density dependence function for determining how many seedlings establish per square meter c in the equations below Used by the Density Dependent Seed Survival behavior Slope of Dropoff Above the Optimum GLI The slope of the line describing the drop off in seedling survival as a function of GLI above the optimum GLI Used by the Light Dependent Seed Survival behavior Slope of Dropoff Below Optimum GLI The slope of the line describing the dropoff in seedling survival as a function of GLI below the optimum GLI Used by the Light Dependent Seed Survival behavior Steepness of Density Dependence The steepness of the density dependence function for determining how many seedlings establish per square meter 6 in the equations below Used by the Density Dependent Seed Survival behavior Snag Age Class 1 Light Extinction Coefficient 0 1 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 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 Used by the Light Dependent Seed Survival behavior Snag Age Class 2 Light Extinction Coefficient 0 1 Fraction of light transmitted through the snag
42. by data species first View by data type first View by behavior This button changes the view to a hierarchical structure that shows behaviors at the top level Each behavior for the current run is listed in order Expanding the tree under a behavior shows the grids and trees to which it applies Clicking on the name of any behavior brings up the Current run behaviors window where you can edit the list of behaviors their order and to what trees they apply Clicking on any grid name brings up the Grid setup window where you can set options for grids Expanding trees shows you the tree types to which the behavior is assigned first by tree type and then by species Clicking on a species name brings up the tree behavior window which you can use to set up the behaviors applied to the chosen tree type and species combination View by data species first This button changes the view to a hierarchical structure that shows grids and trees at the top level In the tree structure portions species is shown at a higher level and tree type life history stage is shown beneath Expanding a tree or grid branching shows what behaviors in order apply Clicking on any grid name brings up the Grid setup window where you can set options for grids Clicking on a tree type below a species name brings up the tree behavior window which you can use to set up the behaviors applied to the chosen tree type and species combination Clicking on
43. each day in the growing season the times of sunrise and sunset are calculated and then the sun s position in the sky grid is tracked at 5 minute intervals throughout the day The equations are below At each solar position the amount of direct beam radiation received from the sun at that position is calculated taking into account atmospheric effects Each sky segment keeps track of the total amount of direct beam radiation coming from it for the duration of the growing season The total amount of light in the sky is the amount of direct beam radiation plus the amount of diffuse radiation Once the total amount of direct beam radiation is known the amount of diffuse radiation is calculated accordingly and added equally to all portions of the sky Each sky segment is then relativized to hold the percentage of total light coming from that segment Determining a tree s light index For each timestep SORTIE calculates the amount of light each tree receives by simulating a fisheye photograph To take the photo the model looks at the hemisphere of sky around and above a tree and determines which portions of it are blocked by neighboring trees It then totals up how much light is left to reach the tree Only tree crowns block light in the model Trunks do not shade Because seedlings are modeled as sticks with no crowns they don t shade either The first step in creating the simulated fisheye photo is to determine how far from the tree to sear
44. 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 and data files in SORTIE ND You can open parameter files this way and then add map files or detailed output files to the run You can load files that may not be complete or valid for a run To check a file you can save it or open the Parameters window and then click OK to trigger a file validation 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 is incorrect 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 yes 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 Last updated 15 Nov 2006 06 53 AM Batch file setup window This window is reached from
45. 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 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 2 DEH y vf Vx i 2 Xb SH where e DBH is of the target tree in cm e Xo is the NCI Size Effect Mode in cm X0 NCI growth parameter e X is 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
46. for GLI Map Creator in rad 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 This value applies to the GLI Map Creator behavior Minimum Solar Angle for GLI Points Creator in rad 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 This value applies to the GLI Points File Creator behavior Minimum Solar Angle for Quadrat Light in rad 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 This value applies to the Quadrat based GLI light behavior if the value should be different from the value being used by the GLI light behavior Number of Altitude Sky Divisions for GLI Light Calculations Number of grid cells into which the sky is divided from horizon to zenith for the purpose of calculating light direction Used by the GLI light behavior as well as the Quadrat based light behavior if a different value is not specified for it Number of Altitude Sky Divisions for GLI Map Creator Calculations Number of grid cells into which the sky is divided from horizon to zenith for the purpose of calculating light direction Used by the GLI Map Creator behavior If the GLI light behavior is also used this value is not required Number of Altitude Sky Divisions for GLI Points Cr
47. 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 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 Storm Damage This grid is created by the Storm disturbance behavior Each grid cell holds a storm damage 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 Susceptibility the resolutions must match Data in the grid Data member Description name A storm damage index for all storms occurring in the past timestep Darago Mex from 0 no damage to total damage Time Since Last The number of years since the last storm occurred in this cell The last Storm storm is an
48. generalized and given different names but when you read the documentation on the individual behaviors you should be able to find the ones you want Then read about the new parameter files Read about your output options with the topics on summary output files and detailed output files You can load an old parameter file into SORTIE ND up to version 6 04 Download and install a version and load your old parameter file using the File menu You can then save it in a new format This file will then be readable by newer versions of SORTIE ND If you need help each version of SORTIE ND has its own user manual that will guide you through Last updated 07 Jun 2005 02 37 PM Run setup and progression 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 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 The model counts off the timesteps until it has finished the specified number then cleans up its memory and shuts down Run parameters e Number of timesteps The number of timesteps for which to run the model e Number of years per timestep The length of the timestep i
49. 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 way 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 Juvenile 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 Unlike adult self thinning there is no upper DBH limit applied There is nothing in this behavior which makes it specifically for juvenile trees the name is to match existing SORTIE conventions How it
50. if Adult tree count there are behaviors which use forest cover Gap Light 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 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 Results 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 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 Type of harvest that occurred in the current timestep or 1 Harvest Type if none has occurred Cut Density species x cut Number of trees cut in the current timestep for the given range y species and cut range Cut Basal Area species x Total basal area cut in the current timestep for the given cut range y species and cut range Merchantable Timber Value This grid is created by the Merchantable T
51. in SORTIE By default no output occurs during a SORTIE run You set up output files and choose what data should be saved in them in order to perform data analysis There are two kinds of output files summary output files and detailed output files Summary output files save high level data for a run like population density and basal area Detailed output files save more detailed data in fact as much detail as you want to have they are very flexible To set up output choose Edit gt Output options Once you have produced output files you can ask SORTIE to display charts and graphs using the data visualization features You can also use certain kinds of output as initial conditions in subsequent runs Output strategies in SORTIE 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 You can see a list of chart types and what they require here Also be aware that for overall data the summary output file is a better choice than the detailed output file 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 ba
52. in meters Height at which the GLI Map Creator behavior calculates GLI Height at Which GLI is Calculated for Quadrats in meters Height at which the Quadrat based GLI light behavior calculates GLI Height of Fisheye Photo 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 Applies to all behaviors making GLI or Sail light calculations Seedlings always get fisheye photos at top of crown no matter what this value is Height of Light Filter in m Height in meters at which the Beer s law light filter hangs Only applies to the Beer s law light filter behavior Last Day of 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 Used by all behaviors making GLI or Sail light calculations Light Transmission Coefficient 0 1 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 Light Filter Light Transmission Coefficient Amount of light that is blocked by the light filter Only applies to the Beer s law light filter behavior Minimum Solar Angle for GLI Light in rad 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 This value applies to the GLI light behavior Minimum Solar Angle
53. 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 Ib 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 Correction 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 Merchantable Timber Value This behavior calculates the value of merchantable timber How it wo
54. light level as calculated by the Basal Area Light behavior Conter Racal Area 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 Area towards the light calculation Carbon Value 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 The amount of carbon in the plot for Species X in metric xX tons Carbon Value for Species x The value of the carbon for Species X Dispersed Seeds This grid is created by the Disperse behaviors 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 Description name Number of seeds for Species K The number of seeds in each grid cell belonging to Species X Whether the cell is in gap true or under closed canopy false Gap status P Only used if there are behaviors which use forest cover The count of adult trees for determining gap status Only used
55. 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 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 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 How it works Light levels 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
56. of any species If you wish to use the light level parameter switch also use the Storm Light behavior Linear bi level growth diam only 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 How it works The equation used by this behavior to increment growth is Y a b diam T where 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 Linear 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 T
57. of the model you can add grid maps to a parameter file for use as initial conditions on another run For more information see Adding to a parameter file e Look at the values edit them and print them out To do this use the Grid setup window 25 Jan 2005 01 02 PM Grid list In this document Average Light grid Basal Area Light grid Carbon Value grid Dispersed Seeds grid Gap Light grid GLI Map grid Harvest Results grid Merchantable Timber Value grid Mortality Episode Results grid Partitioned Biomass grid Planting Results grid Quadrat GLI grid Resource grid Seed Predators grid Storm Damage grid Storm Light grid Storm Susceptibility grid Substrate calcs grid Substrate Favorability grid Substrate grid Windstorm Results grid For more on what grids are see Grids 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 This grid is created by the Basal Area Light behavior Each grid cell holds tree basal area data and a light level 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 a Description name Light The
58. 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 in 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 Last updated 03 Aug 2005 09 42 AM Dead tree remover 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 Currently there is only one Dead tree remover How it works This behavior looks for the death flag as set by the mortality b
59. 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 index 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 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 tha
60. parent species in m e isthe 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 undergo non spatial disperse 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 m5 ote Ding el where 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 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 1s the distance in meters from point i to the kth parent tree e
61. ponei as ymp poe Hn with auto height N Scher oe re Aen Puerto Rico semi stochastic diam oniy Re ative Soni limited to basal area a increment SE diam a Unlimited relative growth behavior diam with auto height Unlimited relative growth behavior diam only Stochastic gap growth How growth is applied Growth behaviors increase the size of a tree A tree has two basic size dimensions diameter and height A growth behavior can increase tree size using one of three methods In the first method the behavior calculates an amount of diameter increase 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 way that growth has been applied in all previous versions of SORTIE and is the method you should choose if you are in doubt about which one you want Behaviors using this method have the tag diam with auto height in their name In the second method the behavior calculates an amount of diameter increase and then adds this amount to the tree s diameter The height is not allowed to change The rationale behind this is that tree diameter and height are not always strictly coupled by the allometry equations sometimes diameter and height should be allowed to vary independently If you use a growth behavior of this type it is required that you pair it with a separate behavior i
62. 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 fall 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 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 How it works 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 spe
63. refreshed 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 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 save DBH and tree volume from the Tree volume calculator behavior 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 MAJ 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 table Detailed output files can display specialized tables for the following grids Harvest Results
64. 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 total tree density or as an absolute amount of tree density Trees of any size except seedlings can be cut 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 c
65. substrate 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 n 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
66. tab delimited tree map file Tree map format Here is an example of a tree map X Y Species Type Diam Height 10 34 62 1 Maple Seedling 0 24 0 9 33838 88 9771 Beech Sapling 4 567 O 5 73746 5 16968 Hemlock Adult 15 887 15 3 127 039 146 606 Beech Snag 35 41 28 7 122 571 14 06372 Oak Sapling 2 91 0 9 31396 50 0366 Maple Adult 23 554 14 82 The first row in the file is assumed to be column headers and is ignored by SORTIE ND 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 increases 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 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 Tree setup window to view the list Case is important 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 thi
67. the Grid setup window When you have a group of related behaviors sharing a group of related grids you can assign them the same grid cell size or even multiples of a size to ensure efficient data transfer between them with fewer approximations You can also add grid maps to set the initial conditions for some grids using the File gt Open file command For more on entering the maps from a detailed output file the most likely source see the detailed output file topic You can also use the Grid layer setup window to directly edit the values of grid maps 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 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 the most likely source see the detailed output file topic Last updated 30 Mar 2005 02 44 PM Output
68. the Storm disturbance behavior Storm 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 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 _ expla DBH lt exp a b DBH 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 they survive it this behavior will not try to kill them again even if they are still damaged A certain proportion
69. 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 and the Storm Light behavior applied Density Dependent Seed Survival This behavior assesses seed survival as a function of the local density of conspecific seeds 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 become survive The number of seeds that survives is calculated as Rsp Ssp i exp c Den where e Rs is the number of surviving seeds of a given species in the seed grid cell e Ss 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 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 Proportional Seed Survival This behavior reduces the number of seeds by a set am
70. 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 perform 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
71. 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 a ShE S 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 2 Y D cg 9 C DBH NCI where e Cis the NCI Crowding Effect Slope C parameter e D isthe 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 NCIis 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 S
72. the third DBH cut range in cm Used by the Selection harvest behavior Selection Harvest Cut Range 3 Target Basal Area m2 ha The target basal area in square meters per hectare of the third cut range Used by the Selection harvest behavior Selection Harvest Cut Range 4 Lower DBH cm The lower bound of the fourth DBH cut range in cm Used by the Selection harvest behavior Selection Harvest Cut Range 4 Upper DBH cm The upper bound of the fourth DBH cut range in cm Used by the Selection harvest behavior Selection Harvest Cut Range 4 Target Basal Area m2 ha The target basal area in square meters per hectare of the fourth cut range Used by the Selection harvest behavior Selection Harvest Initial Age The initial age Used by the Selection harvest behavior Standard Deviation lognormal or normal If the Storm Damage Application parameter is set to Stochastic and the Stochastic Pattern Damage Distribution is set to either Normal or Lognormal this is the standard deviation used when randomizing 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 Used by the Storm disturbance behavior Stochastic Pattern Damage Distribution If the Storm Damage Application parameter is set to Stochastic this is the probability distribution function to use
73. the volume total The volume of a tree trunk segment is found as follows V A Az 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 is 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 d a DAH ay a7 thl OO pbx tal Dts H 4X i 0 i where e X 1 hi H 1 p e Qj 1 hi H e p 1 3 H e 7 h 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 Multip
74. 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 only growth behavior applied Logistic growth w size dependent asymptote diam with auto height How it works This behavior calculates annual diameter increases as y _4 b diana J 4 GLT jj where e Y amount of diameter increase in mm e a Size Dep Logistic Diam Intercept a parameter e b Size Dep Logistic Diam Slope b parameter e c Size Dep Logistic Diam Shape Param 1 c parameter e d Size Dep Logistic Diam Shape Param 2 d parameter 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 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 After applying the amount of diameter increase tree height is allowed to update automatically according to the allometry equations 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 behavio
75. type in its upper DBH bound in the box and click Add To remove an existing class select it in the list to the left and click Remove To define a size class for seedlings add a size class with an upper limit of 0 Grid Setup Window This window is reached using the main SORTIE window menu option Edit gt Grid layer setup It allows you to work with grids for your run It has the following options Choosing a grid to work with Cell length in X E W direction in m Cell length in Y N S direction in m Apply cell size changes View edit save grid values Clear grid map Choosing a grid to work with The first step is to choose the grid you would like to work with The active grids appear in the drop down list that shows the option Please select grid when the window is first displayed The grids that appear in that list depends on the list of behaviors for this run editable using the Edit simulation flow window If none of the behaviors with which a grid is associated are enabled then the grid won t show up in the list When you are finished with a grid you can choose another from this list Cell length in X E W direction in m Displays and sets the size of the grid in the X E W direction in meters Some grids do not allow you to change their cell size consult the documentation for individual grids for any limitations or recommendations You can enter any number that you wish between 0 and the leng
76. up 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 How it works The relative 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
77. what you want to save for each tree of that species You can Ctrl click to select multiple data at once Save every X timesteps Choose how often in timesteps you want to save the data The number saves every timestep The number 0 saves only the first and last timesteps Any other number X saves data every X timesteps Add Use the Add button once you have chosen your data and how often you wish to save it What s being saved This is a list of all of the save settings that are currently set up for this tree type If it is not displayed here it won t be saved Remove If you would like to erase a setting select it in the What s being saved box and click Remove 25 Jan 2005 12 52 PM Set up grid save options This window is reached from the Setup detailed output file window It allows you to choose options for grid data for a detailed output file Each grid has different data associated with it so you must choose them separately You choose each piece of data you want to save and how often you want to save it You can work through the process below as many times as you like until you have your settings the way you want them What you save for output depends on what data you want to be available to you after the run For a list of data visualization options and what you need to save to use them see the Data Visualization topic Select a grid Choose one of the current run s active grids from this drop down list The gri
78. works Self thinning uses a simple linear function of probability of mortality as a function of DBH 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 Juvenile 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 There is nothing about this behavior which makes it only applicable to juveniles The name conforms to old SORTIE standards and allows it to be distinguished from the Adult stochastic mortality behavior so that two different rates can be applied to two different groups of trees How it works For each tree a random number is compared to that species s Juvenile Background Mortality Rate parameter to determine if it falls in the pool of trees that die 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 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 po
79. you can ignore this Otherwise a value must be provided for all species Used by all behaviors making GLI or Sail Light calculations e Snag Age Class 3 Light Transmission Coefficient 0 1 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 Used by all behaviors making GLI or Sail Light calculations e Storm Light Intercept of Light Function Intercept of the function to determine light level Used by the Storm Light behavior e Storm Light Max Radius m for Damaged Neighbors The maximum distance in meters within which the Storm Light behavior searches for damaged trees Used by the Storm Light behavior e Storm Light Max Years Damaged Trees Affect Light The maximum amount of time in years after storm damage that a tree will still be counted in the number of damaged trees Used by the Storm Light behavior e Storm Light Minimum Trees For Full Canopy 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 Used by the Storm Light behavior e Storm Light Slope of Light Function Slope of the function to determine light level Used by the Storm Light behav
80. 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 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 open 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 Tips 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 ac
81. your run 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 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 2 DBA AE 2 Xb SH e where e DBH is of the target tree in cm e Xo is the NCI Size Effect Mode in cm X0 parameter e xX is the NCI Size Effect Variance in cm Xb Shading Effect is calculated as SAE gS 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 Y D cg 9 C DBH NCI where e Cis the NCI Crowding Effect Slope C 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 D isthe NCI Crowding Effect Steepness D paramet
82. 1 log 43 54 mA pa 142 a a T T a Se sie ea pe ae 438 a 1 080 1 310 1 549 719 836 892 953 1 014 1 084 1 154 1 223 1 292 1 366 71 1 441 2 logs 91 111 135 159 185 211 244 277 314 351 392 434 480 525 572 619 673 77 1786 844 1 162 1 416 11 666 1 245 1 522 1 784 1 332 1 628 1 910 1 419 1 734 2 037 11 518 1 859 2 188 11 618 1 984 2 338 1 721 12 109 2 494 1 824 2 234 2 649 11 928 12 368 2 796 12 032 2 502 12 944 111 145 168 135 178 208 159 212 Ras h 185 249 295 f 211 286 342 H 332 398 377 1453 a79 b576 657 537 e49 44 505 722 830 660798 925 1 092 1 173 1 429 1 693 1 330 1 569 1 777 1 918 2 059 2 214 2 368 2 534 2 700 2 874 3 049 3 224 B logs 4 logs 5 logs jor f 1 636 1 790 504 538 Am Aral RTI yal eel i ra Form Class 85 DBH inches 10 1 log 45 56 68 82 con 127 a 164 TA oa perl aera Ba Fen Bal Ba m S 516 11 265 1 546 1 823 907 970 1 037 1 104 1 173 1 242 1 318 1 393 1 476 1 558 74 481 2 logs 94 114 138 163 191 219 252 285 322 360 402 444 490 537 588 638 693 745 807 866 930 1 357 1 664 1 953 1 453 1 782 2 096 1 549 1 901 2 240 1 6
83. 48 2 023 2 387 11 746 2 145 2 534 11 859 2 284 2 706 1 972 2 422 2 877 2 088 2 570 3 042 12 203 2 719 3 208 297 355 252 342 412 388 468 440 1531 492 504 678 550 667 765 609 740 852 675 818950 11 205 1 298 1 588 1 874 1 469 1 741 2 101 2 259 2 431 2 603 2 766 2 929 5 123 3 317 3 512 3 logs 4 logs 5 logs 6 logs 1 689 1 844 1 999 32 550 993 1 391 1 706 2 006 2 321 33 587 1 061 1 488 1 827 2 150 2 495 34 624 1 129 1 586 1 948 2 294 2 669 35 663 1 204 1 692 2 080 2 454 2 846 36 702 1 278 1 797 2 212 2 614 3 022 37 744 1 355 1 912 2 352 2 788 3 219 38 785 1 432 2 027 2 493 2 962 3 416 39 828 1 515 2 144 2 644 3 130 3 614 40 872 1 598 2 260 2 795 3 298 3 813 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 visualizat
84. 7 349 Canham C D and S W Pacala 1994 Linking tree population dynamics and forest ecosystem processes pp 84 93 in C G Jones and J H Lawton eds Linking Species and Ecosystems Chapman and Hall New York Coates K D Canham C D Beaudet M Sachs D L and Messier C 2003 Use of a spatially explicit individual tree model SORTIE BC to explore the implications of patchiness in structurally complex forests For Ecol Manage Vol 186 Issue 1 3 297 310 Coates K D and Burton P J 1999 Growth of planted tree seedlings in response to ambient light levels in northwestern interior cedar hemlock forests of British Columbia Can J For Res 29 1374 1382 Frelich Lee E and Craig G Lorimer 1991 A Simulation of Landscape Level stand dynamics in the northern hardwood region Journal of Ecology 79 223 233 Goldenberg Stanley B Christopher W Landsea Alberto M Mestas Nunez and William M Gray 2001 The Recent Increase in Atlantic Hurricane Activity Causes and Implications Science 293 474 479 Greene David F Charles D Canham K David Coates and Philip T LePage 2004 An evaluation of alternative dispersal functions for trees Journal of Ecology 92 758 766 Hilborn Ray and Marc Mangel 1997 The Ecological Detective Confronting Models with Data Princeton University Press Iqbal Muhammed 1983 An Introduction to Solar Radiation Academic Press Toronto Jenkins J C D C Chojnacky L S Heath an
85. Binomial this is the clumping parameter used when randomizing 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 Negative Binomial Used by the Storm disturbance behavior e 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 Used by the Storm damage applier and Storm killer behaviors e Number of Years Damaged Trees Take to Heal The number of years it takes a damaged tree to heal After this time it is considered undamaged Used by the Storm damage applier behavior e 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 Used by the Storm killer behavior e Plot Storm Susceptibility Pattern How storm damage susceptibility varies 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 Used by the Storm disturbance behavior e Return Interval for Severity Storm Class 0 0 1 The return interval in years of storms of severity 0 0 1 Set this to 0 to turn off storms of this severity Used by the Storm disturbance behavior e Return Interval for Severity
