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User Manual 5.1

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2. g oun c o um t 0 0 Size Class Time yrs The Diameter Distribution plot shows the initial size class distribution in black This distribution 1s static The current year size class distribution 1s shown in red This distribution updates each year according to simulation results The diameter size classes are defined by 10 cm intervals and only trees gt 20 cm diameter are plotted The vertical gray line divides commercial and non commercial trees as determined by the minimum diameter cutting limit The Tree Abundance plot shows the abundance of trees over time The black line tracks the abundance of all trees gt 20 cm diameter The red line tracks the abundance of commercial sized trees The vertical gray lines indicate the harvest years that is 31 61 and 91 years in the example shown 17 Free Landis amp Grogan Mahogany Growth amp Yield 8 3 Harvest Productivity Monitors HARVEST PRODUCTIVITY monitors report the volume of trees logged in the most recent harvest as well as the number and volume of trees logged in all previous harvests Monitors are updated after each logging event HARVEST PRODUCTIVITY Logged Volume m3 Total Logged Volume m3 Total Logged Trees 48 6 590 9 96 Logged Volume reports the volume m of trees logged in the most recent harvest Total Logged Volume reports the volume m of trees logged in all previous harvests Total Logged Trees reports the number of trees logged in
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6. www java com Check your browser s homepage for more information on installing the Java plug in If you think you have the right browser and plug in but the online model still does not work check your browser s preferences to ensure that Java 1s enabled The following web site may be helpful for determining which version of Java you have and for getting the correct version installed and running http www javatester org Browser Memory The Big Leaf Mahogany Growth amp Yield Model applet may require more memory than the browser normally makes available This is more likely to happen when simulating large populations On Windows you can increase the available memory heap space in the Java Control Panel s applet runtime settings In the Java tab of the Java Control Panel view the Java Applet Runtime 10 Free Landis amp Grogan Mahogany Growth amp Yield Settings Enter the following in the Java Runtime Parameters field Xmx1024M Include the initial hyphen but not the final period More information is available here http download oracle com 1avase 1 5 0 docs guide deplovment deplovment guide 1cp html Mac OS X 10 4 users should note that Mac OS X 10 4 initially had a low memory limit for Java applets 64 megabytes A Java update from Apple raised the memory limit to 96 megabytes This update is available through the Software Update but no other options for increasing the Java memory limit are avail
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9. amp Grogan Mahogany Growth amp Yield 2 MANUAL GUIDE This User Manual is intended for both beginning and advanced users working with the Big Leaf Mahogany Growth amp Yield Model to inform management decisions The Manual can be read from front to back for a thorough understanding of how the model works It can also be queried with specific questions using the section guide below MODEL INSTALLATION section 3 details the model installation process HELP BUTTONS section 4 explains where to find help while working in the model interface A BRIEF GUIDE section 5 provides basic instructions for navigating the model interface USER DATA UPLOAD section 9 provides instructions for uploading user data into the model framework SIMULATION EXPERIMENTS section 11 provides directions for running repeat simulations of a single harvest regime or multiple simulations of varied harvest regimes ADVANCED USERS NETLOGO RESOURCES section 12 reviews the advanced NetLogo features and identifies resources for interested users to learn more about NetLogo programming The remaining sections review model features in greater detail and can be read in advance or when specific questions arise If you still have questions after reading this User Manual or have any feedback on the model please contact the authors page 47 3 MODEL INSTALLATION 3 1 CD Installation The following section explains how to install the NetLogo software from the Big Le
10. gamma a A 12 where fruit production by a given tree 1s capped at 750 to avoid unrealistically high values 55 Free Landis amp Grogan Mahogany Growth amp Yield Once fruit production 1s determined for surviving reproductive trees new seedling recruits are added to the population based on the following equation 1 year old seedlings 37 fruit Spruit fgapi feurv 13 where n is the number of reproductive trees in the population fruit is the number of fruit produced by tree i Spuit 1s the mean number of seeds per fruit foap 1s the fraction of seeds landing in gaps for tree i and f 1s the fraction of seeds that germinate and survive to become 1 year old seedlings Spuir and fsury are constant values of 42 4 and 0 085 respectively based on observations at the Marajoara field site The fgeap i fraction represents the proportion of the 0 91 ha seed shadow overlapped by zones of recruitment of contributing treefall gaps and natural disturbances The resulting number of surviving seeds is divided by the number of zone of recruitment patches within the seed shadow Each zone of recruitment patch receives the resulting number of l year old seedlings with diameters drawn randomly from an observed distribution of seedling diameters Model Reset Function The final function in the model procedure resets the trees and landscape before beginning the process again during the next time step the next year First all dead trees
11. 100 STATISTICS The HARVEST STATISTICS section is only displayed if logging is turned on during the simulation This section summarizes the number of harvests number of trees logged and volume of trees logged during the simulation runtime The section also summarizes the results of each harvest by displaying the year and productivity of successive harvest events Finally the SIZE DISTRIBUTION YEAR XXX section summarizes the size distribution of trees gt 20 cm diameter in the final year of simulation The largest tree 1s always contained within the second largest size class that 1s the final size class will always contain 0 trees The number of size classes changes based on the size distribution of trees in the final year but the size class increment 1s always 10 cm diameter 11 SIMULATION EXPERIMENTS BehaviorSpace The NetLogo BehaviorSpace tool allows users to easily run repeat simulations of the Big Leaf Mahogany Growth amp Yield Model using either constant or systematically varied harvest parameter settings The BehaviorSpace tool thus enables users to examine the outcomes of multiple harvest regimes with statistical confidence repeat simulations and methodological ease automated process Results from these simulations are then tabulated into a spreadsheet for analysis 27 Free Landis amp Grogan Mahogany Growth amp Yield The following section explains how to run modify and analyze the six built in BehaviorSpace experim
12. 3es sT5 6 dus eaep z AT1 rO0Z e4ieu eaeq Jesejiep peoT sth eq4ep I ATI p0Z VeI Leu eT ays ejzep Azepunog Ffoz ezeu ej eqd a3esej3ep peor srb ejep Azepunog foz exzew 3eTm dus ea3ep eed434 p0z edeu ejeqg jJesejep peoT sth eaep eed4a poz e e2eu q T o3 w w w 1STT ZejZoweTp y oqur ASO y UT sz a uerp y speew sandur HWVN WTId4 uq ur desn y q pergjroeds aTtF Aso uq su do ASO p prAo4ad desn oy uo4j Si q uerp Hutz04S AOF STI s qzxe dzO NOILV IndOd LEA MHLd4WVIG HS HdVOSQNV I NO SAAAL SLAS SO qQ T29A 90274 burureuoedg y dn s3es yey eunpeoodd y STTI O oueu pourjep dgesn oy YATM erirgjedeus oy ur ea4nqrig33 eu3 WOATF s aeurpaooo peaeroosse y AOF 1 4 WLeTp oy speeN 4STT STUG uo peseq s qaeurpaooo ObOTIEN eua sp irnq pue UOTReEDSOT ASTT 9u3 O4UT e rjedeus y Aq pergjroeds sejaeurpuooo oua speay oa Ttyoedeys 99413 ua FO qu ax SYA OF PTAOM ObDO T39N 9U3 FO qu ax ou43 ses ObO IT349eN OUT e rjedeus poeurgjep Aesn oua FO sea4nqidg33 y Spe q NOILV IndOd HIIAHdVHS AASA AdVOSGNVT NO SHAHAAL SLAS em w w w en oa Oh OD w w w w w w w w w w w w w w w eqep eed43 Aso pe 1x TT1jJ Ndz eqaep z3a ASO 3es epue 3 e e 1T3 you TTuA eoueN er r4 7ESN PrAOM usedo aeTTI 3STT a3 p eed4 ASO YOST SooJ24 ASo dn3es OF s nTrTeA 1za dna s eueN e43nqra33V WVIG D4J3OA on eA A4aagedoud sTb do43ouer