86. CI Storm Effect Medium Damage 0 1 The fraction by which a tree s survival probability is reduced when it has sustained medium storm damage Used in the NCI mortality behavior Species i NCI Lambda The scale of the competitive effect of a neighbor tree s species on the target tree s species Used in the NCI mortality behavior Senescence Mortality Alpha Controls the senescence mortality rate Used by the Senescence behavior Senescence Mortality Beta Controls the senescence mortality rate Used by the Senescence behavior 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 Used by the Stochastic Bi Level Mortality behavior e Stochastic Bi Level High Light Mortality Threshold 0 100 The threshold between low light and high light mortality rates as a value between 0 and 100 Used by the Stochastic Bi Level Mortality behavior e 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 Used by the Stochastic Bi Level Mortality behavior e Weibull Annual a Parameter for Snag Size Class 1 Mortality Weibull annual a parameter for those trees whose DBH is less than or equal to the value in Upper DBH of snag size class 1 Used by the Weibull snag mortality behavior e Weibull Annual a Parameter for Snag Size Class 2 Mortality Weib
87. Class 0 8 0 9 The return interval in years of storms of severity 0 8 0 9 Set this to 0 to turn off storms of this severity Used by the Storm disturbance behavior Return Interval for Severity Storm Class 0 9 1 0 The return interval in years of storms of severity 0 9 1 0 Set this to 0 to turn off storms of this severity Used by the Storm disturbance behavior Selection Harvest Cut Range 1 Lower DBH cm The lower bound of the first DBH cut range in cm Used by the Selection harvest behavior Selection Harvest Cut Range 1 Upper DBH cm The upper bound of the first DBH cut range in cm Used by the Selection harvest behavior Selection Harvest Cut Range 1 Target Basal Area m2 ha The target basal area in square meters per hectare of the first cut range Used by the Selection harvest behavior Selection Harvest Cut Range 2 Lower DBH cm The lower bound of the second DBH cut range in cm Used by the Selection harvest behavior Selection Harvest Cut Range 2 Upper DBH cm The upper bound of the second DBH cut range in cm Used by the Selection harvest behavior Selection Harvest Cut Range 2 Target Basal Area m2 ha The target basal area in square meters per hectare of the second cut range Used by the Selection harvest behavior Selection Harvest Cut Range 3 Lower DBH cm The lower bound of the third DBH cut range in cm Used by the Selection harvest behavior Selection Harvest Cut Range 3 Upper DBH cm The upper bound of
88. Height Diameter Function The allometric relationship used to relate DBH and height for saplings Each of the choices is described in detail below Sapling Linear Function Intercept The intercept of the sapling linear function for DBH and height Any species not using that function can omit this value Sapling Linear Function Slope The intercept of the sapling linear function for DBH and height Any species not using that function can omit this value The Sapling Reverse Linear Function Intercept The intercept of the sapling reverse linear function for DBH and height Any species not using that function can omit this value Sapling Reverse Linear Function Slope The slope of the sapling reverse linear function for DBH and height Any species not using that function can omit this value Seedling Height Diameter Function The allometric relationship used to relate diameter at 10 cm and height for seedlings Each of the choices is described in detail below Seedling Linear Function Intercept The intercept of the seedling linear function for DBH and height Any species not using that function can omit this value Seedling Linear Function Slope The slope of the seedling linear function for DBH and height Any species not using that function can omit this value Seedling Reverse Linear Function Intercept The intercept of the seedling reverse linear function for DBH and height Any species not using that function can omit this value Seedlin
89. I growth behavior diam with auto height and NCI growth behavior diam only behaviors NCI Beta NCI function exponent Used in the NCI growth behavior diam with auto height and NCI growth behavior diam only behaviors NCI Crowding Effect Slope C The slope of the curve for the crowding effect equation Used in the NCI growth behavior diam with auto height and NCI growth behavior diam only behaviors NCI Crowding Effect Steepness D The steepness of the curve for the crowding effect equation Used in the NCI growth behavior diam with auto height and NCI growth behavior diam only behaviors NCI Damage Effect Complete Storm Damage 0 1 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 Used in the NCI growth behavior diam with auto height and NCI growth behavior diam only behaviors NCI Damage Effect Medium Storm Damage 0 1 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 Used in the NCI growth behavior diam with auto height and NCI growth behavior diam only behaviors Species i NCI lambda neighbors The competitive effect of neighbors of species i on the target tree species s growth between 0 and 1 Used in the NCI growth behavior diam with auto height and NCI growth behavior diam only behaviors NCI Maximum
90. 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 density or as an absolute amount of tree density Trees of any size except seedlings can be cut 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 proporti
91. LI Weibull d The d parameter in the Weibull function for calculating annual mortality Used by the Height GLI Weibull Mortality behavior Height GLI Weibull Max Mortality 0 1 The maximum mortality probability for a species expressed as a proportion between 0 and 1 Used by the Height GLI Weibull Mortality behavior Include Snags in NCI Calculations Whether or not to include snags when finding competitive neighbors for NCI Used in the NCI mortality behavior Juvenile Background Mortality Rate The proportion of trees that die each year as a value between 0 and 1 Used by the Juvenile stochastic mortality behavior Juvenile Self Thinning Intercept Intercept of the juvenile self thinning linear function Used by the Juvenile self thinning behavior Juvenile Self Thinning Slope Slope of the juvenile self thinning linear function Used by the Juvenile self thinning behavior Light Dependent Mortality Light dependent mortality Used by the GMF mortality and BC morality behaviors Logistic Bi Level Low Light a The a parameter used in low light conditions Used by the Logistic Bi Level Mortality behavior Logistic Bi Level Low Light b The b parameter used in low light conditions Used by the Logistic Bi Level Mortality behavior Logistic Bi Level High Light a The a parameter used in high light conditions Used by the Logistic Bi Level Mortality behavior Logistic Bi Level High Light b The b parameter used in high ligh
92. Mounds 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 Initial Conditions Proportion of Decayed Logs 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 Adding to a parameter file for information on how to do this then the map values will be used for the initial conditions and this number will be ignored Initial Conditions Proportion of Fresh Logs 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 Adding to a parameter file for information on how to do this then the map values will be used for the initial conditions and this number will be ignored Initial Conditions Proportion of Scarified Soil 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 Adding to a parameter file for information on how to do this then the map values will be used for the initial conditions and this number will be ignored Initial Conditions Proportion of Tip Up Mounds The proportion of plot substrate that is tip up mounds substrate when the run starts as a value between 0 and 1 If
93. NCI Beta parameter for the target tree s species e DBHjx 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 is 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 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 The final total growth amount is added to the tree s DBH Height is calculated according to the appropriate allometric equation How to apply it This behavior can be applied to saplings and adul
94. SORTIE ND User Manual Version 6 07 November 30 2006 Author Lora E Murphy Institute of Ecosystem Studies SORTIE ND User Manual e What s New e What s New Archives e Getting started with SORTIE ND o New users o Users of previous versions e Run setup and progression e The SORTIE ND plot e Using SORTIE ND o Creating a parameter file o Parameter file additions o Output o Batching e The SORTIE ND menu o File menu Batch setup window o Edit menu Tree setup window Edit size classes window Grid setup window Grid value edit window Model flow window Current run behaviors window Tree behavior edit window Tree assignments window Parameters window Episodic events window Edit harvest window Edit mortality episode window Edit planting window 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 window o Model menu o Help menu e Trees o Allometry o Tree data member list e Behaviors Harvest and disturbance behaviors Light behaviors Growth behaviors Mortality behaviors Substrate behaviors Tree removal behaviors Disperse behaviors Seed predation behaviors Establishment behaviors Planting behaviors o Analysis behaviors e Grids o Individual g
95. See Light Behaviors for more on GLI calculations Used by the Light Dependent Seed Survival behavior Light Extinction Coeff of Complete Damage Trees 0 1 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 Light Behaviors for more on GLI calculations Used by the Light Dependent Seed Survival behavior Light Extinction Coeff of Medium Damage Trees 0 1 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 Light Behaviors for more on GLI calculations Used by the Light Dependent Seed Survival behavior Light Extinction Coeff of Undamaged Trees 0 1 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 Light Behaviors for more on GLI calculations Used by the Light Dependent Seed Survival behavior Mean Height of Fresh Log Substrate in m The mean height of fresh log substrate in meters Used by the Establishment with Microtopography behavior Mean Height of Mounds in m The mean height of mounded areas in meters Used by the Establishment with Mic
96. a DBH less than the minimum adult DBH See the trees topic for more Seedling A tree less than 1 35 meters tall See the trees topic for more Senescence The slight increase in tree mortality seen among very old very large trees See the mortality behaviors topic for more Short output file A type of output file which provides summary data for a run Synonymous with summary output file See the summary output file topic Silviculture Forestry science The management of tree harvesting and planting Simulation The process of the model receiving input and performing calculations for a specified number of timesteps Synonymous with run Stochastic Chaotic random Stochastic processes in SORTIE generally make heavy use of the random number generator Submodel In previous versions of the model these were pieces of the SORTIE model designed to do a specific task in the simulation Subplot A subarea of the plot chosen by the user This subarea is tracked separately during data analysis Substrate What seedlings germinate in soil and the organic layers on top of it See the substrate behaviors topic Summary output file A type of output file which provides summary data for a run Synonymous with short output file See the summary output file topic Suppression When juvenile trees are in persistently low light conditions their growth slows considerably This is suppression Different species have different tolerances fo
97. a map of substrate values is included in the parameter file see Adding to a parameter file for information on how to do this then the map values will be used for the initial conditions and this number will be ignored Maximum Number of Years that Decay Occurs The number of years that a substrate disturbance event has effect before it is deleted the lifetime of a substrate cohort Partial Cut Proportion of Decayed Logs 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 Partial Cut Proportion of Fresh Logs 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 Partial Cut Proportion of Scarified Soil 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 Partial Cut Proportion of Tip Up Mounds 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 Proportion of Dead that Fall 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 Proportion of F
98. 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 Quadrat based GLI light For more on what GLI is and how it is calculated see above How it works This behavior uses a grid object called Quadrat GLI to help it assign GLI values to the 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
99. 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 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 above How it works 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 Sail light For more on what the Sail Light index is and how it is calculated see above How it works 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 Constant GLI 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
100. able 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 members 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 24 Oct 2006 09 10 AM Edit diameter at 10 cm This window is reached through the Edit Episodic Events Window by clicking on the Plantings tab and clicking the button marked Edit initial diameter at 10 cm When planting seedlings see more on the planting behavior or the Edit Planting Window you can allow their size to default to the value in the New seedling diameter at 10 cm parameter of the tree population or you can specify values for each species All plantings for a run share the same set of values For each species enter the diameter at 10 cm value for newly planted seedlings of that species Actu
101. ablishment with Microtopography 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 Kstablishment parameters e Beam Fraction of Global Radiation The fraction of total solar radiation that is direct beam radiation as opposed to diffuse Expressed as a value between 0 and 1 See Light Behaviors for more on GLI calculations Used by the Light Dependent Seed Survival behavior e Clear Sky Transmission Coefficient Used to determine the amount of solar radiation seen at the plot location See Light Behaviors for more on GLI calculations Used by the Light Dependent Seed Survival behavior e First Day of Growing Season for GLI Light Calculations The first day of the growing season as a Julian day number between 1 and 365 Seeds only get light during the growing season See Light Behaviors for more on GLI calculations Used by the Light Dependent Seed Survival behavior e Fraction Seeds Germinating on Canopy Decayed Logs The proportion of those seeds that land on decayed logs u
102. actual amount of basal area to kill by multiplying this number by the area to which the planned mortality episode is applied SORTIE will work its way down the trees in the disturbed area in size order killing each one that brings the amount of basal area killed closer to the target amount without going over If the size class range and the disturbed area are both large the amount of basal area killed is likely to be very close to the target Diameter Range s to kill Enter the size class ranges you are killing You must enter at least one For each size class enter the minimum and maximum DBH and the amount to kill in that range The units of amount to kill will depend on what you have entered in Amount of mortality type Kill ranges may not overlap Choosing the area to which to apply the planned mortality episode To specify the plot area to which to apply the planned mortality episode select the appropriate cells on the map Cells are each 8 meters by 8 meters Selected cells will show up in color and unselected cells will be white You can click and drag to mark out an area or click on individual cells Clicking or dragging on selected colored cells causes them to become unselected white 07 Dec 2004 10 55 AM Edit Planting Window This window is reached from the Edit Episodic Events Window by clicking on the Plantings tab and selecting New or Edit This window is where you create a new planting event or edit an e
103. al Gap Annual STR 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 Used by the Gap spatial disperse behavior Lognormal Gap Beta The for the lognormal function under gap conditions see equation below This is only required if the gap probability distribution function is lognormal Used by the Gap spatial disperse behavior Lognormal Gap Xo The mean of the lognormal function under gap conditions see equation below This is only required if the gap probability distribution function is lognormal Used by the Gap spatial disperse behavior Lognormal Gap X The variance of the lognormal function under gap conditions see equation below This is only required if the gap probability distribution function is lognormal Used by the Gap spatial disperse behavior Maximum Parent Trees Allowed in Gap Cell 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 Used by the Gap spatial disperse behavior Maximum Search Distance for Neighbor Parents in m The maximum distance that the Anisotropic disperse behavior will look for neighbor parents from a particular point Used by the Anisotropic spatial disperse behavior Mini
104. al 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 X is the mean of the function the Lognormal Canopy Xo or Lognormal Gap Xo parameters e Xj is the variance of the function the Lognormal Canopy X or Lognormal Gap X parameters e mis the amplitude of the anisotropic effect the Amplitude of Anisotropic Effect parameter e is the azimuth angle of maximum dispersal distance the Azimuth Direction of Max Dispersal Distance in rad parameter e 0 is the azimuth angle from the kth parent tree to point i As an example the lognormal function produces the following graph E 15 00 a 5 z 5 10 00 amp 5 00 gz 3 T oo 0 0 50 0 180 0 270 0 360 0 Direction For each grid cell in the Dispersed Seeds grid all neighbor parent trees within a certain radius are found and the appropriate function above is applied to calculate the seed density at that point That number of seeds is added to the grid cell 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 pa
105. al values will be slightly randomized around these values 07 Dec 2004 10 55 AM Output setup window This window is reached using the Edit gt Output options choice on the menu of the main SORTIE window It is a gateway to managing the output options for a run What you save for output depends on what data you want to be available to you after the run For more on output in SORTIE including a guide on what to save see the Output in SORTIE topic For a list of data visualization options and what you need to save to use them see the Data Visualization topic Save Summary Output File out This button opens the Summary output file setup window for saving short or summary output files As a quick check the text just below this button will tell you if there are currently summary output file save settings Save Detailed Output File This button opens the Setup detailed output file window for saving detailed output files As a quick check the text just below this button will tell you if there are currently detailed output file save settings 25 Jan 2005 12 50 PM Setup detailed output file window This window is reached from the Output setup window It is the first step in setting up a detailed output file What you save for output depends on what data you want to be available to you after the run For a list of data visualization options and what you need to save to use them see the Data Visualization topic Output file name
106. allen that Uproot The proportion of fallen trees that uproot to create new tip up mound substrate as a value between 0 and 1 Proportion of Forest Floor Litter Moss Pool that is Moss 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 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 Scarified Soil Annual Decay Alpha The o exponent in the decay equation a2 aS applied to scarified soil Note that this is annual decay Scarified Soil Annual Decay Beta The B exponent in the decay equation os aS applied to scarified soil Note that this is annual decay Tip Up Mounds Annual Decay Alpha The a exponent in the decay equation ang h a gt 28 as applied to tip up mounds substrate Note that this is annual decay Tip Up Mounds Annual Decay Beta The B exponent in the decay equation _ ote a aS applied to tip up mounds substrate Note that this is annual decay Uprooted Tree Radius Increase Factor for Root Rip Out 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 Use Directional Tree Fall If true dead trees fall in a random direction and possibly contribute new fresh log across several Substrate grid
107. am only behaviors Linear Bi Level Slope for High Light Growth b The slope of the linear growth function used in high light conditions Used in the Linear bi level growth diam with auto height and Linear bi level growth diam only behaviors Linear Bi Level Slope for Low Light Growth b The slope of the linear growth function used in low light conditions Used in the Linear bi level growth diam with auto height and Linear bi level growth diam only behaviors Linear Bi Level Threshold for High Light Growth 0 100 The threshold between low light and high light parameters as a value between 0 and 100 Used in the Linear bi level growth diam with auto height and Linear bi level growth diam only behaviors Logistic Asymptotic Diam Growth Full Light in mm yr a Asymptotic annual growth at full light in mm yr Used by the Logistic growth diam with auto height and Logistic growth diam only behaviors Logistic Asymptotic Height Growth Full Light in cm yr a Asymptotic annual growth at full light in cm yr Used by the Logistic growth height only behavior Logistic Diam Shape Param 1 b Shape parameter 1 Used by the Logistic growth diam with auto height and Logistic growth diam only behaviors Logistic Diam Shape Param 2 c Shape parameter 2 Used by the Logistic growth diam with auto height and Logistic growth diam only behaviors Logistic Height Shape Param 1 b Shape parameter 1 Us
108. and 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 z2 himp Ag r p o Za R gt p F a gal 30 where 2 co I gt m fo ae Ta 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 1s 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 Xj is the variance of the function the Lognormal Canopy X or Lognormal Gap Xp parameters e isa disperse parameter the Lognormal Canopy Beta or Lognormal Gap Beta parameters 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 Non gap spatial disperse is called non gap to distinguish it from gap disperse The non gap means that forest cover is ignored
109. and 100 calculated by a light behavior e T number of years per timestep 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 and a diameter only growth behavior applied Linear growth w exponential shade reduction diam with auto height How it works This behavior calculates an amount of diameter growth as Y a b diam GLI 100 T where e Y amount of diameter increase in mm e a Shaded Linear Diam Intercept in mm yr a parameter e b Shaded Linear Diam Slope b parameter e c Shaded Linear Diam Shade Exponent c parameter 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 After applying the amount of diameter increase tree height is allowed to update automati
110. applies The same amount type applies to all size classes e of density You intend to specify kill amounts as a percentage of total density from 0 to 100 The trees killed will be randomly distributed between the minimum and maximum diameters in the size class For small tree populations the amount actually killed may not be exactly what was entered e Amt density ha You intend to specify kill amounts as a number of trees per hectare SORTIE will calculate the actual number of trees to kill by multiplying this number by the area to which the planned mortality episode is applied The trees are removed in size order starting with the tallest in the size class until the target number has been reached or there are no more trees in that size class e 4 of basal area You intend to specify kill amounts as a percentage of total basal area from 0 to 100 SORTIE will add up the basal area in the size class in the cut area and take the percentage in order to figure out how much to kill SORTIE will work its way down the trees in the disturbed area in size order killing each one that brings the amount of basal area killed closer to the target amount without going over If the size class range and the disturbed area are both large the amount of basal area killed is likely to be very close to the target e Amt basal area m ha You intend to specify kill amounts as an amount of basal area in square meters per hectare SORTIE will calculate the
111. are 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 the Apache Software Foundation http www apache org GNU GENERAL PUBLIC LICENSE Version 2 June 1991 Copyright C 1989 1991 Free Software Foundation Inc 59 Temple Place Suite 330 Boston MA 02111 1307 USA Everyone is permitted to copy and distribute verbatim copies of this license document but changing it is not allowed Preamble The licenses for most software are designed to take away your freedom to share and change it By contrast the GNU General Public License is intended to guarantee your freedom to share and change free software to make sure the software is free for all its users This General Public License applies to most of the Free Software Foundation s software and to any other program whose authors commit to using it Some other Free Software Foundation software is covered by the GNU Library General Public License instead You can apply it to your programs too When we speak of free software we are referring to freedom not price Our General Public Licenses are designed to make sure t
112. arts of the simulation engine Read about trees behaviors and grids a kind of data structure Read a little about how a run progresses Then you should read about parameter files which is the way that you input your settings into SORTIE Once you ve done that you are ready to start building a parameter file To create a file from scratch read the topic creating a parameter file from scratch Once you have a parameter file you can read about advanced additions to it in the topic adding to a parameter file Once you have a parameter file you simply load it using the File menu then choose Model gt Run That s all there is to it Wait for the simulation to end then look at your output files using the model s data visualization capabilities Getting started users of previous versions of SORTIE If you have used SORTIE before you re in luck You can probably start doing runs right away The early versions of SORTIE ND were designed to be backwards compatible your old files should load and run Newer versions of SORTIE ND can then use the files created by the earlier versions Before you do arun you may want to familiarize yourself with what s new First read about behaviors They replace submodels When before you might choose the BC juvenile growth submodel for instance now you will choose a growth behavior All submodels from the old model have been translated to behaviors in the new model They may have been slightly
113. as you step through the timesteps If you change the bin size or number of bins the visualizer will preserve your changes Tree map A tree map is available when you have saved the X Y and DBHs of trees in a detailed output file The tree map does not display seedlings The size of the tree circles corresponds to the size of its DBH The color matches the species in the legend If a tree is quite small it may not show up on the map You can change the minimum DBH to make sure that all the trees that you are interested in are displayed If your trees do not show up well you can change the relative sizes of the circles To do this enter a new value for the DBH Scale Factor and click the Update Map button Larger values make the tree circles bigger smaller values make them smaller 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 scroll 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 th
114. asic parameter file has the tree population list of species defined the run behaviors list assembled and the parameters entered Once that s complete here s some extra additions you might make Output Tree maps Grid setup Replicating a point in another run Output A basic parameter file creates no output by default You can perform a run with it but you will not be able to see any of the results since SORTIE ND s data visualization can only occur on run output 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 Tree maps You can set up an initial tree population using density values in size classes using the Parameters window You can also input a known list of trees in a tree map using the File gt Open file command There are two kinds of tree maps those from detailed output files and those you create directly in tab delimited text For more on entering the maps from a detailed output file the most likely source see the detailed output file topic For more on the tab delimited tree map file format see the tab delimited tree map topic You can combine these methods of defining tree initial conditions or use any one alone Grid setup You can manipulate the settings for grids to further optimize your run For many grids you can set the sizes of the grid cells using
115. asy to manually convert any old stmf files to the new format using a spreadsheet program such as Microsoft Excel All other file types are unsupported Last updated 07 Jun 2005 02 46 PM Data Visualization SORTIE runs produce output which you can then use the SORTIE interface to view graphically You can view 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 doing with that data For more on output including a guide on what to save see the topic Output in SORTIE In this document Loading an output file for data visualization Displaying the data from a file Viewing a chart s raw data Viewing charts from a run as it progresses Tips For details on the chart types available see Output Chart Types Loading an output file for data visualization You can load a file by choosing the menu option File gt Open Run Output 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 Displaying the data from a file 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 th
116. atch 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 par3 You can set up a batch of three runs then set up all the parameters in a single file like this parl_1 par2_1 par3_1 parl_2 par2_2 par3_2 parl_3 par2_3 par3_3 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 How to apply it It is easiest if you add the harvest interface after the rest of your parameter file is complete so 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