13. 91C X u eu 8 1901 801 x IT Z X PZ soyojed 77z 8 9IC X 8 687 L7 8687 rbueqao q eu 8 1901T Ssquuud SNOISNSELXH ZAA ANAL suorsueurg obo T43eN suorsueurq Yo ed aT bue zoey feu 8L LE9 ATepunog euggo uozeuy ezgovV SNOISNHWIG NdVOSGQNV TI 00001 OOT x oqe Z T eu vc 80c equoo ST PTIOM yL 00T Seeza 8 II IT Z X G8 x s u o qaed gg x sayojzed 09 seuo3qed a8 X 09 lt Z TLT X 9 IZI u QpP cCILTI X u 60 9TZT rbueqao q eu7oz taxed aS s zq a T8 eu OOT Se8974 0 CL ey 001 9274 T OL ALISNZG IT Z X 09 eu 804 L14989 1S I GPL S99JI43 EFI IZIS ZAA ANAL suorsu urq obo T43eN suorsueurq Yo ed aT bue zoey eu OL 7O7 aepunog gt SNOISNHWId AdVOSANWT zog z unqa OJ4NI HdVOSGNV I UOZzeulv 3S M 1OV eugcor Ied AS eupoz 4ed AS V4uV SNOILV IndOd eTTAydozsew erueaqerAg Aueboyew jeo b5rq jo epou pper pue yAMoAb uoraeTndod paseq Tenptatput TOTIdX eraeds v OJUI T9pow soroedsg zequtyz TeotdozL JO sburasrT SALIDO Burau u TdurI 203 ueagboaud SHLIO OLLI qLII S4S0 Aazysez0q Teordoar jo 4N4 T4SUI euoraeudoaqur uebory souep s STpueT A933 9W N I9PON PT TA 9 YAMOAD uebouew jJe T 5rgd ooa24 1r udoasrdauo burpung S1O0ua3nv 9I 3TL T PON OjUI T DONW w w w w w w w on enh OR OR OR OD w w w w w w w
14. DBuraano e qeA oT T umururu eu 00T Seed23 G LInAVANG PBurbbor zeqaze seezdg43 rIOJeuuoo jo q4rsuep e qeAOT T UnuTruru pobboT 08 b5burpueas 3gje q asnu 072 LInNWANd burb50T 293g s zqa rodgeuuoo jo uorqu qa 41 unururu e uo 09 Li10Vd4ud burbb50T erodgeuuoo 7AOF Nd eq OF paMOTTe seer FO uo zagea3euerp unururu s002 onxuuvga ANY NVO2ONO WOM SGUYVGNVLS LINYA Und TTITA Suoraeinurs epou y I eura FO ua3bue unurxeu y seuTWASe ep ASPTTS STYL Suorjeinurs epou oua buranp pebboT ede soo2g43 I UYJ YM s urud qa p YORTMS STYL Suorae inurs epou y ur pesn sT uorqaeTndod eed4 YOTYM s urud q p desoouo STUL S IVHO ID HOLIMS ANW HdGdi s em em em w em en en en oui oui oui oui TIV ou seA uoaed zodsjeems e sr uo3ed e deu3euA 4 Buraqaeorpur uee ooq v ou se A uoaed eouequnasip e sr uoa3ed e dgeoua3euA buraeorpur uee ooq v SH IHVINHVA HOLVd sobe sgqeo oou4u3 Tenptsezr yyAMorh sobe szeak om Tenptsez yAMorb sobe ageo ouo Tenptsez yyMo rb Jeo qu s dzd eua ur Tenptsez yyAMo rb sbur pees ageo 434Ss4313j uoo q oq HuTATAANS sp s FO goqunu ooJ3134 e Aq peonpodud qrn4J FO Aequnu Uu3404b5 pue AaejZowetTp uozgj poaeino eo ooud3 e AOF DBurarnag FO AQAtTTtqeqoizd U34045 pue do3euerp uozj p qeTnoTeo za E 4103 KqarTeqad3Ou Fo arrirqeqoad 99213 jo ZA wo qer u3 4o42b Tenuue J9ojeuerp uoz2gj pea3e ino eo 9073 e FO gu eun oA Uqp uozj peyzerTnoTes
15. Marajoara was selectively logged for mahogany during 1992 1994 The population in 204 ha is from a 100 inventory for mahogany trees gt 20 cm diameter The population in 1035 ha contains the 204 ha population but at lower sampling resolution representing gt 80 of trees gt 20 cm diameter in this larger forest area Most of the trees presented here are logged stumps For more details see Grogan et al references section 16 Acre West Amazon presents spatial and diameter data for a mahogany population located 40 km south of Sena Madureira in the western Brazilian state of Acre This data is from a 100 inventory in 685 ha for mahogany trees gt 20 cm diameter At the time of inventory this was an 14 Free Landis amp Grogan Mahogany Growth amp Yield unlogged population The low landscape scale density is typical of western Amazonian mahogany populations USER POPULATIONS User Population xyd For uploading spatial and diameter data from a spreadsheet User Population shp For uploading spatial and diameter data from a shapefile User Population csv For uploading non spatial diameter data from a spreadsheet The site is drawn in the landscape middle field of the model interface If the site is drawn too small for the available space increase the value shown in Patch Area and press the Resize button upper right on interface If the site 1s drawn too large for the available space decrease the value shown in Patch A
16. Simultaneous runs in parallel option 2 maximizes run efficiency e ou Run options X Spreadsheet output V Table output Simultaneous runs in parallel 2 If more than one some runs happen invisibly in the background Defaults to one per processor core Press OK and save the output file anywhere on your computer The output file must be saved as a csv or xls file INCLUDE THE CSV OR XLS FILE EXTENSION IN THE FILE NAME Step 6 Determine Run Settings After saving the output file the Running Experiment window will open in the center of your screen This window graphs the population metrics measured during the experiment and tracks the progress of the experiment by reporting the number of completed steps and elapsed time 32 Free Landis amp Grogan Mahogany Growth amp Yield _ O Running Experiment Population Growth amp Productivit t normal speed 0 count trees lll 1 count trees with 3 2 count trees with 9 3 sum annual har 4 sum annual har El 5 annual harvest 9 6 annual harvest Run 4 of 600 step 53 Total elapsed time 0 04 06 Logging true minimum diameter 40 vi Update view vi Update plots and monitors Abort V The graph will only be shown when measuring every time step therefore you will only see this graph if you change the default experiment settings The graph displays the measure of each population metric over t