117. ating new episodic events Editing existing episodic events Deleting existing episodic events Episodic events edit windows Window layout The purpose of the main window is to display episodic events which have already been defined and to provide the starting point for creating new episodic events or editing existing ones On the left is a panel with three tabs labeled Harvests Plantings and Mortality Episodes For more on harvests and planned mortality episodes see the Disturbance Behaviors topic For more on Plantings see the Planting Behaviors topic On the right is a map of the plot On this map is displayed the plot grid cells to which a episodic event is applied In addition if there has been a tree map defined existing trees are also displayed The color key for these trees is at the far right Note to users of previous versions of SORTIE In the past trees would be displayed on the harvest plot if they had been either created by tree map or by size class initial densities This was because since the interface and the core model were completely integrated the initial density data had already been used to create the initial population of trees Now the interface and the core model are separated there are no trees produced from initial density data until the core model executes when Model gt Run is chosen from the main model window If you need to know the initial tree population and distribution in order to creat
118. behavior Basal Area Light Angiosperm c Parameter The c value used to calculate mean GLI from angiosperm basal area Used by the Basal Area Light behavior Basal Area Light Conifer b Parameter The b value used to calculate mean GLI from conifer basal area Used by the Basal Area Light behavior Basal Area Light Conifer c Parameter The c value used to calculate mean GLI from conifer basal area Used by the Basal Area Light behavior Basal Area Light Lognormal PDF Sigma Sigma value for the lognormal probability distribution Used by the Basal Area Light behavior Basal Area Light Mean GLI a Parameter The a value used to calculate mean GLI from basal area Used by the Basal Area Light behavior 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 Used by the Basal Area Light behavior Basal Area Light Minimum DBH for Trees The minimum DBH in cm of trees that count towards basal area Used by the Basal Area Light behavior Basal Area Light Species Type Whether each species is a conifer or an angiosperm for the purposes of light calculations Used by the Basal Area Light behavior Beam Fraction of Global Radiation The fraction of total solar radiation that is direct beam radiation as opposed to diffuse Expressed as a value between 0 and 1 Used by all behaviors makin
119. both short output files and detailed output files For more details on this option see the Output setup window topic 25 Jan 2005 12 29 PM Tree setup window This window is reached from the menu option Edit gt Tree Setup in the main SORTIE ND window It allows you to control some basic aspects of the tree population Edit list of species The top of the window is devoted to editing the species list The box just below this label is the list of current species You can add and remove species from this list To add a species type its name in the box labeled New species and click the button marked Add To remove a species select a species in the list and click the button marked Remove To change the name of a species select it type the new name in the box and click the button Rename Edit initial densities size classes This button allows you to edit the size classes for tree population initial density by opening the Edit size classes window Size classes help you to define the initial conditions for the tree population Size classes are not required if you do not want to define your initial tree population this way Add tree map This lets you load a tab delimited tree map file and add it to your current parameter file These trees will add to any tree maps already loaded Remove tree map trees If there is a tree map loaded then the button marked Remove tree map trees is enabled If you want to remove all cur
120. bplot with the lower number but you won t be able to see your selections because the subplot with the higher number is covering them up To avoid mistakes you should completely finish each subplot before creating a new one especially if their areas will overlap If you need to make changes to a partially hidden subplot you might want to erase the higher subplot areas and then put them back in when you re done If you are setting up both summary and detailed output and you want to use the same subplots for both there is a button to copy subplots already defined for the other file type to the current file type Displaying additional information Subplots are often used to analyze the effects of specific episodic events such as silvicultural treatments To input episodic events use the Edit Episodic Events Window To help you with this the subplots window will display episodic events for you on the map You can display harvest planned mortality episodes and planting events You scroll through the events in the same order in which they were created in the edit windows The button colors match the colors in which the events will display on the map Note that subplots will cover up episodic events that have the same area and episodic events may cover each other as well If you are having trouble seeing an episodic event use the buttons to set all the other episodic events to display the event number 0 Last updated 18 May 2006 12 56 PM
121. 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 Tree height is allowed to update automatically according to the allometry equations 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 limited to basal area increment diam only 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 and a height incrementing growth behavior applied Unlimited relative growth diam with auto height How it works The amount of increase returned by the relative growth equation is applied to the tree Tree height is allowed to update automatically according to the allometry equations How to apply it This behavior can be applied to seedlin
122. cally according to the allometry equations 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 Linear growth w exponential shade reduction diam only How it works This behavior calculates an amount of diameter growth as Y a b diam GLI 100 T where e Y amount of diameter increase in mm e a Shaded Linear Diam Intercept in mm yr a parameter e b Shaded Linear Diam Slope b parameter e c Shaded Linear Diam Shade Exponent c parameter 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 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 height only growth behavior applied Logistic growth height only How it works The amount of height increase is calculated as a J e GiT i where Y amount of height increase in cm a Logistic Asymptotic Height Growth Full Light in cm yr a b Logistic Height Shape Param 1 b parameter c Logistic Height Shape Param 2 c parameter GLI global light index as a percentage between 0 and 100 calculated b
123. ce c The resource dependent mortality parameter Used by the Exponential Growth and Resource Based Mortality behavior Exponential Growth Resource d Used by the Exponential Growth and Resource Based Mortality behavior Growth Resource Scaling Factor rho Scaling factor to reduce survival at the mode of the survival probability function Used by the Growth and Resource Based Mortality behavior Growth Resource Function Mode mu Determines the mode of the function along a gradient of the resource R the mode is the optimal niche of a species Used by the Growth and Resource Based Mortality behavior Growth Resource Survival Increase with Growth delta Specifies the increase in survival caused by amount of growth Used by the Growth and Resource Based Mortality behavior Growth Resource Low Growth Survival Parameter sigma Affects the shape of the survival probability distribution in low growth conditions Used by the Growth and Resource Based Mortality behavior Height GLI Weibull a The a parameter in the Weibull function for calculating annual mortality Used by the Height GLI Weibull Mortality behavior Height GLI Weibull b The b parameter in the Weibull function for calculating annual mortality Used by the Height GLI Weibull Mortality behavior Height GLI Weibull c The c parameter in the Weibull function for calculating annual mortality Used by the Height GLI Weibull Mortality behavior Height G
124. cells If false dead trees collapse vertically and contribute all their fresh log area to the cell in which they are rooted 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 d
125. ch for shading neighbors For GLI this is done by comparing the height of the fisheye photo to the maximum possible tree height and determining how far away a tree of this height could be and still have its crown appear in the sky above the minimum solar angle All trees within this search radius that are taller than the height of the fisheye photo and thus can be seen by it are added into the photo For Sail Light the search distance is specified by the user To add a shading neighbor to the photo the light behavior determines the amount and location of sky covered by its crown In a GLI calculation neighbor crowns are approximated as cylinders In a Sail Light calculation neighbor crowns are approximated as 2 D rectangles with a width equal to their crown diameter and a height equal to their crown height or as an added simplification the behavior can assume the crowns of shading neighbors extend all the way to the ground The amount of radiation received from the portion of the sky blocked by the shading neighbor is multiplied by the light transmission coefficient for the neighbor s species The effects of multiple neighbors blocking the same patch of sky are multiplicative Once all shading neighbors have been added to the fisheye photo the amount of light that can still be seen from each region of the sky is totaled up into the appropriate index Sky Simulation Equations All equations are from Iqbal 1983 At a given solar tim
126. cies to which this behavior is applied the seeds are eaten with equal enthusiasm the proportions of each type are captured before predation and any leftover seeds are redistributed according to those proportions 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 IR N where e Ois offta
127. coefficient If your run does not work with snags you can ignore this Used by the Light Dependent Seed Survival behavior e Upper Age Yrs of Snag Light Extinction Class 2 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 Used by the Light Dependent Seed Survival behavior Substrate Dependent Seed Survival No Gap Status This behavior assesses seed survival based on substrate conditions 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 list above 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 tho
128. d R A Birdsey 2004 Comprehensive Database of Diameter based Biomass Regressions for North American Tree Species United States Department of Agriculture Forest Service General Technical Report NE 319 http www fs fed us ne Kobe R K S W Pacala J A Silander Jr and C D Canham 1995 Juvenile tree survivorship as a component of shade tolerance Ecological Applications 5 517 532 Kobe R K and K D Coates 1997 Models of sapling mortality as a function of growth to characterize interspecific variation in shade tolerance of eight tree species of northwestern British Columbia Canadian Journal of Forest Research 27 227 236 LePage P Canham C D Coates K D and Bartemucci P 2000 Seed abundance versus substrate limitation of seedling recruitment in northern temperate forests of British Columbia Can J For Res 30 415 427 Messavage C and J W Girard 1956 Tables for estimating board foot volume of timber USDA Forest Service Pacala S W C D Canham and J A Silander Jr 1993 Forest models defined by field measurements I The design of a northeastern forest simulator Canadian Journal of Forest Research 23 1980 1988 Pacala S W C D Canham J A Silander Jr and R K Kobe 1994 Sapling growth as a function of resources in a north temperate forest Canadian Journal of Forest Research 24 2172 2183 Pacala S W C D Canham J Saponara J A Silander Jr R K Kobe and E Ribbens 1996
129. d 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 normal distribution is z2 pt xjax pi airh ono where o is the function standard deviation Mean is zero The lognormal distribution is acre 2 pt xjdx Z y ax xV2n0 where is the function mean and o is the standard deviation The Poisson distribution is 274 JaN where A is the function mean The negative binomial distribution is P x u EEB e Eo Tika lu tk where u is the function mean and k is the clumping parameter This is Equation 3 103 from Hilborn and Mangel Disperse parameters e Amplitude of Anisotropic Effect The amplitude of the anisotropic effect how strongly the distances differ in the maximum and minimum directions Used by the Anisotropic spatial
130. d 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 the previous year The total diameter increment is the sum of the X individual diameter 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 and a height only 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 GLI If a cell is in gap a tree in that cell is randomly chosen out of all the trees to which the behavior 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 Ga
131. danger that redistributors of a free program will individually obtain patent licenses in effect making the program proprietary To prevent this we have made it clear that any patent must be licensed for everyone s free use or not licensed at all The precise terms and conditions for copying distribution and modification follow TERMS AND CONDITIONS FOR COPYING DISTRIBUTION AND MODIFICATION 0 This License applies to any program or other work which contains a notice placed by the copyright holder saying it may be distributed under the terms of this General Public License The Program below refers to any such program or work and a work based on the Program means either the Program or any derivative work under copyright law that is to say a work containing the Program or a portion of it either verbatim or with modifications and or translated into another language Hereinafter translation is included without limitation in the term modification Each licensee is addressed as you Activities other than copying distribution and modification are not covered by this License they are outside its scope The act of running the Program is not restricted and the output from the Program is covered only if its contents constitute a work based on the Program independent of having been made by running the Program Whether that is true depends on what the Program does 1 You may copy and distribute verbatim copies of the Program s sourc
132. 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 can apply planting in one of two ways You can create new planting treatments using the Edit Episodic Events Window by choosing the Edit gt Episodic events option from the main SORTIE window If you have existing harvest regime files with planting data from previous versions of SORTIE you can input them into your run as well For instructions on how to do this see the Adding to a parameter file topic 25 Jan 2005 01 01 PM Analysis behaviors In this document Analysis parameters Carbon Value behavior Dimension Analysis behavior Merchantable Timber Value behavior Partitioned DBH Biomass behavior Partitioned Palm Biomass behavior Tree Bole Volume calculator behavior Tree Age behavior Tree Volume Calculator behavior 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 Analysis parameters Bole Volume Form Class 60 100 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 Used by the Tree Bole Volume Calculator behavior Bole Volume Parameter b0 The b0 parameter for the bole volume equatio
133. disperse behavior e Azimuth Direction of Max Dispersal Distance in rad The azimuth direction in radians north zero east positive of the maximum dispersal distance Used by the Anisotropic spatial disperse behavior e Beta for Stumps 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 Used by the Gap spatial disperse and Non gap spatial disperse behaviors e Canopy Function Used The probability distribution function to be used to distribute seeds in canopy conditions For the behaviors Non gap spatial disperse and Anisotropic disperse these PDFs are always the ones used Used by the Non gap spatial disperse Gap spatial disperse and Anisotropic spatial disperse behaviors e Gap Function Used The probability distribution function to be used to distribute seeds in gap conditions Used by the Gap spatial disperse behavior e Intercept of Mean Non Spatial Seed Rain seeds m7 yr The intercept of the non spatial seed rain function This is the bath seed rain term Set this value to zero to turn off bath non spatial seed rain Used by the Non spatial disperse behavior e Lognormal Canopy Annual STR 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 distrib
134. does not yet yield good results and needs tweaking It is recommended that you NOT use it How it works Extra parameters are added to the Weibull and lognormal probability distribution functions to allow for anisotropy For Weibull R RS ir pat ID x cos p 6 m k l where ses jer eee Emi D 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 Weibull Canopy Annual STR or Weibull Gap Annual STR parameters e DBH is the DBH in cm of the k 1 T parent trees within a specified radius of location 1 e Disa species specific dispersion 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 e mis the amplitude of the anisotropic effect the Amplitude of Anisotropic Effect parameter e isthe azimuth angle of maximum dispersal distance the Azimuth Direction of Max Dispersal Distance in rad parameter e 0 is the azimuth angle from the kth parent tree to point i For lognormal in Mik a To ecos DBH B oe gE Some k l where in Mit PE EE EA aa xy n fe 0 and where e Riis the density m2 of seedlings at a given point i e STR the standardized tot
135. ds that appear in that list depends on the list of behaviors for this run editable using the Edit simulation flow window If none of the behaviors with which a grid is associated are enabled then the grid won t show up in the list Save every X timesteps Choose how often in timesteps you want to save this grid s data The number saves every timestep The number 0 saves only the first and last timesteps Any other number X saves data every X timesteps For this grid save Choose the data to save for this grid Ctrl click to select multiple items For an explanation of what each grid s data is see the individual grid documentation Add Use the Add button once you have chosen your data and how often you wish to save it What s being saved This is a list of all of the save settings that are currently set up for all grids Remove If you would like to erase a setting select it in the What s being saved box and click Remove 25 Jan 2005 12 53 PM Summary output file setup window This window is reached from the Output setup window It allows you to set options for a summary output file Only one of these files may be saved per run What you save for output depends on what data you want to be available to you after the run For a list of data visualization options and what you need to save to use them see the Data Visualization topic Output File Name Enter your output file name here or choose the Browse button to navi
136. e Dependent Seed Survival With Gap Status behavior Fraction Seeds Germinating on Gap Scarified Soil 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 Used by the Substrate Dependent Seed Survival With Gap Status behavior Fraction Seeds Germinating on Gap Tip Up 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 Used by the Substrate Dependent Seed Survival With Gap Status behavior Fraction Seeds Germinating on Ground Decayed Logs 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 Used by the Substrate Based Seed Survival With Microtopography behavior Fraction Seeds Germinating on Ground Forest Floor Litter 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 Used by the Substrate Based Seed Survival With Microtopography behavior Fraction Seeds Germinating on Ground Forest Floor Moss 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 Used by the Substrate Based Seed Survival With Microtopography behavior Fract
137. e 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 e 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 each 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
138. e the sun s zenith angle is calculated by cos 0 sin sing cos 6 cos Q COS and its azimuth angle is calculated by cos y sina sin Q sind cos a cos Q where e angle from zenith in degrees e solar declination in degrees e g Plot Latitude in decimal degrees parameter from Plot e a the solar altitude angle from horizon in degrees e the hour angle solar time Azimuth here is south zero east positive Solar declination is calculated by 0 006918 0 399912 cos I 0 070257 sin T 0 006758 cos 2I 0 000907 sin 2T 0 002697 cos 3I 0 00148 sin 3I where solar declination in radians and J is the day angle in radians The day angle is calculated by J 2z d 1 365 where I is the day angle in radians and dis the Julian day number day of the year between 1 and 365 So once we finally have the azimuth and altitude angles for the sun s position in the sky we can calculate the amount of direct beam radiation coming from it and add it to the appropriate grid cell The direct beam radiation equation is I Eo t cos 0 where e J is the beam radiation Eo is the earth s eccentricity Tis the Clear Sky Transmission Coefficient parameter mis the optical mass of the atmosphere 0 is the zenith angle of the sun Eccentricity is calculated by Eo 1 000110 0 034221 cos I 0 001280 sin I 0 000719 cos 2I 0 000077 sin 2T where J is the day angle equation above Optica
139. e Puerto Rico storm bi level growth diam with auto height behavior PR Storm Bi Level Intercept for Low Light Growth a The intercept of the linear growth function used in low light conditions Used in the Puerto Rico storm bi level growth diam with auto height behavior PR Storm Bi Level Slope for Low Light Growth b The slope of the linear growth function used in high light conditions Used in the Puerto Rico storm bi level growth diam with auto height behavior Relative Michaelis Menton Growth Diameter Exponent The exponent to be used with diameter when calculating relative growth Used in the Relative growth behaviors Shaded Linear Diam Intercept in mm yr a Intercept of the size dependent growth potential in mm yr Used by the Linear growth w exponential shade reduction diam with auto height and Linear growth w exponential shade reduction diam only behaviors Shaded Linear Diam Shade Exponent c Effect of shading Used by the Linear growth w exponential shade reduction diam with auto height and Linear growth w exponential shade reduction diam only behaviors Shaded Linear Diam Slope b Slope of the size dependent annual growth potential Used by the Linear growth w exponential shade reduction diam with auto height and Linear growth w exponential shade reduction diam only behaviors Shaded Linear Height Intercept in cm yr a Intercept of the size dependent growth potential in cm yr Used by t
140. e 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 multiple 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 Last Updated 01 Nov 2006 06 04 AM Growth behaviors In this document How growth is applied Growth parame ors Absolute growth behaviors Absolute growth limited to radial increment behavior diam with auto height Absolute growth limited to radial increment behavior diam only Absolute growth limited to basal area increment behavior diam with auto height Absolute growth limited to basal area increment behavior diam only Unlimited absolute growth behavior diam with auto height Unlimited absolute growth behavior diam only Allometric height incrementer Basal area NCI growth diam with auto height Basal area NCI growth diam only stant basal area growth behavior diam with auto heig Constant basal area growth behavior diam only S onsa ata eet behavior diam with auto height ht ar vel growth Tas with aut Linear bi level growth diam only 19 eight Linear growth w er meas a a ae Logistic promt o ht only Logistic ie grow w size caer dent asymptote height only i ic growth wi size i
141. e behavior s assignment to any other trees Apply to species type There is a button marked Apply to species type to apply your changes to the tree type species combination for instance Apply to Species 1 Saplings Behaviors you have added to the list are applied to that species type combination Behaviors you have removed have that species type combination deleted from their list If a tree dependent behavior no longer applies to anything as a result of your choice it is removed from the run If you have made an invalid behavior assignment you will receive an error message and be given the opportunity to correct your choices Apply to all type There is a button marked Apply to type to apply your changes to all species of the specified tree type All existing behavior applications for any species of the specified type are deleted and replaced with the behavior choices listed If a tree dependent behavior no longer applies to anything as a result of your choice it is removed from the run If you have made an invalid behavior assignment you will receive an error message and be given the opportunity to correct your choices Tree assignments window This window is reached from the Current run behaviors window or from the Edit harvest interface window It modifies the trees to which a behavior is applied The current list of tree species type combinations is shown on the right hand side of the window The left hand side a
142. e center of each grid 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 number of heavily damaged trees N is counted 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 Snags that were created because a tree was killed by a process other than a storm are not counted 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 Basal Area Light behavior This behavior calculates light levels as a function of the ba
143. e code as you receive it in any medium provided that you conspicuously and appropriately publish on each copy an appropriate copyright notice and disclaimer of warranty keep intact all the notices that refer to this License and to the absence of any warranty and give any other recipients of the Program a copy of this License along with the Program You may charge a fee for the physical act of transferring a copy and you may at your option offer warranty protection in exchange for a fee 2 You may modify your copy or copies of the Program or any portion of it thus forming a work based on the Program and copy and distribute such modifications or work under the terms of Section 1 above provided that you also meet all of these conditions e a You must cause the modified files to carry prominent notices stating that you changed the files and the date of any change e b You must cause any work that you distribute or publish that in whole or in part contains or is derived from the Program or any part thereof to be licensed as a whole at no charge to all third parties under the terms of this License e c If the modified program normally reads commands interactively when run you must cause it when started running for such interactive use in the most ordinary way to print or display an announcement including an appropriate copyright notice and a notice that there is no warranty or else saying that you provide a warranty and that users may
144. e 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 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 Viewing a chart s raw data You can save the raw data used to make any chart to a tab delimited text file suitable for viewing in spreadsheet 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 Viewing charts from a run as it progresses 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
145. e 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 the 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
146. e now species specific Getting started with SORTIE In this document How does SORTIE work How do I start working with SORTIE How does SORTIE work It is important when starting with SORTIE to understand a little bit about how SORTIE works SORTIE is a program designed to simulate the life cycles of individual trees and assess the impacts of various external events on them SORTIE does this by creating individual virtual trees and allowing certain processes chosen by the user to act on these trees These processes are called behaviors and usually correspond to biological processes For instance a simulation might consist of three behaviors 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 The behaviors have a certain order in which they act When all of the behaviors have acted once that s a single timestep The process is repeated for the number of timesteps that you set and that s a single simulation or run Different species have different requirements of course and trees undergo different processes at various points within their life cycle Behaviors can be applied to very specific tree subsets and you can use different versions of a similar behavior to get the effects you wish to achieve How do I start working with SORTIE First you may want to familiarize yourself with the various p
147. e 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 Stochastic bi level mortality This behavior applies a constant rate of mortality to trees with different rates for high light and low light conditions How it works 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 Stochastic Bi Level High Light Mortality Threshold 0 100 parameter 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 Leve
148. e 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 detailed output file for analysis Tree Bole Volume Calculator This behavior calculates merchantable tree volume Make sure to distinguish between this behavior and the other tree volume behavior How it works Tree volume is calculated as follows V b0 bl 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 de
149. e your episodic events use a tree map If you want to create a tree map with a random distribution of trees from size class data do the following Load your parameter file without episodic event information 2 Enter the appropriate size classes using Edit gt Tree Setup and the appropriate initial density information using Edit gt Parameters In the parameters set the length of the run to be 1 timestep 4 Using Edit gt Output Options create a detailed output file with the X Y and DBH of the saplings and adults of each species 5 Save the parameter file under a different name 6 Choose Model gt Run from the main SORTIE window or run one timestep This causes the model to be run A tree map of the initial density data you entered is then created 7 Load your original parameter file again 8 Use the instructions in the detailed output files topic to get the detailed output timestep file for timestep 0 and add it to the parameter file 9 Proceed to enter your episodic events 09 Displaying current episodic events To display existing episodic events choose the tab of the type of episodic event you would like to see The episodic events are numbered in the order that they were entered You will see the currently displayed episodic event and what its number is of the total for example Showing harvest 3 of 5 Use the backward and forward buttons to move back and forth through the current episodic
150. ead snags and live trees there is a certain probability 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 Tip up mounds Scarified sail Fresh logs Decayed Relationships 1 2 4 and 6 represent the decay of the different substrates as a function of substrate age according to the equation y aso where t is time in years Graphed this equation looks like this Hypothetical Substrate Loss Function _ Remaining ae ee dd 9 Losthyr 0 5 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 8 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
151. ear return interval as a value between 0 no mortality and 1 complete devastation Used by the Windstorm behavior Windstorm Severity for 5 Year Return Interval Storm The severity of storms with a 5 year return interval as a value between 0 no mortality and 1 complete devastation Used by the Windstorm behavior Windstorm Severity for 10 Year Return Interval Storm The severity of storms with a 10 year return interval as a value between 0 no mortality and 1 complete devastation Used by the Windstorm behavior Windstorm Severity for 20 Year Return Interval Storm The severity of storms with a 20 year return interval as a value between 0 no mortality and 1 complete devastation Used by the Windstorm behavior Windstorm Severity for 40 Year Return Interval Storm The severity of storms with a 40 year return interval as a value between 0 no mortality and 1 complete devastation Used by the Windstorm behavior Windstorm Severity for 80 Year Return Interval Storm The severity of storms with a 80 year return interval as a value between 0 no mortality and 1 complete devastation Used by the Windstorm behavior Windstorm Severity for 160 Year Return Interval Storm The severity of storms with a 160 year return interval as a value between 0 no mortality and 1 complete devastation Used by the Windstorm behavior Windstorm Severity for 320 Year Return Interval Storm The severity of storms with a 320 year return int
152. eator Number of grid cells into which the sky is divided from horizon to zenith for the purpose of calculating light direction Used by the GLI Points File Creator behavior If the GLI light behavior is also used this value is not required Number of Altitude Sky Divisions for Quadrat Light Calculations Number of grid cells into which the sky is divided from horizon to zenith for the purpose of calculating light direction Used by the Quadrat based light behavior If the GLI light behavior is also used this value is not required Number of Azimuth Sky Divisions for GLI Light Calculations Number of grid cells into which the sky is divided around the horizon for the purpose of calculating light direction Used by the GLI light behavior as well as the Quadrat based light and GLI Map Creator behaviors if different values are not specified for them Number of Azimuth Sky Divisions for GLI Map Creator Calculations Number of grid cells into which the sky is divided around the horizon for the purpose of calculating light direction Used by the GLI Map Creator behavior If the GLI light behavior is also used this value is not required Number of Azimuth Sky Divisions for GLI Points Creator Number of grid cells into which the sky is divided around the horizon for the purpose of calculating light direction Used by the GLI Points File Creator behavior If the GLI light behavior is also used this value is not required Number of Azimuth Sky Divisions
153. ect 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 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 How it works The equation used by this behavior to calculate survival probability is m Ee ltexp at 5 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 Logistic 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 diam 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 th
154. ect it in the list labeled Current behavior order then click Up or Down to move it You cannot move it past a dashed line This ensures behavior orders that make sense Removing behaviors the Remove button To remove a behavior from the run select it in the list labeled Current behavior order and click the button marked Remove Changing behavior assignments the Modify assigned data button This button changes the trees to which a behavior applies if the behavior is of a kind applied to trees and most are Select a behavior in the list labeled Current behavior order and then click the Modify assigned data button This brings up the Tree assignments window to allow you to modify the assignments Tree behavior edit window This window is reached through the Edit simulation flow window It edits the list of behaviors for a given tree combination of species and type life history stage The combination being edited is displayed in the top of the window The current list of behaviors in order appears in the box labeled Assigned behaviors In this window Adding new behaviors Removing behaviors Apply to species type Apply to all type Adding new behaviors The left hand side of the window is devoted to choosing new behaviors to apply to this tree type species combination Begin by choosing an overall behavior grouping using the drop down list that shows Please select a behavior group when the w
155. ected Partial cut under Cut type Enter how you intend to specify the amount to cut in each size class you want to cut The same cut amount type applies to all size classes e 9 of density You intend to specify cut amounts as a percentage of total density to remove from 0 to 100 The trees removed will be randomly distributed between the minimum and maximum diameters in the size class For small tree populations the amount actually removed may not be exactly what was entered e Amt density ha You intend to specify cut amounts as a number of trees per hectare to remove SORTIE will calculate the actual number of trees to remove by multiplying this number by the area to which the harvest is applied The trees are removed in size order starting with the tallest in the size class until the target number has been reached or there are no more trees in that size class e of basal area You intend to specify cut amounts as a percentage of total basal area to remove from 0 to 100 SORTIE will add up the basal area in the size class in the cut area and take the percentage in order to figure out how much to cut SORTIE will work its way down the trees in the cut area in size order removing each one that brings the amount of basal area removed closer to the target amount without going over If the size class range and the cut area are both large the amount of basal area removed is likely to be very close to the target e Amt basal area m7
156. ecutable form under the terms of Sections and 2 above provided that you also do one of the following e a Accompany it with the complete corresponding machine readable source code which must be distributed under the terms of Sections 1 and 2 above on a medium customarily used for software interchange or e b Accompany it with a written offer valid for at least three years to give any third party for a charge no more than your cost of physically performing source distribution a complete machine readable copy of the corresponding source code to be distributed under the terms of Sections 1 and 2 above on a medium customarily used for software interchange or e c Accompany it with the information you received as to the offer to distribute corresponding source code This alternative is allowed only for noncommercial distribution and only if you received the program in object code or executable form with such an offer in accord with Subsection b above The source code for a work means the preferred form of the work for making modifications to it For an executable work complete source code means all the source code for all modules it contains plus any associated interface definition files plus the scripts used to control compilation and installation of the executable However as a special exception the source code distributed need not include anything that is normally distributed in either source or binary form with the major componen
157. ed by the Logistic growth height only behavior Logistic Height Shape Param 2 c Shape parameter 2 Used by the Logistic growth height only behavior Lognormal Bi Level Max Growth in High Light m The maximum height growth in meters under high light conditions Used by the Lognormal bi level growth height only behavior Lognormal Bi Level Max Growth in Low Light m The maximum height growth in meters under low light conditions Used by the Lognormal bi level growth height only behavior Lognormal Bi Level X0 for High Light Growth The Xo parameter to use under high light growth conditions Used by the Lognormal bi level growth height only behavior Lognormal Bi Level X0 for Low Light Growth The Xo parameter to use under low light growth conditions Used by the Lognormal bi level growth height only behavior Lognormal Bi Level Xb for High Light Growth The X parameter to use under high light growth conditions Used by the Lognormal bi level growth height only behavior Lognormal Bi Level Xb for Low Light Growth The X parameter to use under low light growth conditions Used by the Lognormal bi level growth height only behavior Lognormal Bi Level Threshold for High Light Growth 0 100 Used by the Lognormal bi level growth height only behavior Lognormal Diam Effect of Shade c Effect of shade Used by the Lognormal with exponential shade reduction diam with auto
158. ee 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 foot logs pA log 3log 4 log tree 5 log tree 6 log tree DBH tree 7 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 ie Waa ee e ee ee ee eee ea eee a ee erin em e 12 1 6 11 3115 1 11 4 1 9 e 14 17 i4li6i2iasy2 W W W W IW qa qe fe ye ia WRG NOS 1S aT Weel ces Ieee cae ct Pee Wee Mae i8 Ia oa Pet Wis p av h he e e ee ie
159. ee 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 it is not actually created Tree life history stage transitioning growth and death Trees transition between life history stages as they grow When a seedling reaches the maximum 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 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 The reasons why a tree is killed are natural causes harvest insects fi
160. ees upon which to act Tree population initial conditions When setting up a simulation a key part is to define the initial tree population 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 by describing a particular pattern of densities by species and size range size class You define size classes in the Tree setup window and enter densities in the Parameters window The second way is to directly list a particular set of trees in a tree map within the parameter file Tree parameters e Initial Densities The density of trees in number per hectare for that size class Trees are randomly placed within the chosen size range which starts at the value of the size class beneath or 0 if there is none and ends at the value for the current size class The aim is for an even distribution You can also set up a size class for seedlings Seedlings set up this way are given a slightly randomized value of New seedling diameter at 10 cm below You can further specify seedling initial densities using the seedling height class parameters You can set up size classes in the Tree setup window e Initial Density ha Seedling Height Class 1 Number of seedlings per hectare to create in the first seedling height class not required The lower bound of this class is 0 cm and the upper bound is the value in the Seedling Height Class 1 Up
161. ehaviors For each tree that it finds with that flag it sends a request to the tree population to kill the tree The reason passed to the tree population for the death of the tree is natural death How to apply it This behavior should be applied to all tree species and tree types All trees to which this behavior is applied must also have a light behavior applied This is a signal to this behavior that the trees are going to have their data set up in the expected way 24 Jun 2004 12 38 PM Disperse behaviors In this document Seed randomization Disperse parameters Non spatial disperse behavior Spatial disperse behaviors Non gap spatial disperse behavior Gap spatial disperse behavior Anisotropic spatial disperse behavior 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 You can change this grid s cell resolution 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 Trees these seeds are not individuals but merely numbers in a grid You coul
162. em 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 IMPORTANT The new coordinates are different from the older versions of SORTIE in which the axes were switched When the new version converts older files the coordinate conversions are made automatically 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 parameters e Plot Length in the X
163. endent 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 The proportion of seeds of Species X expected to germinate Species X in that cell Windstorm Results 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 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 Last updated 08 Nov 2006 11 33 AM The parameter file In this document What is a parameter file Contents of a parameter file Editing a parameter file Validating a parameter file Making a human readable copy of the parameter file What is a parameter file
164. ength 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 diam with auto height 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 Tree height is allowed to update automatically according to the allometry equations 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 Absolute growth limited to radial increment diam only 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 increm
165. ensity Adult Abs Den e Sapling relative basal area Sapl Rel BA e Sapling absolute basal area Sapl Abs BA Sapling relative density Sapl Rel Den Sapling absolute density Sapl Abs Den Seedling absolute density Sdl Abs Den Snag tree relative basal area Snag Rel BA 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 and absolute data types also include a total across species For a definition of the different tree types see the Trees topic You can define areas within the plot to track separately These are called subplots These subplots do not have to be continuous and you can define more than one In order to define subplots use the Edit Subplot window The output options you choose for the main window will apply to the subplots too You cannot define separate options for them 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 arow for each subplot for each timestep You can view graphs of summary output files using SORTIE s data visualization functions
166. ent asymptote diam only and Logistic growth w size dependent asymptote diam with auto height behaviors Size Dep Logistic Diam Shape Param 2 d Shape parameter 2 for shade reduction of annual growth Used by the Logistic growth w size dependent asymptote height only and Logistic growth w size dependent asymptote diam with auto height behaviors Size Dep Logistic Diam Slope b Slope of the size dependent annual growth potential Used by the Logistic growth w size dependent asymptote diam only and Logistic growth w size dependent asymptote diam with auto height behaviors Size Dep Logistic Height Intercept a Intercept of the size dependent annual growth potential Used by the Logistic growth w size dependent asymptote height only behavior Size Dep Logistic Height Shape Param 1 c Shape parameter for shade reduction of annual growth Used by the Logistic growth w size dependent asymptote height only behavior Size Dep Logistic Height Shape Param 2 d Shape parameter 2 for shade reduction of annual growth Used by the Logistic growth w size dependent asymptote height only behavior Size Dep Logistic Height Slope b Slope of the size dependent annual growth potential Used by the Logistic growth w size dependent asymptote height only behavior Slope of Growth Response S Slope of the Michaelis Menton growth function at zero light for relative and absolute growth behaviors S in the equatio
167. ent 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 and a height incrementing growth behavior applied Absolute growth limited to basal area increment diam with auto height 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 Tree height is allowed to update automatically according to the allometry equations 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 Absolute growth limited to basal area increment diam only 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 T
168. ependent Seed Survival No Gap Status and Substrate Dependent Seed Survival With Gap Status behaviors Fraction Seeds Germinating on Canopy Tip Up The proportion of those seeds that land on tip up mounds substrate under canopy conditions that survive to become seedlings Expressed as a value between 0 and 1 Used by the Substrate Dependent Seed Survival No Gap Status and Substrate Dependent Seed Survival With Gap Status behaviors Fraction Seeds Germinating on Gap Decayed Logs 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 Used by the Substrate Dependent Seed Survival With Gap Status behavior Fraction Seeds Germinating on Gap Fresh Logs 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 Used by the Substrate Dependent Seed Survival With Gap Status behavior Fraction Seeds Germinating on Gap Forest Floor Litter 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 Used by the Substrate Dependent Seed Survival With Gap Status behavior Fraction Seeds Germinating on Gap Forest Floor Moss 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 Used by the Substrat
169. equation below Used by the Tree Volume Calculator behavior e Taper Equation Height Exponent a2 The az parameter in the taper equation below Used by the Tree Volume Calculator behavior e Taper Equation X Exponent 1 b1 The b parameter in the taper equation below Used by the Tree Volume Calculator behavior e Taper Equation X Exponent 2 b2 The bz parameter in the taper equation below Used by the Tree Volume Calculator behavior e Taper Equation X Exponent 3 b3 The b parameter in the taper equation below Used by the Tree Volume Calculator behavior e Taper Equation X Exponent 4 b4 The b4 parameter in the taper equation below Used by the Tree Volume Calculator behavior e Taper Equation X Exponent 5 b5 The bs parameter in the taper equation below Used by the Tree Volume Calculator behavior e Taper Equation X Exponent 6 b6 The be parameter in the taper equation below Used by the Tree Volume Calculator behavior e Diameter Outside Bark Constant a1 The a parameter in the equation for calculating tree diameter outside bark below Used by the Tree Volume Calculator behavior e Diameter Outside Bark First Degree Parameter a2 The a parameter in the equation for calculating tree diameter outside bark below Used by the Tree Volume Calculator behavior e Diameter Outside Bark Second Degree Parameter a3 The a3 parameter in the equation for calculating tree diameter outside bark below Used by the Tree Volume Calculator
170. er 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 NCI is calculated as 8 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 yis 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
171. erent assumptions but if so they should be clearly stated in that behavior s documentation Seedlings in SORTIE ND do not have crowns Saplings and adults and in some cases snags all use the same relationships to describe crown shape Allometry parameters e Adult Crown Height Height Function The allometric relationship used to relate tree height in m and height or length of the crown in m for adult trees Each of the choices is described in detail below e Adult Crown Radius Diameter Function The allometric relationship used to relate DBH in cm and crown radius in m for adult trees Each of the choices is described in detail below e Adult Height Diameter Function The allometric relationship used to relate DBH and height for adult trees Each of the choices is described in detail below e Adult Linear Function Intercept The intercept of the adult linear function for DBH and height Any species not using that function can omit this value e Adult Linear Function Slope The slope of the adult linear function for DBH and height Any species not using that function can omit this value e Adult Reverse Linear Function Intercept The intercept of the adult reverse linear function for DBH and height Any species not using that function can omit this value e Adult Reverse Linear Function Slope The slope of the adult reverse linear function for DBH and height Any species not using that function can omit this value e Chapman Richards A
172. erval as a value between 0 no mortality and 1 complete devastation Used by the Windstorm behavior Windstorm Severity for 640 Year Return Interval Storm The severity of storms with a 640 year return interval as a value between 0 no mortality and 1 complete devastation Used by the Windstorm behavior Windstorm Severity for 1280 Year Return Interval Storm The severity of storms with a 1280 year return interval as a value between 0 no mortality and 1 complete devastation Used by the Windstorm behavior Windstorm Severity for 2560 Year Return Interval Storm The severity of storms with a 2560 year return interval as a value between 0 no mortality and 1 complete devastation Used by the Windstorm behavior Windstorm Storm Cyclicity Sine Curve d 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 Used by the Windstorm behavior Windstorm Storm Cyclicity Sine Curve f Parameter that controls the cyclicity of storm frequency This value is part of the sine curve term and controls the sine frequency Used by the Windstorm behavior Windstorm Storm Cyclicity Sine Curve g 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 Used by the Windstorm behavior e Windstorm Storm Cyclicity Trend Function Inte
173. es 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 Light Dependent Seed Survival This behavior assesses seed survival as a function of the Global Light Index 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 The effects of light levels on seed survival is graphed as Sio Shi Light Effect Proportion Established Lopt 0 GLI 100 How it works To assess the effects of light level on the number of seeds that survive this behavior calculates the
174. etailed output file topic You are not required to create subplots Last updated 18 May 2006 12 55 PM Setup tree save options window For more on the different tree types see the trees topic For more on the data available to save see the tree data member list topic This window is reached from the Setup detailed output file window It allows you to choose options for tree data for a detailed output file What you save for output depends on what data you want to be available to you after the run For a list of data visualization options and what you need to save to use them see the Data Visualization topic There are four tabs at the top of the window one each for seedlings saplings adults and snags For each of these tree types you choose each piece of data that you want to save and how often you want to save it Some of the data always apply and will always be available Other types of data only exist when certain behaviors that need them have been chosen for the current run Each piece of data may not be available for all species The window will sort out and ignore any invalid combination You can work through the process below as many times as you like until you have your settings the way you want them Select one or more species Begin here by choosing the species of the data you want to save You can Ctrl click to select multiple species at once For each tree save For the species that you have selected click on
175. eters 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 height and width relationships The Chapman Richards equation for calculating crown radius is rad i a 1 e PBR where e rad is 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 height is ch i a 1 e where 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 height 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 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 seedli
176. ethod 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 highly susceptible to damage The pattern of storm susceptibility can be either Uniform meaning all locations within 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 three possible probability distribution functions for stochastic damage application normal lognormal and negative binomial The normal distribution is x Panel a20 dx pt xjax 2x0 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 acer 2 pt xjax a 2 ax xV 2n07 where is the function mean and o is the standard deviation The negative binomial distribution is x k Piz jap EN a 44 rix etk k where u is the function mean and k is the clumping parameter This is Equation 3 103 from Hilborn and Mangel Combining these two parameters provides four possibilities for
177. events On the left you will see information about the episodic event On the map to the right the current episodic event cells are displayed in color Untreated plot cells are white For more on what displayed information means see the topics on episodic event entry below Creating new episodic events Choose the tab of the type of episodic event you would like to create Then click New A new window will come up where you can enter the episodic event For more on how to enter the episodic event see the topics on episodic event entry below Editing existing episodic events Choose the tab of the type of episodic event you would like to edit Use the backward and forward buttons to navigate through the episodic events and display the one you want to edit Then click Edit A new window will come up displaying the episodic event Edit it as you wish For more see the topics on episodic event entry below Deleting existing episodic events Choose the tab of the type of episodic event you would like to delete Use the backward and forward buttons to navigate through the episodic events and display the one you want to delete Then click Delete Episodic events edit windows For more on how to enter episodic events see the individual episodic event edit topics Edit Harvest Edit Mortality Episode Edit Planting Edit planting diameter at 10 cm 04 Jun 2004 02 30 PM Edit Harvest Window This window is reached from the Edit E
178. f a tree species 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 Say that you do not have data on separate diameter and height growth for adults so 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 Allometric height incrementer behavior was developed to help bridge this gap When used with a behavior that only increments diameter it will preserve height differences that have developed across individuals in a species Growth parameters e Adult Constant Area Growth in sq cm yr The constant amount of basal area by which to increase a tree s basal area Used in basal area increment limited behaviors and constant basal area growth behaviors e Adult Constant Radial Growth in mm yr The constant value by which to increase a tree s radius at breast height Used in radial increment limited grow
179. ffects e The Storm damage applier behavior can create tip ups from storm killed trees e New harvest behavior Selection harvest that allows SORTIE ND to decide when to perform harvests based on target basal area levels e New behavior GLI Points File Creator which calculates GLI at certain specific points e New light behavior Storm Light behavior that uses storm damage as a proxy for finding light levels e New growth behavior Puerto Rico semi stochastic growth e New growth behavior Linear bi level growth that can grow trees with two sets of parameters based on light level e New growth behavior Lognormal bi level growth that can grow trees with two sets of parameters based on light level New mortality behavior Logistic Bi Level Mortality that can use two sets of parameters based on light level NCI growth and NCI Mortality now each have a flag for whether or not to include snags in NCI calculations Refinement of substrate dynamics for snags allowing them to tip up at different rates from live trees Version 6 03 released April 6 2005 New in version 6 03 New function form for the NCI Mortality behavior New mortality behavior which calculates mortality as a function of neighbor density the Density Self Thinning Mortality behavior New format for tab delimited tree maps which can be prepared in any spreadsheet program and added to SORTIE ND New data visualization chart type h
180. for Quadrat Light Calculations Number of grid cells into which the sky is divided around the horizon for the purpose of calculating light direction Used by the Quadrat based light behavior If the GLI light behavior is also used this value is not required Sail Light Maximum Shading Neighbor Distance in meters The radius in meters from a tree for which neighbors will be searched who can shade that tree Used only in the Sail Light behavior Sail Light Minimum Solar Angle in degrees The azimuth angle in degrees below which it is assumed trees will see no light Used only by the Sail Light behavior Snag Age Class 1 Light Transmission Coefficient 0 1 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 Used by all behaviors making GLI or Sail Light calculations Snag Age Class 2 Light Transmission Coefficient 0 1 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
181. g GLI or Sail Light calculations See equations above for more on how this is used Calculated Crown Depth When the shape of a tree s shading neighbors is 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 Used only by the Sail light behavior Clear Sky Transmission Coefficient Used to determine the amount of solar radiation seen at the plot location Applies to all behaviors making GLI or Sail Light calculations See equations above for more on how this is used Constant GLI Constant GLI Value 0 100 The GLI value assigned to all trees Used by the Constant GLI behavior behavior First Day of Growing Season The first day of the growing season as a Julian day number between 1 and 365 Trees only get light during the growing season Used by all behaviors making GLI or Sail light calculations GLI Points Input File 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 File format is below Used by the GLI Points File Creator behavior GLI Points Output File The file to which the GLI Points File Creator behavior will write its results each timestep Any existing data in this file will be overwritten at the start of the run Height at Which GLI is Calculated for GLI Map
182. g Reverse Linear Function Slope The slope of the seedling reverse linear function for DBH and height Any species not using that function can omit this value Slope of Asymptotic Crown Height Slope of the standard equation for determining crown height Any species not using that function can omit this value Slope of Asymptotic Crown Radius Slope of the standard equation for determining crown radius Any species not using that function can omit this value Slope of Asymptotic Height Exponential decay term in the adult and sapling standard function for DBH and height Any species not using that function can omit this value Slope of DBH to Diameter at 10 cm Relationship The slope 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 Height Diameter at 10 cm Relationship The slope of the seedling standard function for diameter at 10 cm and height Any species not using that function can omit this value standard crown height and width relationships Crown radius is calculated as where rad C DBH rad is the crown radius in meters C is the Slope of Asymptotic Crown Radius parameter a is the Crown Radius Exponent parameter DBH is the tree s DBH in cm Crown radius is limited to a maximum of 10 meters Crown height is calculated as ch C height j where e chis the distance from the top to the bottom of the crown cylinder in m