17. To specify a different download location right click on the link and select the Download Linked File As option Step 2 Unzip Model Package Contents The contents of the Model zip zip file must be unzipped using built in zip software On most operating systems double clicking the zip file accesses the zip software However some systems may require you to right click the Model zip file and select the unzip or uncompress options Follow the unzip instructions of your software and extract the Model folder anywhere on your computer Step 3 View the Model Folder Contents If you successfully unzip the Model zip zip file you will see the Model folder This folder contains all the files necessary to install the NetLogo software and run the growth amp yield model Double click the Model folder to view its contents It contains six elements 1 Growth amp Yield Model file 4 User folder 2 User Manual file 5 Results folder 3 Data folder 6 NetLogo folder The Growth amp Yield Model file 1s the NetLogo file nlogo containing the growth amp yield model This file will only run after installing the NetLogo software The User Manual file 1s a copy of this User Manual in PDF format The Data folder contains all the data files necessary to run the growth amp yield model NEVER ALTER OR REMOVE ANY FILES IN THIS FOLDER Free Landis amp Grogan Mahogany Growth amp Yield The User folder contains example user upload
18. Trees gt 20 cm diameter count trees with diameter gt minimum diameter Commercial Trees sum annual harvest number Logged Trees sum annual harvest volume Logged Tree Volume m annual harvest number Harvest Number List yr annual harvest volume Harvest Volume List m yr 34 Free Landis amp Grogan Mahogany Growth amp Yield If you would like to query the model for additional information please refer to Command Line and BehaviorSpace Experiments below sections 12 1 amp 12 2 Step 8 Analyze Simulation Data Before analyzing the data you may be interested in adding a few data columns such as total density commercial density and harvest year statistics The abundance count values can be converted to density values using the following formula Density Abundance Site Area 100 where site area 1s measured in hectares ha and density 1s measured in trees per 100 hectares The harvest number and volume lists can be broken into individual years using the Text to Columns feature available in most spreadsheet programs First highlight the two list columns and use the Find and Replace feature to remove the brackets from the cells Then use the Text to Columns feature with data delimited by spaces to convert the text data to column data This will better facilitate the examination of harvest productivity across time The post processing of the harvest value lists can be avoided by using the direct
19. all previous harvests 9 USER DATA UPLOAD You can simulate population growth and harvest outcomes of a mahogany population at your own site using the DATA UPLOAD portion of the model interface At minimum you will need diameter data for the trees within your site If you have both spatial distribution mapping and tree diameter data you can upload the data from a spreadsheet or if available from a GIS shapefile Refer below to Spatial Diameter Data User Spreadsheet and Spatial Diameter Data User Shapefile sections 9 1 amp 9 2 respectively for instructions If you only have diameter data you can upload the data from a spreadsheet but you will need to know or estimate the dimensions or approximate area of your site Refer to Non Spatial Diameter Data User Spreadsheet section 9 3 below 9 1 Spatial Diameter Data User Spreadsheet This section describes the procedures necessary to upload diameter data with spatial location information from a user spreadsheet The spatial diameter data must be formatted according to the instructions below for the model to accept the user data Step I Data Structure and Format The first step 1s to structure your data so the computer can read the information into the model Create an Excel xls type spreadsheet to organize the data into three columns X coordinates Y coordinates and tree diameters The columns must be listed in this order for your data to be read into the model Column A