183. g trees A tree s maximum potential growth rate is reduced due to competitiveness and several other possible factors How it works 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 PGA SH e where e DBH is 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 Crowding Effect is calculated as CE exp C DBH BA 1000 where e Cis the NCI Crowding Effect Slope C 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 Dis the NCI Crowding Effect Steepness D parameter e BA is the sum of the basal areas in square cm of trees with a DBH larger than the target tree s DBH When calculating BAg 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 target tree s DBH and larger than the values set in the NCI Minimum Neighbor DBH
184. gate to a path If you do not enter a path the file may be hard to find after the run The extension that will be added if you haven t added it already is out Set up subplots Opens the Edit Subplots window The other options allow you to choose saving options for different types life history stages of trees For the definition of seedling sapling adult and snag see the trees topic Save absolute density Saves the density of trees of each species of that type in number per hectare Save relative density Saves the density of trees of each species of that type as a proportion of total tree density for that type Save absolute basal area Saves the amount of basal area of trees of each species of that type in square meters per hectare Save relative basal area Saves the amount of basal area of trees of each species of that type as a proportion of total tree basal area for that type 16 Nov 2004 12 39 PM Edit Subplots Window You reach this window by clicking the Set up subplots button on either the Summary output file setup window or the Setup detailed output file window This window allows you to define subplots for output Subplots are subareas of the plot for which statistics will be tracked separately They can be as small as a single plot grid cell or as large as the entire plot They do not have to be continuous in area you could define several separate patches and put them together in a single subpl
185. gs saplings and adults of any species Any tree species type combination to which it is applied must also have a light behavior applied Unlimited relative growth diam only 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 and a height incrementing growth behavior applied Double resource relative growth diam with auto height 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 Relative growth is calculated with the equation AHC R GL AEE rr eel GL 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 GLIis 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 fo
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187. he Linear growth w exponential shade reduction height only behavior Shaded Linear Height Shade Exponent c Effect of shading Used by the Linear growth w exponential shade reduction height only behavior Shaded Linear Height Slope b Slope of the size dependent annual growth potential Used by the Linear growth w exponential shade reduction height only behavior Simple Linear Diam Intercept in mm yr a Intercept of the linear growth function or growth at no light in mm yr Used by the Linear growth diam with auto height and Linear growth diam only behaviors Simple Linear Diam Slope b Slope of the linear growth function Used by the Linear growth diam with auto height and Linear growth diam only behaviors Simple Linear Height Intercept in cm yr a Intercept of the linear growth function or growth at no light in cm yr Used by the Linear growth height only behavior Simple Linear Height Slope b Slope of the linear growth function Used by the Linear growth height only behavior Size Dep Logistic Diam Intercept a Intercept of the size dependent annual growth potential Used by the Logistic growth w size dependent asymptote diam only and Logistic growth w size dependent asymptote diam with auto height behaviors Size Dep Logistic Diam Shape Param 1 c Shape parameter for shade reduction of annual growth Used by the Logistic growth w size depend
188. he 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 and a height incrementing growth behavior applied Unlimited 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 Tree height is allowed to update automatically according to the allometry equations 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 Unlimited absolute growth diam only 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 and a height incrementing growth behavior applied Constant basal area growth diam with auto height How it works The amount of diameter increase is calculated from a constant basal area increment The increase 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
189. he 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 Amount of palm leaf biomass for species X in X Mg Mg Bole Palm Biomass for species Amount of palm bole biomass for species X in X Mg Planting Results 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 resolution 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 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 eps Description name GLI value or 1 if there were no trees to which to assign a GLI value GLI in that grid cell Resource This grid holds values for a second growth resource
190. height and Lognormal with exponential shade reduction diam only behaviors Lognormal Diam Growth Increment at Diam 36 in mm yr a Annual growth increment at diameter 36 in mm yr Used by the Lognormal with exponential shade reduction diam with auto height and Lognormal with exponential shade reduction diam only behaviors Lognormal Diam Shape Parameter b Shape parameter Used by the Lognormal with exponential shade reduction diam with auto height and Lognormal with exponential shade reduction diam only behaviors Lognormal Height Effect of Shade c Effect of shade Used by the Lognormal with exponential shade reduction height only behavior Lognormal Height Growth Increment at Diam 36 in cm yr a Annual growth increment at diameter 36 in cm yr Used by the Lognormal with exponential shade reduction height only behavior Lognormal Height Shape Parameter b Shape parameter Used by the Lognormal with exponential shade reduction height only behavior Mortality Threshold for 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 Used in absolute growth behaviors NCI Alpha NCI function exponent Used in the NC
191. hen 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 uninitialized in newly created trees If you want the new data members to be wri
192. his 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 height only growth behavior applied If you wish to use the light level parameter switch also use the Storm Light behavior Lognormal bi level growth height only 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 How it works The equation used by this behavior to increment growth is 2 H yf 2 X T MG Ye 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 X0 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 Stor
193. iam 36 in cm yr a parameter e b Lognormal Height Shape Parameter b parameter e c Lognormal Height Effect of Shade c parameter 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 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 and a diameter only growth behavior applied Lognormal with exponential shade reduction diam with auto height How it works This behavior calculates annual height increases as in diam 36 2 0 f Biden e Y a eg b oe 100 where e Y amount of height increase in cm e az Lognormal Diam Growth Increment at Diam 36 in mm yr a parameter e b Lognormal Diam Shape Parameter b parameter e c Lognormal Diam Effect of Shade c parameter e GLI global light index a
194. ich 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 to learn how run order might affect a behavior Behaviors work on data in sequence Some behaviors require that a specific step has been taken before they can do their job This means that in order to use some behaviors you must also use certain other behaviors The individual behavior documentation will tell you about its requirements To change the order in which behaviors act use the Model flow window Behavior data Behaviors help define trees and grids based on the work they need to do They will create a grid if they need one or they may attach a new piece of data to the trees to which they are applied Other behaviors rely on the presence of the grids and tree data members in order to read the results of previous behaviors and make their own calculations For specifics on these data and what behaviors create them see the list of grids that can be created and list of tree da
195. icked Changed the way neighbor storm damage was treated for NCI growth and NCI mortality What s New archive Last updated 28 Nov 2006 11 55 AM What s New Archive Version 6 06 released March 31 2006 Note If you have a parameter file from an earlier version and you are using behaviors that have been updated in version 6 05 load your file and save it SORTIE ND will automatically make any needed adjustments to your parameter file New in version 6 06 New allometry equation for saplings the power diameter height relationship Updated allometry equation the DBH diameter at 10 cm relationship now has an intercept term New seed survival behavior Storm Light Dependent Seed Survival which works with the light levels produced by the Storm Light behavior New mortality behavior Stochastic Bi Level Mortality which uses two different mortality rates in high and low light New disturbance behavior Windstorm which follows a given storm regime to produce storms and kill trees as a result New growth behavior Basal Area NCI Growth which calculates tree growth as a function of neighborhood basal area New light behavior Basal Area Light which calculates light levels as a function of neighborhood basal area of angiosperms and conifers New disturbance behavior Storm Killer that kills trees damaged in storms This behavior takes over and expands a function previously performed by the Storm Damage Applier behavior Ne
196. id 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 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 The effects of light levels on seed survival is graphed as mk on Sio Shi Light Effect Proportion Established Lopt 0 GLI 100 How it works 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 GLI LE 1 Si GLIop GLD e If GLI GLlop LE 1 e If GLI gt GLlop LE 1 Spi GLI GLIopt where GLI is the light level at the center of the Dispersed Seeds grid cell 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
197. ighbor has sustained medium storm damage Set this to 1 if you are not including storms in your run Used in the NCI growth behavior diam with auto height and NCI growth behavior diam only behaviors NCI Shading Effect Coefficient m The coefficient in the shading effect equation Set this value to 0 if you do not wish to use shading Used in the NCI growth behavior diam with auto height and NCI growth behavior diam only behaviors NCI Shading Effect Exponent n The exponent in the shading effect equation If you set the NCI Shading Effect Coefficient m parameter to 0 this value is ignored Used in the NCI growth behavior diam with auto height and NCI growth behavior diam only behaviors NCI Size Effect Mode in cm X0 The mode of the size effect curve Used in the NCI growth behavior diam with auto height and NCI growth behavior diam only behaviors NCI Size Effect Variance in cm Xb The variance of the size effect curve Used in the NCI growth behavior diam with auto height and NCI growth behavior diam only behaviors NCI Size Sensitivity to NCI gamma The sensitivity of a tree s growth rate to its DBH Set this to 0 to remove the DBH term altogether Used in the NCI growth behavior diam with auto height and NCI growth behavior diam only behaviors behaviors PR a Parameter for Deterministic Growth a parameter used to calculate deterministic growth when a tree is below the stochastic height threshold Used
198. ill apply and in what order they will run Defining the scope of a behavior s actions Behaviors act on data to achieve a result The data in the model is trees and grids For those behaviors that act on trees you must tell them what trees to act on For instance if you had a behavior which applied a Michaelis Menton growth function to trees you may tell it to act on saplings of species 1 2 and 3 adults of those species may have a different growth behavior applied to them The individual behavior documentation tells you how each behavior can be applied 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 or warn you against things that don t make sense Therefore it is important to carefully check the behavior setup yourself before starting a run Common mistakes include applying two different behaviors of the same type to the same set of trees and failing to provide a complete set of behaviors to a particular type of tree These types of situations make computer sense and a simulation can be run when they occur However they do not make scientific sense and unexpected results may occur To choose which behaviors to include in the run and how to apply them use the Model flow window Behavior order and dependencies The parameter file specifies which behaviors to include in the simulation and in wh
199. imber 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 Results 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 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 Cut Density species x cut Number of trees killed in the current timestep for the given range y species and cut range Cut Basal Area species x Total basal area killed in the current timestep for the given cut range y species and cut range Partitioned Biomass 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 t
200. in the Puerto Rico semi stochastic diam only behavior PR b Parameter for Deterministic Growth b parameter used to calculate deterministic growth when a tree is below the stochastic height threshold Used in the Puerto Rico semi stochastic diam only behavior PR DBH Standard Deviation for Stochastic Growth Standard deviation for DBH values when a tree uses stochastic growth This is the standard deviation of the DBH value NOT the amount of growth Used in the Puerto Rico semi stochastic diam only behavior PR Height Threshold for Stochastic Growth m The tree height threshold in meters between deterministic and stochastic growth Used in the Puerto Rico semi stochastic diam only behavior 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 Used in the Puerto Rico semi stochastic diam only behavior PR Storm Bi Level Threshold for High Light Growth 0 100 The threshold between low light and high light equations as a value between 0 and 100 Used in the Puerto Rico storm bi level growth diam with auto height behavior PR Storm Bi Level High Light a The a value in the high light growth function Used in the Puerto Rico storm bi level growth diam with auto height behavior PR Storm Bi Level High Light b The b value in the high light growth function Used in th
201. indow is first opened When you have chosen a group a list of individual behaviors for that grouping shows in the box underneath Select the one you wish to add then click the button marked gt gt to add it to the list It automatically inserts itself in the correct place in the behavior list based on the order of the master behavior list Use the Current run behaviors window to edit the order of the behaviors in a run At this time you must add new behaviors one at a time It is possible to select multiple individual behaviors but the gt gt button will apply to only the first one selected If you have chosen a behavior that is already on the list nothing happens Not all behaviors can be assigned to all species type combinations If you have made an invalid choice you will see an error message when you click an Apply to button and you will be given the opportunity to change it See the documentation for individual behaviors for information on how they can be applied Certain special behaviors cannot be added using this window If you try to add them you will see a message saying Use this behavior s own dialog This means that it has options that can be set up through a window accessible from the main SORTIE menu Removing behaviors To remove a behavior from the list assigned to this species type combination select it in the list labeled Assigned behaviors and click the button marked Remove This does not affect th
202. int it levels off To assess whether a tree will die due to senescence the following function is evaluated gi t ACDBH DBH Y m g A DBH DBR where 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 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 How it works The behavior uses a Weibull function to determine the number of snags of a certain age left standing at a given time The equation is g aT where e Sis proportion of snags still standing between 0 and 1 e aand bare Weibull parameters Weibull Annual
203. ion Seeds Germinating on Ground Fresh Logs The proportion of those seeds that land on fresh logs ground substrate that survive to become seedlings Expressed as a value between 0 and 1 Used by the Substrate Based Seed Survival With Microtopography behavior Fraction Seeds Germinating on Ground Scarified Soil 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 Used by the Substrate Based Seed Survival With Microtopography behavior Fraction Seeds Germinating on Ground Tip Up 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 Used by the Substrate Based Seed Survival With Microtopography behavior Fraction Seeds Germinating on Mound Decayed Logs 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 Used by the Substrate Based Seed Survival With Microtopography behavior Fraction Seeds Germinating on Mound Forest Floor Litter 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 Used by the Substrate Based Seed Survival With Microtopography behavior Fraction Seeds Germinating on Mound Forest Floor Moss The proportion of those seeds that land on forest floor moss mound substrate that survi
204. ion system Partitioned DBH Biomass This behavior calculates biomass as a linear function of DBH partitioned into leaf branch and bole biomass How it works The biomass of leaves boles and branches is calculated using the same equation but using different parameters The equation is Bio a DBH bi where e Bio biomass in kg dry weight of either leaves branches or the bole e a either the Partitioned DBH Biomass Leaf Slope a Partitioned DBH Biomass Branch Slope a or Partitioned DBH Biomass Bole Slope a parameters e b either the Partitioned DBH Biomass Leaf Intercept b Partitioned DBH Biomass Branch Intercept b or Partitioned DBH Biomass Bole Intercept b parameters 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 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 Palm Biomass This behavior calculates biomass as a linear function of tree height partitioned into leaf and bole biomass How it works The bi
205. ior e Storm Light Std Dev or Clump Parameter If the value in the Storm Light Stochasticity parameter is Normal or Lognormal the standard deviation of the probability distribution function if the value is Negative Binomial the clumping parameter for the PDF if Deterministic this value is ignored Used by the Storm Light behavior e Storm Light Stochasticity What method to use for randomizing light values if desired Used by the Storm Light behavior e Upper Age Yrs of Snag Light Transmission Class 1 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 Used by all behaviors making GLI or Sail Light calculations e Upper Age Yrs of Snag Light Transmission Class 2 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 Used by all behaviors making GLI or Sail Light calculations Average Light This behavior averages GLI values to produce
206. is Weibull Used by the Gap spatial disperse Non gap spatial disperse and Anisotropic spatial disperse behaviors In the case of the last two the canopy probability distribution function is the only one used for a species e Weibull Canopy Dispersal The dispersal value for the Weibull function under canopy conditions see equation below This is only required if the canopy probability distribution function is Weibull Used by the Gap spatial disperse Non gap spatial disperse and Anisotropic spatial disperse behaviors In the case of the last two the canopy probability distribution function is the only one used for a species e Weibull Canopy Theta The 0 for the Weibull function under canopy conditions see equation below This is only required if the canopy probability distribution function is Weibull Used by the Gap spatial disperse Non gap spatial disperse and Anisotropic spatial disperse behaviors In the case of the last two the canopy probability distribution function is the only one used for a species e Weibull Gap Annual STR 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 Used by the Gap spatial disperse behavior e Weibull Gap Beta The value for the Weibull function under gap conditions see equation below Th
207. is is only required if the gap probability distribution function is Weibull Used by the Gap spatial disperse behavior e Weibull Gap Dispersal 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 Used by the Gap spatial disperse behavior e Weibull Gap Theta 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 Used by the Gap spatial disperse behavior 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 How it works Non spatial disperse calculates how many seeds to distribute as A p BA k where e is 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
208. is not used Clear Cut Proportion of Tip Up Mounds 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 Decayed Log Annual Decay Alpha The a exponent in the decay equation ae as applied to decayed logs Note that this is annual decay Decayed Log Annual Decay Beta The exponent in the decay equation PA O T nae as applied to decayed logs Note that this is annual decay Fresh Log Annual Decay Alpha The a exponent in the decay equation PA G oe as applied to fresh logs Note that this is annual decay cyte Fresh Log Annual Decay Beta The B exponent in the decay equation as applied to fresh logs Note that this is annual decay Gap Cut Proportion of Decayed Logs 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 Gap Cut Proportion of Fresh Logs 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 Gap Cut Proportion of Scarified Soil 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 Gap Cut Proportion of Tip Up
209. istograms for grid values New behavior for calculating tree volume the Tree bole volume calculator behavior Updated Substrate behavior documentation New behavior for calculating tree biomass the Dimension analysis behavior New feature for running batches NCI behaviors NCI Mortality and NCI growth now have a parameter for minimum DBH of crowding neighbors The Storm damage applier behavior now can kill trees immediately as a result of storm damage Changes to the File menu options Version 6 02 released March 10 2005 New in version 6 02 New tree data members for Light level and Diameter Growth New behavior for creating GLI maps Gap Light behavior New line graphs in data visualization for relative volume and absolute volume Seedling initial density can now be controlled by three height classes New growth based mortality behavior Competition Mortality New mortality as a function of growth and a second resource Growth and Resource Based Mortality New function form for the NCI growth behaviors New growth functions using a double Michaelis Menton function of light and a second resource Double resource relative growth New light behavior which simplifies GLI calculations for extremely competitive gap dynamics Gap Light behavior e New growth behavior for simulating extremely competitive gap dynamics Stochastic gap growth e Snag size classes for the Weibull snag mortality behavior ar
210. ith a DBH greater than this value experience no further increase in the mortality rate Used by the Senescence behavior Density Self Thinning Asymptote A The asymptote of the density self thinning function Used by the Density Self Thinning Mortality behavior Density Self Thinning Density Effect S The parameter controlling the density effect of the density self thinning function Used by the Density Self Thinning Mortality behavior Density Self Thinning Diameter Effect C The parameter controlling the effect of neighbor mean diameter of the density self thinning function Used by the Density Self Thinning Mortality behavior Density Self Thinning Minimum Density for Mortality ha The minimum density of neighbors in stems ha for density self thinning mortality A tree with a lower density of neighbors than this value will not die Used by the Density Self Thinning Mortality behavior Density Self Thinning Neighborhood Radius in m The maximum radius in m within which to search for neighbors to calculate neighbor density for density self thinning Used by the Density Self Thinning Mortality behavior Exponential Growth Resource a The mortality at zero growth scaled as a function of the resource Used by the Exponential Growth and Resource Based Mortality behavior Exponential Growth Resource b The light dependent mortality parameter Used by the Exponential Growth and Resource Based Mortality behavior Exponential Growth Resour
211. ke total number of seeds consumed e IR 1s per capita seed offtake e Nis the number of predators Per capita seed offtake is IR 1 where e c 1s the Max Intake Rate seeds per predator per day parameter e Sis the number of seeds per predator per day e Dis the Foraging Efficiency parameter The number of predators in each cell s population is calculated as N Ni 1 enl where e N is number of predators for the current timestep e N is number of predators in the previous timestep e 7 1S instantaneous rate of change in predator abundance for the previous timestep The instantaneous rate of change r is calculated as r a d IR g N where e ais the Max Decline Rate in Absence of Food predators week parameter e dis the Predator Population Demographic Efficiency parameter e gis the Density Dependent Coefficient parameter e Nis number of predators 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 15 Aug 2004 10 11 PM Establishment behaviors In this document Establishment parameters Substrate Dependent Seed Survival No Gap Status Substrate Dependent Seed Survival With Gap Status Substrate Based Seed Survival With Microtopography Light Dependent Seed Survival Storm Light Dependent Seed Survival Density Dependent Seed Survival Proportional Seed Survival Seed Establishment Est
212. killed 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 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 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 tree
213. l 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 You must also use the Storm Light behavior Height GLI Weibull Mortality This behavior calculates the probability of mortality using a Weibull function of tree height and GLI light level How it works The equation used by this behavior to calculate mortality probability is P Mmax exp a H c GLI where e p annual probability of mortality Mma the Height GLI Weibull Max Mortality 0 1 parameter e a the Height GLI Weibull a parameter e b the Height GLI Weibull b parameter c the Height GLI Weibull c parameter d the Height GLI Weibull d parameter H tree height in meters 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 J 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 direct
214. l mass of the atmosphere is calculated by m sec 0 where is the zenith angle of the sun SORTIE uses a numerical approximation method instead of the sec to correct at low altitudes This process is repeated for each day in the growing season The growing season starts with the First Day of Growing Season parameter and ends with the Last Day of Growing Season parameter Snags in light calculations Snags are standing dead trees more in the trees topic They can block light like live trees do For SORTIE purposes snag crowns are frozen in the shape they had when the tree died but they transmit more and more light as they lose branches SORTIE tracks a snag s age in order to replicate this decay You define three snag age classes and a light transmission coefficient for each For as long as a snag stands it will block the light of neighboring trees but to a lesser degree through time You don t have to include snags in light calculations If you do not have any behaviors in your run that either create snags or directly work with them then your run is classified as snag unaware and snags will not be created In this case the snag parameters are not required However if your run is snag aware and snags may be created you must supply the snag light transmission parameters Light parameters Basal Area Light Angiosperm b Parameter The b value used to calculate mean GLI from angiosperm basal area Used by the Basal Area Light
215. lated as described in the Constant radial growth behavior Tree height is allowed to update automatically according to the allometry equations 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 Relative growth limited to radial increment diam only 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 and a height incrementing growth behavior applied Relative growth limited to basal area increment diam with auto height 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
216. lier a0 parameter e ais the Taper Equation DBH Exponent a1 parameter e dis the Taper Equation Height Exponent a2 parameter b is the Taper Equation X Exponent 1 b1 parameter bz is the Taper Equation X Exponent 2 b2 parameter b3 is the Taper Equation X Exponent 3 b3 parameter bz is the Taper Equation X Exponent 4 b4 parameter bs is the Taper Equation X Exponent 5 b5 parameter e bs is 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 a 3DBH where e Dis the diameter outside the bark in cm e DBH is the diameter inside the bark in cm SORTIE s DBH e a is the Diameter Outside Bark Constant a1 parameter e ais the 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 carefully 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
217. lity GME Mortality Growth and Resource Based Mortality Height GLI Weibull Mortality Juvenile Self Thinning Juvenile Stochastic Mortality Logistic Bi Level Mortality NCI Mortality Senescence Stochastic Bi Level Mortality Weibull Snag Mortality The mortality behaviors cause tree death due to natural life cycle causes and competition Tree death due to disturbance is covered by other behaviors Mortality 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 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 Mortality parameters Adult Background Mortality Rate The proportion of trees that die each year as a value between 0 and 1 Used by the Adult stochastic mortality behavior Adult Self Thinning Intercept Intercept of the adult self thinning linear function Used by the Adult self thinning behavior Adult Self Thinning Slope Slope of the adult self thinning linear function Used by the Adult self thinning behavior Competition Mortality Maximum Parameter max The maximum relative increment of growth subject to mortality Used by the Competition Mortality behavior Aggregated
218. ll 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 The proportion of cell area that is scarified soil added soil substrate in this cohort Substrate cohort new tip up The proportion of cell area that is tip up mounds mounds substrate substrate added in this cohort The proportion of cell area that is fresh logs added in Substrate cohort new fresh logs this cohort Substrate calcs 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 pap meua 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 grid cell area Fresh logs X timesteps ago Substrate favorability This grid is created by either the Substrate Dependent Seed Survival No Gap Status or the Substrate Dep
219. llometry equation appropriate to the tree type to calculate a height for each diameter The amount of height increase is the difference between these heights 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 only growth behavior applied Linear growth height only How it works This behavior calculates an amount of height growth as Y a b GLI T where e Y amount of height increase in cm e a Simple Linear Height Intercept in mm yr a parameter e b Simple Linear Height Slope b parameter 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 and a diameter only growth behavior applied Linear growth diam with auto height How it works This behavior calculates an amount of diameter growth as Y a b GLI T where e Y amount of diameter increase in mm e a Simple Linear Diam Intercept in mm yr a parameter e b Simple Linear Diam Slope b parameter e GLI global light index as a percentage between 0 and 100 calculated by a light behavior e T number of years per timestep After applying the amoun
220. llows you to choose a new species type combination Choose the appropriate combination where it says Please choose a species and Please choose a tree type Then click the button marked gt gt to add your choice to the list You can remove a choice by selecting it in the list on the right then clicking the Remove button Not all behaviors can be assigned to all species type combinations If you have made an invalid choice you will see an error message when you click the OK button and you will be given the opportunity to change it See the documentation for individual behaviors for information on how they can be applied 23 Oct 2006 11 27 AM 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 In this window Choose which parameters to display Editing values Saving the values to a file for review Error messages when you click OK 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 acti
221. ls on this format see tab delimited tree maps Creating your own map analyses If you would like to take the map data and analyze it in other ways you can have the model interface output the values into a tab delimited text format For grid maps you can do this in the Edit menu by choosing Grid layer setup for tree maps choose Tree Setup See those topics for exact instructions The tab delimited text format is for your own use SORTIE cannot accept it as input Last updated 30 Mar 2005 02 40 PM Tab delimited tree maps You can use tab delimited tree maps to directly enter tree map data Tab delimited text means that columns of data are separated by tabs You can save files of this type in many programs particularly spreadsheet programs like Microsoft Excel Requirements for 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 Files must be in plain text with a txt extension Using tree maps 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 Tree setup window SORTIE ND will not alter your
222. lue Grids can and usually do carry more than one value per cell Grid cell size applies to all values in the grid The amount of memory required for a grid cell 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 in the X and Y directions by using the Grid setup window You do not have to choose the size of a grid s cells all grids have default values However there are times when it makes sense to adjust these values When choosing a 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 its speed 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 Viewing and using grid maps During the simulation the model can write out a grid map the data in a grid into a detailed output file You can choose what you would like saved from a grid by using the Output setup window Things you can do with grid maps e Look at graphical representations of grid maps To do this use the model s data visualization capabilities e Use them as initial conditions Since grid values help represent the internal state
223. ly assign a tree its light level It is expected that this is a GLI value from 0 to 100 of full sun How to apply it This behavior can be applied to seedlings saplings and adults of any species You must also use a light behavior Last updated 28 Nov 2006 10 17 AM Substrate behaviors In this document Substrate parameters Substrate behavior 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 Substrate parameters e Clear Cut Proportion of Decayed Logs The proportion of substrate that is decayed 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 e Clear Cut Proportion of Fresh Logs 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 e Clear Cut Proportion of Scarified Soil 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
224. lysis Use Correction Factor parameter for this species is false Used by the Dimension Analysis behavior Dimension Analysis DBH Units 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 Used by the Dimension Analysis behavior Dimension Analysis Equation ID The biomass equation ID to use when calculating biomass for a particular species Used by the Dimension Analysis behavior Dimension Analysis Parameter a The value for a 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 Used by the Dimension Analysis behavior Dimension Analysis Parameter b 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 Used by the Dimension Analysis behavior Dimension Analysis Parameter c 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 Used by the Dimension Analy
225. m 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 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 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
226. me 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 executable 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 execut
227. ms or to contest validity of any such claims this section has the sole purpose of protecting the integrity of the free software distribution system which is implemented by public license practices Many people have made generous contributions to the wide range of software distributed through that system in reliance on consistent application of that system it is up to the author donor to decide if he or she is willing to distribute software through any other system and a licensee cannot impose that choice This section is intended to make thoroughly clear what is believed to be a consequence of the rest of this License 8 If the distribution and or use of the Program is restricted in certain countries either by patents or by copyrighted interfaces the original copyright holder who places the Program under this License may add an explicit geographical distribution limitation excluding those countries so that distribution is permitted only in or among countries not thus excluded In such case this License incorporates the limitation as if written in the body of this License 9 The Free Software Foundation may publish revised and or new versions of the General Public License from time to time Such new versions will be similar in spirit to the present version but may differ in detail to address new problems or concerns Each version is given a distinguishing version number If the Program specifies a version number of this License which applies
228. mum DBH for Reproduction in cm The minimum DBH at which a tree can reproduce This value does not have to match the Minimum adult DBH Used by all disperse behaviors e Seed Distribution The distribution method to be applied to seeds randomization Used by all disperse behaviors Choices are o Deterministic no randomization o Poisson use the number of seeds as the mean in a Poisson probability distribution function See the equation above o 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 See the equation above o 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 See the equation above o Negative binomial use the number of seeds as the mean in a negative binomial probability distribution function You must then supply a clumping parameter See the equation above e Seed Dist Clumping Parameter Neg Binomial 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 Used by all disperse behaviors e Seed Dist Std Deviation Normal or Lognormal If you have chosen the normal or lognormal probability distribution functions for Seed distribution
229. n Used by the Tree Bole Volume Calculator behavior Bole Volume Parameter b1 The b parameter for the bole volume equation Used by the Tree Bole Volume Calculator behavior Bole Volume Parameter b2 The b2 parameter for the bole volume equation Used by the Tree Bole Volume Calculator behavior Bole Volume Parameter b3 The b3 parameter for the bole volume equation Used by the Tree Bole Volume Calculator behavior Bole Volume Parameter b4 The b4 parameter for the bole volume equation U B U Jsed by the Tree Bole Volume Calculator behavior ole Volume Parameter b5 The b5 parameter for the bole volume equation Jsed by the Tree Bole Volume Calculator behavior Carbon Value Carbon Amount of Biomass 0 100 The percentage of biomass that is carbon as a value between 0 and 100 Used by the Carbon Value behavior Carbon Value Price Per Metric Ton Carbon The price per metric ton of carbon The currency is unimportant Used by the Carbon Value behavior Dimension Analysis Biomass Units 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 Used by the Dimension Analysis behavior Dimension Analysis Correction Factor The correction factor needed by some biomass equations that calculate In biomass log o biomass or logjo9 biomass This value is ignored if the value for the Dimension Ana
230. n 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 Last updated 15 Nov 2006 07 14 AM Edit menu 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 silvicultural treatments and episodic mortality For more details on this option see the Edit Episodic Events Window topic Tree setup Use this option to edit the basics of the tree population For more details on this option see the Tree setup window topic Grid layer setup Use this option to edit the basics 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 Output options Use this option to set up output for a run By default no output is saved This controls
231. n 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 The name in parentheses is the name SORTIE uses Light level Light Light level for the tree This could be GLI or percent shade if Sail Light is used This is created by any of the light behaviors except the Beer s Law light filter Diameter growth Growth Amount of diameter growth per year in mm This is created by any of the growth behaviors that increment diameter growth Light filter respite counter If_count Created by the Beer s law light filter behavior It contains the years of respite for a new seedling from the effects of the light filter Rooting height z The height in mm above ground level at which a seedling is rooted Created by the Beer s law light filter behavior Years released ylr The length of the current release period in years Created by the absolute growth behaviors Years suppressed yls The length of the current suppression period in years Created by the absolute growth behaviors Dead flag dead A boolean flag for whether a tree has died Created by any of the mortality behaviors This is used by the dead tree remover behavior to find the trees it sh
232. n years It is recommended that this value be a whole number e Random seed 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 Plot In this document The SORTIE coordinate system The Torus Forest Plot parameters The plot in SORTIE is the simulation of the physical space in which the model runs 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 be 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 Syst
233. nags in NCI Calculations parameter NCI is calculated as 8 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 n is 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 DBHjx 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 is 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 st
234. 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 Extracting the data to perform your own analyses If you want to perform your own analysis of the data in a detailed output file you can translate it into tab delimited text files that you can then open with a spreadsheet See the topic detailed output files for instructions on how to do this 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
235. nces 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 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 Anisotropic spatial disperse Anisotropic spatial disperse allows for a directionality in the seed probability distribution function Seeds are still evenly distributed at all azimuth angles around a parent tree but the distance varies with azimuth direction This behavior can simulate things like prevailing wind direction IMPORTANT This behavior
236. ncrementing height Behaviors using this method have the tag diam only in their name In the third method the behavior calculates an amount of height increase and then adds this amount to the tree s height The diameter is not allowed to change The rationale is the same as that for the second method If you use a growth behavior of this type it is required that you pair it with a separate behavior incrementing diameter Behaviors using this method have the tag height only in their name Growth behaviors using the second and third method must work together in pairs Behaviors using the first method work alone If you pair a behavior using method one with a behavior using method three the height incrementing behavior will be ignored When incrementing a tree s diameter with new growth seedlings and saplings have the amount of growth increase 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 trees topic 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 mixing different growth methods for different life history stages o
237. nder canopy conditions that survive to become seedlings Expressed as a value between 0 and 1 Used by the Substrate Dependent Seed Survival No Gap Status and Substrate Dependent Seed Survival With Gap Status behaviors e Fraction Seeds Germinating on Canopy Fresh Logs 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 Used by the Substrate Dependent Seed Survival No Gap Status and Substrate Dependent Seed Survival With Gap Status behaviors e Fraction Seeds Germinating on Canopy Forest Floor Litter 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 Used by the Substrate Dependent Seed Survival No Gap Status and Substrate Dependent Seed Survival With Gap Status behaviors Fraction Seeds Germinating on Canopy Forest Floor Moss 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 Used by the Substrate Dependent Seed Survival No Gap Status and Substrate Dependent Seed Survival With Gap Status behaviors Fraction Seeds Germinating on Canopy Scarified Soil 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 Used by the Substrate D
238. ndex 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 and a height only growth behavior applied Logistic growth w size dependent asymptote height only How it works This behavior calculates annual height increases as y b diam J a GLT jj where e Y amount of height increase in cm e a Size Dep Logistic Height Intercept a parameter e b Size Dep Logistic Height Slope b parameter e c Size Dep Logistic Height Shape Param 1 c parameter e d Size Dep Logistic Height Shape Param 2 d parameter 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 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
239. ng and adult life history stages Adults use only DBH DBH and diam are related as follows DBH diamo R I where e DBH is the DBH in cm e diamyjo is 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 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 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 diamj 9 height function is height 0 1 30 1 e amp 4 where e height is tree height in meters e ais the Slope of Height Diameter at 10 cm Relationship parameter e diamyjg is tree diameter at 10 cm height in cm The linear diameter height
240. no further action is taken The previous timestep s GLI and basal area values are kept For each grid cell in which a new GLI is to be calculated a mean GLI value is calculated as follows GLI CGI 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 cc is the Basal Area Light Conifer c Parameter e BA is the conifer basal area for that grid cell in square meters where This mean GLI is translated into a value for the lognormal random draw as follows In GLIn 07 2 where GLI is the mean GLI value calculated above and a 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 eer 2 pt xjax i a ax Xy Aro 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 adult
241. ns below Used in absolute and growth behaviors e Years Exceeding Threshold Before a Tree is Suppressed The number of years for which a tree s growth must be below the defined suppression threshold before it is considered to be suppressed Used in absolute growth behaviors Relative growth behaviors Several behaviors apply a relative growth version of the Michaelis Menton function Relative growth is calculated with the equation A GLI A Ay GLI 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 GLIis 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 Xis the Relative Michaelis Menton Growth Diameter Exponent parameter Relative growth is discussed in Pacala et al 1996 Relative growth limited to radial increment diam with auto height 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 calcu
242. nsities between SORTIE timesteps parameter Predator Population Demographic Efficiency The seed predator population demographic efficiency See equation below Preserve Predator Densities Between SORTIE Timesteps 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 Proportion of Seeds Removed Each Week During Germination Period During the period that germination occurs this is the fraction of the seed pool that is removed due to those seeds having germinated Expressed as a value between 0 and 1 Seed Predation Output Filename If Desired The filename where the mini model will store its intermediate results for later analysis if desired This value is not required Week During Predation Model Run Germination Begins The week timestep 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 Weeks to Run Seed Predation Model 1 52 The number of weeks timesteps to run the behavior s mini model This number must be between 1 and 52 Functional response seed predation This behavior simulates functional response seed
243. obe 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 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 How it works The probability of survival for a tree is calculated with the following equation R py Prob p e 2 8G 0 7 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 mis 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 is the Growth Resource Survival Increase with Growth delta parameter which specifies the increase in survival caused by amount of
244. 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 other storm killed trees Saplings that are killed in storms never become snags They are killed in the manner de
245. 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 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 r
246. omass of leaves and boles is calculated using the same equation but using different parameters The equation is Bio a Height bi where e Bio biomass in kg dry weight of either leaves branches or the bole e a either the Partitioned Palm Biomass Leaf Slope a or Partitioned Palm Biomass Bole Slope a parameters e b either the Partitioned Palm Biomass Leaf Intercept b or Partitioned Palm 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 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 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 Thes
247. ometry equations 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 Constant radial growth diam only 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 p gt 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 height incrementing growth behavior applied NCI growth diam with auto height 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
248. on 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 It is similar to the other storm behaviors with a few key differences For those long time users of SORTIE this is the same as the Windstorm submodel in the pre 6 versions of SORTIE 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
249. ons to each other 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 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 There are two ways to add Harvest events to a SORTIE run To define a new harvest use the Edit Episodic Events Window If you are a user of a previous version of SORTIE and have a harvest regime file you would like to use there are instructions for adding it to your run in the Adding to a parameter file topic Episodic Mortality 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
250. oose Negative Binomial you must provide a function clumping value in the Clumping Parameter neg binomial 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 undamaged 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 How it works 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 expla h e DBH d LT a expla b e DBH where e iis the damage category either 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 bi
251. or a respite from the Beer s law light filter behavior 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 distribution controlled by the Mean Height of Mounds in m and Standard Deviation of Mo
252. orms 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 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 Competition Mortality Competition mortality is a growth based mortality behavior It uses the results of the NCI growth behavior How it works NCI growth in SORTIE is calculated in the
253. ot You can define up to five separate subplots Subplots can overlap In the center of the window is a map displaying the subplots At the right is the legend for any tree map trees which may exist Along the left panel of the window you will see a space for the names of five subplots The colored squares indicate in what color that subplot will show up on the map in the center of the window At the bottom left are some controls for displaying additional useful information that may help you in defining your subplots Defining a subplot Begin by clicking the radio button for the subplot you want to define for instance Subplot 1 Type a name for this subplot Then choose the squares on the map which define the subplot s area You can click single squares or click and drag to select a rectangle You can unselect a square by clicking it again The selected cells will show up in the current subplot s color Everything you click on the map is assumed to apply to the subplot that is currently selected until you select a new one If two subplots overlap only one of the subplot s colors will show up the one with the greater number The hidden subplot still exists it is okay for subplots to overlap However the entire map is still active even for a subplot that is partly covered up Say you select a subplot and then click cells that are covered by a subplot with a higher number Your clicks are still selecting and de selecting cells for the su
254. ould remove Storm Damage Value stm_dmg 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 Created by the Storm damage applier behavior Tree Bole Volume Bole Vol The volume of a tree in cubic feet Created by the Tree bole volume calculator behavior Tree Volume Volume Volume of the tree in cubic meters Created by the Tree volume calculator behavior Tree Biomass Biomass Biomass of the tree in metric tons Mg Created by the Dimension analysis behavior Tree Age Tree Age Age of the tree in years Created by the Tree age behavior Last updated 28 Nov 2006 11 51 AM Behaviors In this document Defining the scope of a behavior s actions Behavior order and dependencies Behavior data Links to individual behavior documentation Behaviors perform all the action when a simulation is running Each behavior represents a step in the overall simulation It retrieves data manipulates it and stores the result Usually a behavior roughly corresponds to a biological process such as tree growth When you define a simulation the most important step is to choose which behaviors will run to what data they w
255. ount How it works In 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 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 f
256. our file and save it SORTIE ND will automatically make any needed adjustments to your parameter file New in version 6 05 e The Substrate behavior has been rewritten to combine all current substrate models into one behavior e New establishment behavior Establishment with Microtopography that allows seedlings to have a rooting height above the ground e Two new allometry equations for crown shape the Chapman Richards function e The stock and stand tables for detailed output now have a mean DBH column e The equation for mean annual increment in the stock table has changed e Bug fix seedlings that use either the GLI light or Sail light behaviors automatically use a top of crown fisheye photo point e Changes have been made to the Parameters window to make parameter editing easier e Changes have been made to output table formatting to make them easier to read Version 6 04 released May 16 2005 Note If you have a parameter file from an earlier version and you are using behaviors that have been updated in version 6 04 load your file and save it SORTIE ND will automatically make any needed adjustments to your parameter file New in version 6 04 e You can now choose the appropriate allometry equation for each species for each life history stage e You can now set the height boundary between seedlings and saplings for trees e The establishment behaviors have been restructured allowing you to mix and match seed survival e
257. 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 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 Last updated 01 Apr 2005 01 29 PM 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 Tree setup 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
258. 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 as described above 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 Tree setup Last updated 18 May 2006 12 46 PM Summary output files For more on output including a guide on what to save see the topic Output in SORTIE The summary output file contains basic summary data for each timestep in the run It is exactly like it was in previous versions of SORTIE You choose what data you want SORTIE to save using Edit gt Output options The choices 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 d
259. p Light behavior applied Linear bi level growth diam with auto height 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 How it works The equation used by this behavior to increment growth is Y a b diam T where 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 Linear 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
260. pe 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 diamjo 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 The power diam height function is height a dj where e heightis tree height in m e ais the Power Function a parameter e bis the Power Function Exponent b parameter e dois diameter at 10 cm in cm Last updated 25 Jan 2006 03 17 PM 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 Data that is always present Some data are fundamental to a tree and are always available for saving They are e X The coordinate of the tree in meters on the X axis in the SORTIE plot e Y The coordinate of the tree in meters on the Y axis in the SORTIE plot e DBH The diameter at breast height of a tree in cm This does not apply to seedlings e Diameter at 10 cm diam10 The tree s diameter at 10 cm height in cm This applies only to seedlings and saplings e Height The tree s height in meters e Age The time since death in years Only for snags Behavior specific data Certai
261. per Bound in cm parameter e Initial Density ha Seedling Height Class 2 Number of seedlings per hectare to create in the second seedling height class not required 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 e Initial Density ha Seedling Height Class 3 Number of seedlings per hectare to create in the third seedling height class not required The lower bound of this class is the value in the Seedling Height Class 2 Upper Bound in cm parameter and the upper bound is 135 cm the tallest possible seedling height e Minimum Adult DBH The minimum DBH at which trees are considered adults See more about tree life history stages above e Max Seedling Height meters The maximum seedling height in meters Trees taller than this height are saplings See more about tree life history stages above 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 e Seedling Height Class 1 Upper Bound in cm The upper bound of the first seedling height class in cm for specifying seedling initial densities not required The lower bound of the size class is 0 e Seedling Height Class 2 Upper Bound in cm The upper bound of the second seedling height clas
262. pisodic Events Window by clicking on the Harvest tab and selecting New or Edit This window is where you create a new harvest event or edit an existing one Along the left portion of the window you enter data about the harvest On the map in the center you select the area of the plot to which to apply your harvest If a tree map has been entered those trees are displayed on the map and the species key is to the right For more on tree maps and episodic events see the Edit Episodic Events Window topic In this document Entering data about the harvest Choosing the area to which to apply the harvest Entering data about the harvest Timestep Enter the timestep in which you wish the harvest to occur You can create more than one harvest per timestep Species applied to Put a checkbox next to each species to which this harvest is to apply If a species is not checked no trees of that species will be cut You can cut the same species more than once in a timestep but if the cut areas of the two harvests overlap there is no attempt to consolidate them and you may not get the results you expect Cut type Select the type of cut you are performing The cut type makes no difference to the way that trees are selected for harvest Its main effect is to change the substrate composition of the plot If you want to select multiple size classes for cutting select Partial cut Cut amount type This only applies if you have sel