20. and disturbances are removed from the landscape Second the tree variables associated with reproduction fruiting probability fruit production and number of surviving seeds are reset to default values to prevent the values of a reproductive year from carrying over into a non reproductive year 56 Free Landis amp Grogan Mahogany Growth amp Yield APPENDIX D MODEL CODE This section provides a fully annotated copy of the model code This code is identical to the code in the Procedures tab of the NetLogo interface The structure of the model code is summarized in Model Procedure Code section 12 3 and reviewed briefly below The head of the model code provides basic information about the model the title the authors the funders the landscape dimensions etc The EXTENSIONS BREEDS AND VARIABLES section declares the code extensions and variables used throughout the model The MODEL SETUP section sets up the model by checking for errors setting variable values drawing the landscape setting the plots and monitors and establishing the initial population on the landscape The RUN MODEL section successively grows logs kills disturbs and reproduces the trees on the landscape This section also contains the code for exporting data and resetting the trees and landscape for the next year of simulation The procedures are color coded according to the following scheme keywords are GREEN constants are ORANGE comments are built
21. annual harvest volume volume of logged trees in harvest 1 item 1 annual harvest volume volume of logged trees in harvest 2 item 2 annual harvest volume volume of logged trees in harvest 3 item 1 X annual harvest volume volume of logged trees in harvest X The item code numbers items in a list from zero onwards so item 0 is harvest 1 item 1 is harvest 2 item 3 1s harvest 4 etc You must enter an item reporter for each expected harvest You can determine the expected number of harvests using the following formula floor Time Limit Cutting Cycle 1 where the floor of a number of harvests is the largest integer less than or equal to the number Adding Stop Conditions If you are interested in including stop conditions different from the defaults which stop simulations after the time limit or when all trees die or are harvested whichever happens first you can enter new conditions in the Stop condition prompt The model stops when conditions become true For example if you want to halt simulations after the first harvest you would enter length annual harvest number gt 0 Alternatively if you want to halt simulations when commercial abundance falls below a certain threshold you would enter count trees with diameter gt minimum diameter lt 10 More information on BehaviorSpace experiments can be found on the NetLogo website or in the NetLogo User Manual Please see NetLogo Resources section 12 4 below 12 3 Model Pro
22. can replace a statistical statement in the provided commands Likewise any tree variable alive diameter mort rate surv seeds etc can replace a tree variable in the provided commands 12 2 Modifying BehaviorSpace Experiments SIMULATION EXPERIMENTS BehaviorSpace section 11 provides a thorough review of the NetLogo BehaviorSpace feature If you are interested in personalizing the built in experiments further or in creating your own experiments entirely please review the section below Varying Multiple Parameters Pre defined BehaviorSpace experiments are designed to test either a single harvest regime or to test the sensitivity of population growth amp yield to a single harvest parameter It 1s also possible to examine multiple harvest regimes within a single simulation experiment This can be achieved by varying more than one harvest parameter in the BehaviorSpace variable settings For example rather than only varying minimum diameter both minimum diameter and retention rate could be varied using the following code minimum diameter 40 10 80 retention rate 10 5 30 The BehaviorSpace experiment would simulate each combination of minimum diameter and retention rate for the specified number of repetitions In other words each minimum diameter cutting limit beginning with 40 cm and ending with 80 cm at 10 cm increments would be simulated with each retention rate beginning with 1096 and ending with 30 at 5 increm
23. create canopy gaps proportional to stem diameter based on the equations In the Mortality Function section below Mortality Function The mortality function estimates the probability of mortality as a binary logistic regression of the current year stem diameter and diameter increment using the following equation log odds mortality 2 11 1 337 growth rate 0 107 diameter 3 0 1305 max 0 diameter 23 0 0197 max 0 diameter 86 which 1s subsequently used to calculate the probability of mortality with the logit transformation mortality probability exp log odds 1 exp log odds 4 where the fate of each tree Is determined by comparing its probability of mortality to a random number between 0 and 1 If the randomly selected number is smaller than the probability of mortality the tree is marked as dead Before its removal from the population a dead tree 1s given a 50 chance of dying standing and a 50 chance of dying before seeding A tree dying after seeding will fruit and disperse seeds before being removed from the population whereas a tree dying before seeding will be removed from the population without fruiting A tree dying standing will be removed from the population without creating a treefall gap whereas a tree resulting 1n a treefall gap will create a disturbance area according to the following equation disturbance area m 25 171 1 398 dbh 0 02 dbh 2 5 whe
24. experiment Edit opens the selected BehaviorSpace experiment for editing Duplicate duplicates the selected BehaviorSpace experiment Delete deletes the selected BehaviorSpace experiment Run runs the selected BehaviorSpace experiment 28 Free Landis amp Grogan Mahogany Growth amp Yield Before running an experiment you should select the Edit option and familiarize yourself with the experiment s settings The modification of these settings and the creation of new experiments are discussed more below section 12 2 Step 3 Choose a BehaviorSpace Experiment Choose a baseline BehaviorSpace experiment to match your experimental goals The Population Growth No Logging experiment simulates the initial population without logging in order to examine the natural projection of the population The Population Growth amp Productivity Standard Logging experiment simulates the initial population under current default harvest standards in order to examine the projection of the initial population following these legal guidelines The four Population Growth amp Productivity Harvest Parameter experiments examine the effect of each harvest parameter on population growth and harvest productivity by varying a single harvest parameter and keeping the other parameters constant The final Population Growth amp Productivity Custom Logging experiment provides a place for the user to define a single custom harvest regime to simulate the recovery and p
25. false Large Dead Tree Abundance show count trees with alive false and diameter gt 60 Dead Tree Diameter List cm show diameter of trees with alive false 37 Free Landis amp Grogan Mahogany Growth amp Yield Disturbance Statistics disturb trees Landscape Disturbance show count patches with disturbance true count patches Landscape Sweetspot Vo show count patches with sweetspot true count patches Landscape Disturbance ha show count patches with disturbance true 100 10000 Landscape Sweetspot ha show count patches with sweetspot true 100 10000 Reproduction Statistics reproduce trees Reproductive Tree Abundance show count trees with reproduce true Mean Reproductive Tree Diameter show mean diameter of trees with reproduce true Max Large Tree Fruit Probability show max fruit prob of trees with diameter lt 30 Median Fruit Production show median num fruit of trees with reproduce true Potential Seed Production show floor sum num fruit of trees seeds per fruit Actual Seed Production show sum surv seeds of trees Disturbance Seedling Datasets Median Disturbance Area m show median disturbance dataset Disturbance Dataset Sample Size show length disturbance dataset View Disturbance Dataset show disturbance dataset Mean First Year Seedling Diameter show mean seed diam list disturbance dataset a list of the disturbance area sizes m obser
26. have been specified press the Setup button under MODEL SETTINGS to draw your site on the model interface The site should be drawn using a Patch Area of 1 00 pixel but a larger or smaller Patch Area may be preferred depending on the dimensions of your site If the site 1s drawn too small for the available space increase the Patch Area by entering 2 00 and press the Resize button If the site 1s drawn too large for the available space decrease the Patch Area by entering 0 50 and press the Resize button Continue to make adjustments by increasing or decreasing the Patch Area until you are satisfied with the size of your site on the model interface Step 4 Trouble Shooting If you require quick assistance press the button for a summary of the DATA UPLOAD features or refer to this manual See Error Messages Trouble Shooting section 9 4 below for a discussion of error messages you may encounter when uploading your data into the model 22 Free Landis amp Grogan Mahogany Growth amp Yield 9 3 Non Spatial Diameter Data User Spreadsheet This section describes the procedures necessary to upload diameter data without spatial location information into the model interface Although spatial diameter data 1s not required for this data upload feature you must know or estimate the physical dimensions or area ha of your field site Step I Data Structure and Format The first step 1s to structure your data so the computer can read the inf