263. pisodic Events Window by clicking on the Mortality Episodes tab and selecting New or Edit This window is where you create a new planned mortality episode or edit an existing one Along the left portion of the window you enter data about the planned mortality episode On the map in the center you select the area of the plot to which to apply your planned mortality episode If a tree map has been entered those trees are displayed on the map and the species key is to the right For more on tree maps and episodic events see the Edit Episodic Events Window topic In this document Entering data about the planned mortality episode Choosing the area to which to apply the planned mortality episode Entering data about the planned mortality episode Timestep Enter the timestep in which you wish the planned mortality episode to occur You can create more than one planned mortality episode per timestep Species applied to Put a checkbox next to each species to which this planned mortality episode is to apply If a species is not checked no trees of that species will be killed You can kill trees of the same species more than once in a timestep but if the areas of the two planned mortality episodes overlap there is no attempt to consolidate them and you may not get the results you expect Amount of mortality type Enter how you intend to specify the amount of trees to kill in each size class to which the planned mortality episode
264. ply 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 this 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 How it works The paper above outlines 9 different biomass equations in Table 6 as follows ID Equation 1 log10 biomass a b log10 dia 2 In biomass a b dia c In dia D 3 In biomass a b In dia c d e In dia 4 biomass a b dia c dia 4 5 biomass a b dia c dia d dia 6 biomass a exp b c In dia d dia 7 biomass a b dia dia d 8 log100 biomass a b log10 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
265. r biomass equation for leaves Used by the Partitioned DBH Biomass behavior Partitioned DBH Biomass Branch Slope a The slope in the linear biomass equation for branches Used by the Partitioned DBH Biomass behavior Partitioned DBH Biomass Branch Intercept b The intercept in the linear biomass equation for branches Used by the Partitioned DBH Biomass behavior Partitioned DBH Biomass Bole Slope a The slope in the linear biomass equation for boles Used by the Partitioned DBH Biomass behavior Partitioned DBH Biomass Bole Intercept b The intercept in the linear biomass equation for boles Used by the Partitioned DBH Biomass behavior Partitioned Palm Biomass Leaf Slope a The slope in the linear biomass equation for leaves Used by the Partitioned Palm Biomass behavior e Partitioned Palm Biomass Leaf Intercept b The intercept in the linear biomass equation for leaves Used by the Partitioned Palm Biomass behavior e Partitioned Palm Biomass Bole Slope a The slope in the linear biomass equation for boles Used by the Partitioned Palm Biomass behavior e Partitioned Palm Biomass Bole Intercept b The intercept in the linear biomass equation for boles Used by the Partitioned Palm Biomass behavior e Taper Equation Initial Multiplier a0 The ap parameter in the taper equation below Used by the Tree Volume Calculator behavior e Taper Equation DBH Exponent al The a parameter in the taper
266. r suppression some will die while some can tolerate being suppressed for decades See the growth behaviors topic for more Tab delimited text file An ASCII text file organized as a table with columns separated by tabs and rows separated by returns Timestep The basic unit of time in SORTIE Timesteps are defined in years in the parameter file The basic run cycle is repeated once per timestep See the run setup and progression topic Torus A donut shape This is the shape of the forest in SORTIE See the plot topic 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 softw
267. r 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 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 GMF mortality GMF mortality is a growth based mortality behavior How it works The GMF mortality model evaluates the following function to determine the probability of a tree s mortality m G m m e where e mis the probability of mortality e mz is 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 this timestep 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 K
268. r applied Logistic growth w size dependent asymptote diam only How it works This behavior calculates annual diameter increases as ye at b diana 1 gt a GLT where e Y amount of diameter increase in mm e a Size Dep Logistic Diam Intercept a parameter e b Size Dep Logistic Diam Slope b parameter e c Size Dep Logistic Diam Shape Param 1 c parameter e d Size Dep Logistic Diam Shape Param 2 d parameter 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 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 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 height only growth behavior applied Lognormal with exponential shade reduction height only How it works This behavior calculates annual height increases as 2 in diam 36 la e y 100 where e Y amount of height increase in cm e az Lognormal Height Growth Increment at D
269. r 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 Unlimited relative growth behavior How it works 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 Once growth has been calculated and applied to the tree s diameter tree height is allowed to update automatically according to the allometry equations 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 must also enter a map of second resource values into the Resource grid Double resource relative growth diam only How it works This behavior calculates growth exactly like the Double resource relative growth diam with auto height behavior Height is updated separately using another 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 ligh
270. r your own review in a spreadsheet or text editor program Choose File gt Save window as file Each value for each data member in the map is saved separately and there will be a heading for it even if there were no values in the map For an explanation of the values that were saved consult the documentation for individual grids Saving the window view to a file is not the same as saving the values in SORTIE You still need to click OK to save any changes you ve made The tab delimited text file is just for your review It cannot be used as input to SORTIE directly although you could copy and paste values from it 16 Sep 2004 10 04 AM Model flow window This window is reached using the main SORTIE window menu option Edit gt Model flow It allows you to choose the behaviors for a run put them in a particular order and assign them to trees The current behaviors and their tree assignments is displayed in a hierarchical structure You can view the data in three structures ordered by different hierarchies so that you can quickly find the information you want Clicking on different parts of the structure bring up windows to edit those options You will find that there are multiple ways to find view and edit the same information Once you have experience with this window you may use different methods to edit behaviors depending on the nature of the edit you need to do This window has the following options View by behavior View
271. ram the recipient automatically receives a license from the original licensor to copy distribute or modify the Program subject to these terms and conditions You may not impose any further restrictions on the recipients exercise of the rights granted herein You are not responsible for enforcing compliance by third parties to this License 7 If as a consequence of a court judgment or allegation of patent infringement or for any other reason not limited to patent issues conditions are imposed on you whether by court order agreement or otherwise that contradict the conditions of this License they do not excuse you from the conditions of this License If you cannot distribute so as to satisfy simultaneously your obligations under this License and any other pertinent obligations then as a consequence you may not distribute the Program at all For example if a patent license would not permit royalty free redistribution of the Program by all those who receive copies directly or indirectly through you then the only way you could satisfy both it and this License would be to refrain entirely from distribution of the Program If any portion of this section is held invalid or unenforceable under any particular circumstance the balance of the section is intended to apply and the section as a whole is intended to apply in other circumstances It is not the purpose of this section to induce you to infringe any patents or other property right clai
272. rameters choose the appropriate probability distribution function for each species for each forest cover type This behavior cannot be applied to stumps Last updated 22 Aug 2004 08 36 PM 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 Only one predator population can be modeled Seed predation parameters Density Dependent Coefficient The coefficient describing the effect that density dependent factors have on the predator population instantaneous rate of change See equation below Foraging Efficiency The predator population foraging efficiency See equation below Max Decline Rate in Absence of Food predators week The maximum rate of decline in the predator population in the absence of any food in predators per week Max Intake Rate seeds per predator per day The maximum number of seeds that can be eaten by one predator in one day Number of Weeks in Which Seedfall Occurs The number of weeks at the beginning of the behavior mini model run that seedfall occurs The number of seeds that fall is evenly distributed over that number of weeks Predator Initial Density num sq m 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 Preserve predator de
273. rcept i 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 Used by the Windstorm behavior e Windstorm Storm Cyclicity Trend Function Slope m 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 Used by the Windstorm behavior e Windstorm Storm Intensity Coefficient c The c value in the equation used to determine the mortality of an individual tree as a result of a storm Used by the Windstorm behavior e Windstorm Timestep to Start Storms The first timestep that storms are allowed to occur Used by the Windstorm behavior Harvest 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
274. re and disease there may not be behaviors set up to create tree death for all of these reasons 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 If the tree is an adult killed by harvest and the run is not stump aware it is deleted from memory e If the tree is an adult killed for any reason other than harvest and the run is snag aware the tree is converted to a snag e Ifthe 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 Tree organization Trees are organized by location and size in what is called the tree population The tree population indexes trees into 8 m by 8 m areas lined up by height The population acts as a librarian for behaviors that wish to find certain sets of tr
275. re considered to be in size class 3 Used by the Weibull snag mortality behavior Adult 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 There is nothing in this behavior which makes it specifically for adult trees the name is to match existing SORTIE conventions How it works Self thinning uses a simple linear function of probability of mortality as a function of DBH 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 Adult 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 There is nothing about this behavior which makes it only applicable to adults The name conforms to old SORTIE standards and allows it to be distinguished from the Juvenile stochastic mortality behavior so that two different rates can be applied to two different groups of trees How it works For each tree a random number is compared to that species s Adult Background Mortality Rate parameter to determine if it falls in
276. redistribute the program under these conditions and telling the user how to view a copy of this License Exception if the Program itself is interactive but does not normally print such an announcement your work based on the Program is not required to print an announcement These requirements apply to the modified work as a whole If identifiable sections of that work are not derived from the Program and can be reasonably considered independent and separate works in themselves then this License and its terms do not apply to those sections when you distribute them as separate works But when you distribute the same sections as part of a whole which is a work based on the Program the distribution of the whole must be on the terms of this License whose permissions for other licensees extend to the entire whole and thus to each and every part regardless of who wrote it Thus it is not the intent of this section to claim rights or contest your rights to work written entirely by you rather the intent is to exercise the right to control the distribution of derivative or collective works based on the Program In addition mere aggregation of another work not based on the Program with the Program or with a work based on the Program on a volume of a storage or distribution medium does not bring the other work under the scope of this License 3 You may copy and distribute the Program or a work based on it under Section 2 in object code or ex
277. 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 The linear diam height function is height a b diam where 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 diam o 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 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 slo
278. rently loaded tree map trees click this button This action cannot be undone even if you click Cancel for the window Write tree map to text file If there is a tree map loaded then the button marked Write tree map to text file is enabled Click this button to write the contents of the currently loaded tree map to a tab delimited text file which you can open in a spreadsheet or text editor Files created this way are only for your own use SORTIE ND cannot accept them as run input However you can probably transform them yourself into a tab delimited map file that SORTIE ND can accept see the Tab delimited tree map topic Last updated 15 Nov 2006 07 24 AM Edit size classes window This window is reached from the Tree setup window It allows you to edit the size classes for the tree population Size classes help you define an initial tree population for your run When you have size classes set up you can specify an initial density of trees in each size class in the Parameters window You can have as many size classes as you want The upper DBH bound of a size class is its number The lower bound of the size class is the size class below it or zero if there is no lower class This means you may need one extra class in order to define a lower bound for your smallest class if you want its lower bound to be greater than zero The list of currently defined size classes is in the list at the left of the window To add a new size class
279. rid documentation e Files in SORTIE ND o Parameter files Detailed output files Summary output files Detailed output map files Tab delimited tree map files o Files from previous versions of SORTIE e Data visualization o Output chart types e References e Glossary e SORTIE ND License e GPL License What s New Version 6 07 released November 30 2006 a S a E H E o E e e E A e e a e OO Ov Or 3 Note If you have a parameter file from an earlier version and you are using behaviors that have been updated in version 6 05 load your file and save it SORTIE ND will automatically make any needed adjustments to your parameter file New in version 6 07 e You can now track subplots for detailed output files e The File menu now has an option for setting a working directory e New analysis behavior Partitioned DBH Biomass which calculates biomass separated out by branch leaf and bole e New analysis behavior Partitioned Palm Biomass which calculates biomass separated out by leaf and bole New light behavior Average Light which averages together existing GLI calculations New disturbance behavior Harvest Interface which provides a link between SORTIE and a separate application for doing harvests New mortality behavior Aggregated Mortality which clumps together tree death in both time and space New mortality behavior Exponential Growth and Resource Based Mortality which calculates mortali
280. rks 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 behavior 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 tr
281. rotopography behavior Minimum Solar Angle for GLI Calculations in rad 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 Light Behaviors for more on GLI calculations Used by the Light Dependent Seed Survival behavior Number of Altitude Sky Divisions for GLI Light Calculations Number of grid cells into which the sky is divided from horizon to zenith for the purpose of calculating light direction See Light Behaviors for more on GLI calculations Used by the Light Dependent Seed Survival behavior Number of Azimuth Sky Divisions for GLI Light Calculations Number of grid cells into which the sky is divided around the horizon for the purpose of calculating light direction See Light Behaviors for more on GLI calculations Used by the Light Dependent Seed Survival behavior 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 Used by the Establishment with Microtopography behavior Proportion Germinating Between 0 and 1 The proportion of seeds of a species that survive germination as a value between 0 and 1 Used by the Proportional Seed Survival behavior Proportion of Plot Area that is Mound The proportion of plot area that is mound area as opposed to ground area Expressed as a value
282. s makes decisions about which to kill then writes those trees to kill to another text file You tell SORTIE where to find this executable 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 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 file that SORTIE will write on the Edit Harvest Interface window SORTIE doe
283. s in cm for specifying seedling initial densities not required 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 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 setup window Last updated 02 May 2005 07 32 PM Allometry In this document Allometry parameters The standard crown height and width relationships The Chapman Richards crown height and width relationships DBH diameter at 10 cm relationship The standard diameter height relationships The linear diameter height relationship The reverse linear diameter height relationship The power diameter height relationship Allometry is the relationships between various aspects of a tree s size and shape A tree may use different relationships for different life history stages You can choose the relationship used by each life history stage of each species These can be freely mixed and matched Definitions DBH diameter at breast height is the diameter of a tree trunk at 1 35 meters above the ground Diameter at 10 cm or diamyo is the diameter of a tree trunk 10 cm above the ground In general crowns are modeled as cylinders with a radius and a height Specific behaviors may make diff
284. s 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 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 the previous year The total diameter increment is the sum of the X individual diameter increments After applying the amount of diameter increase tree height is allowed to update automatically according to the allometry equations 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 Lognormal with exponential shade reduction diam only How it works This behavior calculates annual height increases as 2 in diam 36 0 3 E Y a eg b 100 where e Y amount of height increase in cm e az Lognormal Diam Growth Increment at Diam 36 in mm yr a parameter e b Lognormal Diam Shape Parameter b parameter e c Lognormal Diam Effect of Shade c parameter 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 Assume that the number of years per timestep is X In order to fin
285. s a percentage of full sun See the light behaviors topic GMF Great Mountain Forest northwestern Connecticut One of the primary SORTIE field sites Submodels often contain a version whose simulations are based on field data from GMF and are thus intended primarily to simulate GMF conditions Grid A way of storing data in SORTIE that varies over space Grids are the same size as the plot and contain cells which can each contain several values See the grids topic for more Grid cell A single area in a grid object Harvest Logging Julian day A method for expressing dates The days in the year are numbered consecutively from 1 to 365 Juvenile tree A seedling or sapling tree which has not yet reached adult status See the trees topic for more Parameter file A file with all of the settings and data needed to run SORTIE See the parameter file topic for more Partial cut A type of harvest Plot SORTIE s underlying dimensions See the plot topic for more Quadrat A small grid cell Recruitment The process by which seeds become seedlings Release When a suppressed juvenile tree is exposed to higher light conditions it is released Release is characterized by a rapid increase in growth rate See the growth behaviors topic for more Run The process of the model receiving input and performing calculations for a specified number of timesteps Synonymous with simulation Sapling A tree at least 1 35 meters in height with
286. s 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 Tree Setup 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 internal SORTIE name of the data member which is what is displayed to you w
287. s of any species GLI Points File Creator behavior This behavior calculates GLI values for individual points in the plot 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 X Y Height m 12 4 136 5 1 2 128 7 19 5 0 68 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 th
288. s 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 storm damage You may not apply this behavior to seedlings If you wish to use the Storm 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
289. s the function of the Storm damage applier behavior How it works Storm severity is assessed on a scale from 0 no damage to 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 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 class 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 the damage is additive up to a maximum value of 1 total damage 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 m
290. s 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 P x ju k EA 1 7 f rd lute k 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 Adult 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 killed 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 How it works The BC mortality model evaluates the following function to determine the probability of a tree s mortality m l e T ne where e mis the probability of mortality e Tis the number of years per timestep e mz is the
291. s 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 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 Converting pre 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 16 Mar 2006 01 49 PM Files from versions of SORTIE prior to 6 01 If you used previous versions of SORTIE you may have a collection of files you used for runs This version of SORTIE can read some of those files If you have not used previous versions of SORTIE this topic is probably irrelevant for you Supported file types e Harvest regime files
292. s window allows you to directly work with the data in the grid maps for a single grid You can look at the values for maps loaded from a parameter or detailed output file make changes to existing maps or enter new values to use as initial conditions You reach this window from the Grid Setup window When you open this window you will notice that it is composed of one or more tables There is one table for each grid data member see the individual grid documentation for what each grid data member represents If a table is completely blank that means that there is currently no map loaded for this grid or at least for that data member If there is a map loaded you will see values in the tables You load grid maps using the File gt Open file command For more on entering the maps from a detailed output file the most likely source see the detailed output file topic Editing map values To edit a value double click its cell You can copy and paste back and forth from Excel and within the 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 If there is a cursor blinking in a cell when you click OK the value for that cell might not save Whenever you re done entering data it s a good idea to click outside the last cell so that this won t happen Saving grid map as text The window can be saved as tab delimited text fo
293. sal area The cross sectional area of a tree trunk at 1 35 meters DBH Batch Grouping SORTIE runs together to automatically run consecutively See the batch topic for more BC British Columbia Date Creek area central BC One of the primary SORTIE field sites Submodels often contain a version whose simulations are based on field data from BC and are thus intended primarily to simulate BC conditions Behavior A unit of work in the model which makes calculations and updates tree and grid data A simulation consists of a chosen list of behaviors working in sequence A behavior usually corresponds to a biological process See the behaviors topic for more Canopy The branches and leaves of a tree Synonymous with crown Clear cut A type of harvest Crown The branches and leaves of a tree Synonymous with canopy DBH Diameter at Breast Height The diameter of a tree s trunk at a height of 1 35 meters Deterministic Not random predictable Diameter at 10 cm The diameter of a tree taken at a height of ten centimeters Fisheye photograph A photograph taken with a fisheye lens which captures a complete hemisphere in two dimensions A fisheye photograph taken of the sky would see from horizon to horizon in all directions See the light behaviors topic Gap A small open area in a forest canopy Gap cut A type of harvest GLI Global Light Index A measure of the amount of light that reaches a certain point in space expressed a
294. sal 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 will might 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 distribution 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
295. sal 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 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 NOTE The parameters for this behavior are dependent on the size of the cells in the Basal Area Light grid Changing the size of the cells without changing the parameters may give different results The behavior begins by calculating the total basal area and angiosperm basal area in each of the Basal Area Light grid cells Whether a species counts as angiosperm or conifer is set 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
296. saved less frequently Subplots of a detailed output file 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 detailed output file When you do this your SORTIE run will produce a detailed output file for the whole plot and one for each subplot you define up to five They will all contain the same kinds of data 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 Setup detailed output file window 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 Using the example above here s how you would use a spreadsheet to read map data from timestep three of the my detailed output gz tar detailed output file 1 To give context to the map data you must load the original parameter file using File gt Open file Form the run above either testpar xml could be used or its copy in the detailed output file my detailed output xml If you choose the file my detailed output gz
297. scribed 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 Selection harvest This behavior allow you to specify target basal areas for a tree population as a method of harvest input instead of designing specific harvest events 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 behavior 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 documentati
298. se 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 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
299. sis behavior Dimension Analysis Parameter d 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 Used by the Dimension Analysis behavior Dimension Analysis Parameter e 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 Used by the Dimension Analysis behavior Dimension Analysis Use Correction Factor Whether or not the chosen biomass equation requires a correction factor to be multiplied by the result Used by the Dimension Analysis behavior Merchantable Timber Value Form Class The form class of the species Valid values are 78 79 80 81 84 and 85 Used by the Merchantable Timber Value behavior behavior Merchantable Timber Value Price 1000 Board Feet The price per thousand board feet for each species The currency used doesn t matter Used by the Merchantable Timber Value behavior behavior Partitioned DBH Biomass Leaf Slope a The slope in the linear biomass equation for leaves Used by the Partitioned DBH Biomass behavior Partitioned DBH Biomass Leaf Intercept b The intercept in the linea
300. symptotic Crown Height The asymptotic crown height or length in m of the Chapman Richards crown height equation Any species not using that function can omit this value e Chapman Richards Asymptotic Crown Radius The asymptotic crown radius in m of the Chapman Richards crown radius equation Any species not using that function can omit this value Chapman Richards Crown Height Intercept The intercept of the Chapman Richards crown height equation This represents the crown height in m of the smallest possible sapling Any species not using that function can omit this value Chapman Richards Crown Height Shape 1 b The first shape parameter b of the Chapman Richards crown height equation Any species not using that function can omit this value Chapman Richards Crown Height Shape 2 c The second shape parameter c of the Chapman Richards crown height equation Any species not using that function can omit this value Chapman Richards Crown Radius Intercept The intercept of the Chapman Richards crown radius equation This represents the crown radius in m of the smallest possible sapling Any species not using that function can omit this value Chapman Richards Crown Radius Shape 1 b The first shape parameter b of the Chapman Richards crown radius equation Any species not using that function can omit this value Chapman Richards Crown Radius Shape 2 c The second shape parameter c of the Chapman Richards crown radius equation
301. t conditions Used by the Logistic Bi Level Mortality behavior 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 Used by the Logistic Bi Level Mortality behavior Maximum DBH for Adult Self Thinning Maximum DBH at which adult self thinning applies Above this value no mortality occurs Used by the Adult self thinning behavior Mortality at Zero Growth Mortality rate at zero growth Used by the GMF mortality and BC morality behaviors NCI Crowding Effect Slope C The slope of the curve for neighbor effects Used in the NCI mortality behavior NCI Crowding Effect Steepness D The steepness of the curve for neighbor effects Used in the NCI mortality behavior NCI Max Radius of Crowding Neighbors in m The maximum distance from a target tree at which neighbors can have a competitive effect Used in the NCI mortality behavior NCI Max Survival Probability 0 1 The maximum annual probability of survival as a value between 0 and 1 Used in the NCI mortality behavior NCI Minimum Neighbor DBH in cm The minimum DBH for trees of that species to compete as neighbors Used for all neighbor species not just those using NCI mortality Used in the NCI mortality behavior NCI Neighbor DBH Effect alpha The effect of the DBH of a neighbor tree on its competitiveness for a target species Used in the NCI mortality behavior NCI
302. t behavior and a height incrementing growth behavior applied You must also enter a map of second resource values into the Resource grid Absolute growth behaviors Several behaviors apply an absolute growth version of the Michaelis Menton function Absolute growth is calculated with the equation A GEI A Ay GLi where Y loglO 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 GLIis 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 L
303. t 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 How it works 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 The behavior then go
304. t of diameter increase tree height is allowed to update automatically according to the allometry equations 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 Linear growth diam only How it works This behavior calculates an amount of diameter growth as Y a b GLI T where e Y amount of diameter increase in mm e a Simple Linear Diam Intercept in mm yr a parameter e b Simple Linear Diam Slope b parameter 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 and a height only growth behavior applied Linear growth w exponential shade reduction height only How it works This behavior calculates an amount of height growth as Y a b diam GLI 100 T where e Y amount of height increase in cm e a Shaded Linear Height Intercept in cm yr a parameter e b Shaded Linear Height Slope b parameter e c Shaded Linear Height Shade Exponent c parameter e diam diameter diameter at 10 cm for seedlings and saplings DBH for adults e GLI global light index as a percentage between 0
305. ta members that can be added To view this data save a detailed output file Usually a behavior also needs settings and inputs from you to do its job This data is included in the parameter file To edit settings for behaviors use the Parameters window If a behavior does not have all of the data it requires you will receive an error message Links to individual behavior documentation Harvest and disturbance behaviors Light behaviors Growth behaviors Mortality behaviors Substrate behaviors Tree removal behaviors Disperse behaviors Seed predation behaviors Establishment behaviors Planting behaviors Analysis behaviors Last Updated 16 May 2005 08 49 AM Disturbance behaviors Disturbance behaviors simulate different kinds of forest disruption These behaviors cause tree damage and death due to a variety of processes In this document Disturbance parameters Harvest Planned episodic mortality Storm disturbance Storm damage applier Storm killer Selection harvest Windstorm Harvest interface Disturbance parameters Note the Harvest and Planned episodic mortality behaviors do not have their parameters entered through the Parameters Window Set up these behaviors using the Edit Episodic Events Window e Clumping Parameter neg binomial If the Storm Damage Application parameter is set to Stochastic and the Stochastic Pattern Damage Distribution is set to Negative
306. tar from File gt Open file you can choose the file my detailed output xml within it 2 Load the individual timestep file using File gt Open file and choosing my detailed output gz tar You will be able to choose the individual timestep file within it 3 Use the Grid layer setup option or the Tree setup in the Edit menu to save the files as tab delimited text You can then open it from your spreadsheet application or a text editor 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 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 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 You don t have to use all the maps in the file more on this later 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
307. termine 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 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 erie 4 log tree 5 log tree 6 log tree DBH tree i 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 w aa WEZ ta Wese Wee Wess ass Was Miass esdas e w lae ishias Wahia pia fa he Wes Ai ffe e e a i ay Maaie hra Nisha W hos is
308. th behaviors and constant radial increment behaviors e Asymptotic Diameter Growth A Asymptote of the Michaelis Menton growth function at high light in absolute and relative growth behaviors A in the equations below Used in absolute and relative growth behaviors e Double resource Influence of Resource C The parameter governing the influence of the second resource on the double resource Michaelis Menton equation Used by the Double resource relative growth diam with auto height and Double resource relative growth diam only behaviors e Include Snags in NCI Calculations Whether or not to include snags when finding competitive neighbors for NCI Used in the NCI growth behavior diam with auto height and NCI growth behavior diam only behaviors e Length of Current Release Factor Controls the magnitude of the effects of release Used in absolute growth behaviors e Length of Last Suppression Factor Controls the magnitude of the effects of suppression Used in absolute growth behaviors e Linear Bi Level Intercept for High Light Growth a The intercept of the linear growth function used in high light conditions Used in the Linear bi level growth diam with auto height and Linear bi level growth diam only behaviors e Linear Bi Level Intercept for Low Light Growth a The intercept of the linear growth function used in low light conditions Used in the Linear bi level growth diam with auto height and Linear bi level growth di
309. th of the plot in the X direction The number does not have to be an integer Once you have entered your desired value you must click Update this grid to save your changes Cell length in Y N S direction in m Displays and sets the size of the grid in the Y N S direction in meters Some grids do not allow you to change their cell size consult the documentation for individual grids for any limitations or recommendations You can enter any number that you wish between 0 and the length of the plot in the Y direction The number does not have to be an integer Once you have entered your desired value you must click Update this grid to save your changes Apply cell size changes Use this button to update the current grid with any changes you have made to the cell size If you do not click this button your changes will be lost You must click this button for each grid you wish to update View edit save grid values Use this button to open the Grid Value Edit window This window allows you to view and change values for grid maps and write them out to tab delimited text files Clear grid map If there is a map loaded for this grid then the button marked Clear grid map is enabled If you want to remove a currently loaded map click this button This erases all map values for the current grid This action cannot be undone even if you click Cancel for the window 15 Sep 2004 02 45 PM Grid Value Edit Window Thi
310. 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 to add You should make this a fully qualified name i e C my files parameter file 1 xml rather than parameter file 1 xm1 This ensures that the model will be able to find the file when it comes time to run the batch Of course it also means that you should have your parameter files in the right locations before preparing your batch file for greatest ease 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 ru
311. the name of any behavior brings up the Current run behaviors window where you can edit the list of behaviors their order and to what trees they apply View by data type first This button changes the view to a hierarchical structure that shows grids and trees at the top level In the tree structure portions tree type life history stage is shown at a higher level and species is shown beneath Expanding a tree or grid branching shows what behaviors in order apply Clicking on any grid name brings up the Grid setup window where you can set options for grids Clicking on a tree species name below a tree type brings up the tree behavior window which you can use to set up the behaviors applied to the chosen tree type and species combination Clicking on the name of any behavior brings up the Current run behaviors window where you can edit the list of behaviors their order and to what trees they apply Current run behaviors window This window is reached through the Edit simulation flow window It edits the set of behaviors for a run the order they are in and the trees to which they apply if it is appropriate for them to apply to trees The current list of behaviors in order appears in the box labeled Current behavior order In this window Adding new behaviors Changing behavior order the Up and Down buttons Removing behaviors the Remove button Changing behavior assignments the Modify assigned data bu
312. the pool of trees that die How to apply it This behavior can be applied to seedlings saplings and adults of any species Aggregated Mortality Aggregated Mortality is similar to the Adult 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 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 R7 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 the parameter gives an annual rate the actual mortality rate is 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 tree
313. the tree population Grid Layer Setup to configure grids Model flow to specify the behaviors to use and in what order Parameters to provide parameter values and Output options to set up reporting 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 process It is certainly possible however to be working with a parameter file that has a problem of some sort especially if you started with an existing parameter file instead of from scratch The file will be validated before you run it but if you want to do a double check beforehand you can either save it from the File menu or view all its parameters in the Parameters window and then click OK These methods may not catch every problem but they will catch most of them 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 The model can make you tab delimited text versions of your data that you can open in any text editor or spreadsheet program Unfortunately there is currently no support for outputting all data at once If your parameter file contains both parameters and maps you must convert them separately 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
314. 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 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 If you ch
315. 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 Used by all disperse behaviors e Slope Mean Non Spatial Seed Rain seeds m ha of BA yr 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 Used by the Non spatial disperse behavior e STR for Stumps 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 Used by the Non gap spatial disperse Gap spatial disperse behaviors e Weibull Canopy Annual STR 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 Used by the Gap spatial disperse Non gap spatial disperse and Anisotropic spatial disperse behaviors In the case of the last two the canopy probability distribution function is the only one used for a species e Weibull Canopy Beta The B for the Weibull function under canopy conditions see equation below This is only required if the canopy probability distribution function
316. this way are for your reference only They cannot be used as input Last updated 07 Jun 2005 02 39 PM Detailed output files In this document What is a detailed output file Contents of a detailed output file Subplots of a detailed output file Viewing the data in a detailed output file Detailed output files as input to other runs For more on output including a guide on what to save see the topic Output in SORTIE What is a detailed output file 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 1s 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 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 exampl
317. to it and any later version you have the option of following the terms and conditions either of that version or of any later version published by the Free Software Foundation If the Program does not specify a version number of this License you may choose any version ever published by the Free Software Foundation 10 If you wish to incorporate parts of the Program into other free programs whose distribution conditions are different write to the author to ask for permission For software which is copyrighted by the Free Software Foundation write to the Free Software Foundation we sometimes make exceptions for this Our decision will be guided by the two goals of preserving the free status of all derivatives of our free software and of promoting the sharing and reuse of software generally NO WARRANTY 11 BECAUSE THE PROGRAM IS LICENSED FREE OF CHARGE THERE IS NO WARRANTY FOR THE PROGRAM TO THE EXTENT PERMITTED BY APPLICABLE LAW EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT HOLDERS AND OR OTHER PARTIES PROVIDE THE PROGRAM AS IS WITHOUT WARRANTY OF ANY KIND EITHER EXPRESSED OR IMPLIED INCLUDING BUT NOT LIMITED TO THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE PROGRAM IS WITH YOU SHOULD THE PROGRAM PROVE DEFECTIVE YOU ASSUME THE COST OF ALL NECESSARY SERVICING REPAIR OR CORRECTION 12 INNO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR
318. torm 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
319. tput file 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 How it works 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 increases 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
320. 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 Used by the Light Dependent Seed Survival behavior Snag Age Class 3 Light Extinction Coefficient 0 1 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 Otherwise a value must be provided for all species Used by the Light Dependent Seed Survival behavior Standard Deviation of Fresh Log Substrate Height in m The standard deviation of height of fresh log substrate in meters Used by the Establishment with Microtopography behavior Standard Deviation of Mound Height in m The standard deviation of the height of mounded areas in meters Used by the Establishment with Microtopography behavior Upper Age Yrs of Snag Light Extinction Class 1 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
321. 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 Last updated 08 Nov 2006 08 55 AM Grids In this document Defining grid cell size Viewing and using grid maps A grid is a structure for holding model data that varies across space You can picture a grid by thinking of a spreadsheet Each cell in the spreadsheet holds a distinct value which is identified by location coordinates row and column numbers Behaviors use grids to store data and to share it between behaviors Defining 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 Each cell within the grid is a rectangle with a separate X and Y size 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 va
322. ts compiler kernel and so on of the operating system on which the executable runs unless that component itself accompanies the executable If distribution of executable or object code is made by offering access to copy from a designated place then offering equivalent access to copy the source code from the same place counts as distribution of the source code even though third parties are not compelled to copy the source along with the object code 4 You may not copy modify sublicense or distribute the Program except as expressly provided under this License Any attempt otherwise to copy modify sublicense or distribute the Program is void and will automatically terminate your rights under this License However parties who have received copies or rights from you under this License will not have their licenses terminated so long as such parties remain in full compliance 5 You are not required to accept this License since you have not signed it However nothing else grants you permission to modify or distribute the Program or its derivative works These actions are prohibited by law if you do not accept this License Therefore by modifying or distributing the Program or any work based on the Program you indicate your acceptance of this License to do so and all its terms and conditions for copying distributing or modifying the Program or works based on it 6 Each time you redistribute the Program or any work based on the Prog
323. ts 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 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 NCI growth diam only This behavior works exactly like the NCI growth diam with auto height behavior to calculate an amount of diameter increase 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 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 Basal area NCI growth diam with auto height 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 neighborin
324. tten 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 code 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 executables that read setup parameters from a file You may wish to set up a SORTIE b
325. tton Adding new behaviors The left hand side of the window is devoted to choosing new behaviors for this run Begin by choosing an overall behavior grouping using the drop down list that shows Please select a behavior group when the window is first opened When you have chosen a group a list of individual behaviors for that grouping shows in the box underneath Select the one you wish to add then click the button marked gt gt to add it to the list It automatically places itself with other behaviors in its group or in the correct place between other groups if it is the first of its group Behavior groups are separated by dashed lines At this time you must add new behaviors one at a time It is possible to select multiple individual behaviors but the gt gt button will apply to only the first one selected If you have chosen a behavior that is already on the list nothing happens Certain special behaviors cannot be added this way If you try to add them you will see a message saying Use this behavior s own dialog This means that it has options that can be set up through a window accessible from the main SORTIE menu You can however remove these special behaviors from the run from this dialog Changing behavior order the Up and Down buttons You can change the behavior order within the overall behavior groupings Behavior groups are separated by dashed lines To change a behavior s position in the list sel
326. tually 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 With 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 Last updated 25 Jan 2005 01 05 PM Output Chart Types When you create output files you can use SORTIE s data visualization capabilities to look at their data in various ways SORTIE has several chart types that it can create from detailed output files and summary output files The chart types that you can view depend on the data you have saved in your output files Customizing saving and printing the charts Extracting the data to perform your own analyses Line graphs Histograms Tree maps Grid maps Tables Customizing saving and printing the charts 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 box Unchecking the box next to a species removes it from all of that file s charts Clicking on the color next to the species
327. ty as a probability of growth and a second resource New light behavior Constant GLI which provides the same value of GLI to every tree this behavior replaces the Constant full GLI behavior Added the possibility of cyclicity in storm frequency and intensity through time to Windstorm Minor changes and bug fixes Clicking on an output graph to bring it to the front causes its legend to come to the front as well The extra step of clicking a button to save a file has been eliminated when editing a batch file The XY Tree Map now has a minimum display DBH control If multiple output files are open and you choose File gt Close output file from the main menu you will have an option to close all of the files at once The Tree setup window has a new button for adding a tree map to the current parameter file If multiple behaviors use the same grid that grid will display correctly for entering grid maps The Grid value edit window now correctly saves the last value entered even if the cell is still in edit mode Fixed bug that caused changes to output settings for members of grids to become new entries rather than replacement entries this also caused the output settings for grids and trees to behave in the same way Fixed a bug allowing Puerto Rico semi stochastic growth to set a negative tree DBH in some circumstances Fixed a bug that caused designing complicated subplots to slow and eventually crash when too many cells were cl
328. ull 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 Used by the Weibull snag mortality behavior e Weibull Annual a Parameter for Snag Size Class 3 Mortality Weibull annual a parameter for those trees whose DBH is greater than the value in Upper DBH of snag size class 2 Used by the Weibull snag mortality behavior e Weibull Annual b Parameter for Snag Size Class 1 Mortality Weibull annual b parameter for those trees whose DBH is less than or equal to the value in Upper DBH of snag size class 1 Used by the Weibull snag mortality behavior e 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 Used by the Weibull snag mortality behavior e Weibull Annual b Parameter for Snag Size Class 3 Mortality Weibull annual b parameter for those trees whose DBH is greater than the value in Upper DBH of snag size class 2 Used by the Weibull snag mortality behavior e Weibull Upper DBH of Snag Size Class 1 The upper DBH value of trees in size class 1 Used by the Weibull snag mortality behavior e Weibull Upper DBH of Snag Size Class 2 The upper DBH value of trees in size class 2 Trees with a value greater than this a
329. un you would save less data For more information on using detailed output output as initial conditions see the detailed output files topic 18 May 2006 12 51 PM 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 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
330. und 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 Last updated 16 Nov 2005 09 40 AM Planting behaviors Planting Planting directly creates new seedlings When you create a new planting you specify the timestep in which to plant
331. unts 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 instead 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 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 dista
332. ut 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 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 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 i
333. ution function is lognormal Used by the Gap spatial disperse Non gap spatial disperse and Anisotropic spatial disperse behaviors In the case of the last two the canopy probability distribution function is the only one used for a species Lognormal Canopy Beta The for the lognormal function under canopy conditions see equation below This is only required if the canopy probability distribution function is lognormal Used by the Gap spatial disperse Non gap spatial disperse and Anisotropic spatial disperse behaviors In the case of the last two the canopy probability distribution function is the only one used for a species Lognormal Canopy Xo The mean of the lognormal function under canopy conditions see equation below This is only required if the canopy probability distribution function is lognormal Used by the Gap spatial disperse Non gap spatial disperse and Anisotropic spatial disperse behaviors In the case of the last two the canopy probability distribution function is the only one used for a species Lognormal Canopy X The variance of the lognormal function under canopy conditions see equation below This is only required if the canopy probability distribution function is lognormal Used by the Gap spatial disperse Non gap spatial disperse and Anisotropic spatial disperse behaviors In the case of the last two the canopy probability distribution function is the only one used for a species Lognorm
334. ve 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 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 find it by looking at the header that the piece of data is under 16 Nov 2004 06 47 AM Edit Episodic Events Window This window is reached using the menu option Edit gt Episodic events from the main window This window allows you to set up silvicultural treatments and planned mortality episodes In this document Window layout Displaying current episodic events Cre
335. ve to become seedlings Expressed as a value between 0 and 1 Used by the Substrate Based Seed Survival With Microtopography behavior Fraction Seeds Germinating on Mound Fresh Logs 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 Used by the Substrate Based Seed Survival With Microtopography behavior Fraction Seeds Germinating on Mound Scarified Soil 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 Used by the Substrate Based Seed Survival With Microtopography behavior Fraction Seeds Germinating on Mound Tip Up The proportion of those seeds that land on tip up mound substrate that survive to become seedlings Expressed as a value between 0 and 1 Used by the Substrate Based Seed Survival With Microtopography behavior GLI of Optimum Establishment 0 100 The GLI value of optimum survival for seeds as a value between 0 and 100 Used by the Light Dependent Seed Survival behavior Height in m At Which to Calculate GLI The height in meters at which to calculate GLI at the center of each grid cell Used by Light Dependent Seed Survival behavior Last Day of Growing Season for GLI Light Calculations The last day of the growing season as a Julian day number between 1 and 365 Seeds only get light during the growing season
336. w analysis behavior Tree Age which tracks tree ages New mortality behavior Height GLI Weibull Mortality which calculates tree mortality as a function of tree height and light levels New growth behavior Puerto Rico Storm Bi Level Growth which uses two functions to calculate growth before and after storms New analysis behavior Merchantable Timber Value which calculates the value of merchantable timber in a plot New analysis behavior Carbon Value which calculates the amount of carbon in a plot and its value Stand and Stock output tables now display species specific values as well as plot total values The Storm Light behavior has an updated equation for light calculation The main window is now equipped with scroll bars to allow you to use more space when viewing charts and graphs The Tree Setup window is now capable of changing the name of a species The Density Dependent Seed Survival behavior s survival area has been standardized to per square meter The Relative Michaelis Menton growth behaviors now have an additional exponent on diameter The Substrate behavior uses a new equation for decayed log decay Developers The C model code has been ported to the GCC compiler set and the Eclipse development environment Version 6 05 released August 3 2005 Note If you have a parameter file from an earlier version and you are using behaviors that have been updated in version 6 04 load y
337. w different aspects of tree shape are calculated can be found in the Allometry topic In addition a tree may carry data added to it by Behaviors to help simulate different processes Tree life history stages 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 The seed life history stage is currently not used by any behavior but is available if there is a need to model seeds as individuals 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 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 Stumps exist only for the timestep in which they were created and then disappear e Snag Snags are standing dead trees They can be produced when saplings and adults die due to normal tr
338. 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 GLI Map Creator For more on what GLI is and how it is calculated see above How it works 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 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 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 a grid object called
339. xisting one Along the left portion of the window you enter data about the planting On the map in the center you select the area of the plot to which to apply your planting If a tree map has been entered those trees are displayed on the map and the species key is to the right For more on tree maps and episodic events see the Edit Episodic Events Window topic In this document Entering data about the planting Choosing the area to which to apply the planting Entering data about the planting Timestep Enter the timestep in which you wish the planting to occur You can create more than one planting per timestep Percentage of each species For each species enter the percentage of total trees planted that should be of that species as a value between 0 and 100 Enter zero in order to not plant a species Values should add up to 100 When SORTIE plants a seedling it compares a random number to these values to determine its species This ensures a random distribution of species in the planted population but it also means that if the number of seedlings to plant is small the actual percentages of each species planted may not exactly match the entered values Plant spacing Select the seedling spacing If you select Gridded the seedlings are placed at a fixed distance from each other If you select Random the seedlings are randomly scattered around the plant area total trees ha You enter this value if the Plant spacing
340. y 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 and a diameter only growth behavior applied Logistic growth diam with auto height How it works The amount of diameter increase is calculated as a e J GLI K where e Y amount of diameter increase in mm e a Logistic Asymptotic Diam Growth Full Light in mm yr a parameter e b Logistic Diam Shape Param 1 b parameter e c Logistic Diam Shape Param 2 c parameter e GLI global light index as a percentage between 0 and 100 calculated by a light behavior e T number of years per timestep After applying the amount of diameter increase tree height is allowed to update automatically according to the allometry equations 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 Logistic growth diam only How it works The amount of diameter increase is calculated as a ae Crap k where e Y amount of diameter increase in mm e a Logistic Asymptotic Diam Growth Full Light in mm yr a parameter e b Logistic Diam Shape Param 1 b parameter e c Logistic Diam Shape Param 2 c parameter e GLI global light i
341. y storm at all of any strength Storm Light 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 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 Description name A storm damage susceptibility for each cell from 0 not susceptible pusee pully to damage to gt 1 very susceptible to damage Substrate 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 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 ce

SORTIE 6.07 User Manual - sortie-nd

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