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30. should contain the X coordinates longitude of each tree Column B should contain the Y coordinates latitude of each tree Column C should contain the diameter In centimeters 18 Free Landis amp Grogan Mahogany Growth amp Yield of each tree DO NOT GIVE THE COLUMNS HEADERS The head of your file should look like the example file shown on the next page The XY coordinates longitude latitude must be measured in either meters or decimal degrees In the example above coordinates are given in UTM Universal Transverse Mercator geographic coordinate units taken from a standard GPS unit Alternatively coordinates could be given in user assigned meter units derived from a field based inventory Coordinates cannot be given in degrees minutes and seconds Coordinates measured in this format can be converted here http www fcc gov mb audio bickel DDDMMSS decimal html X Coordinates Y Coordinates Diameters o A B C D 1 579775 8 9136498 4 71 3 2 579744 8 9136501 6 79 4 3 580177 6 9135822 6 66 1 4 580265 1 9135770 8 80 4 Trees 5 580300 9 9135752 5 45 5 6 580317 3 9135686 3 64 7 7 580343 1 9135666 1 72 5 8 580406 1 9135441 5 79 0 Diameters must be measured in centimeters cm Tree diameter measurements should be taken at 1 3 m above the forest floor or at least 30 cm above the reach of the tallest buttress Step 2 Save As Text File The model software cannot read data from Excel xls files so the data must be save
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33. 0 of commercial sized trees the prohibition of logging in areas with population densities lt 0 05 trees ha 5 commercial trees 100 ha and a cutting cycle of 25 30 years 15 Free Landis amp Grogan Mahogany Growth amp Yield LOGGING PARAMETERS P i a n w s 1 Harvest parameters can be changed according to user preference Each parameter can be reset using the computer cursor to move the red bar across the green slider Movements to the right increase the parameter values while movements to the left decrease the parameter values The minimum value maximum value and value increment are listed for each parameter below Minimum Diameter 0 100 em 5 cm increments Retention Rate 0 100 95 retention 596 retention increments Minimum Density 0 20 trees 100 ha 1 tree 100 ha increments Cutting Cycle 0 100 years 5 year increments Pressing the Defaults button will return the logging parameters to default conditions Minimum Diameter 60 cm Minimum Retention 20 trees Minimum Density 5 trees 100 ha Cutting Cycle 30 years If you do not want to simulate logging turn logging off using the Logging switch discussed above 8 SIMULATION RESULTS The model interface provides information to allow users to observe simulations as they progress 8 1 Population Monitors The YEAR 0 POPULATION and CURRENT POPULATION monitors report total tree density commercial tree density and commercial tree
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35. 1 61 B6 B6 This section of the file records basic information about the simulation experiment including 1 the version of NetLogo run 2 the name of the model 3 the name of the experiment 4 the date and time the experiment was run and 5 the dimensions of the field site Numbers in the above list correspond to the line number in the experiment results file The field site dimensions are reported in terms of NetLogo patches but can be converted to meters by multiplying each value by 10 meters The length of the X axis of the site is the sum of minimum min pxcor and maximum max pxcor X coordinate The length of the Y axis of the site 1s the sum of minimum min pycor and maximum max pycor Y coordinate Additionally we recommend inserting a few lines under the header to record additional information about the simulation experiment For recordkeeping it would be useful to record the field site name area and dimensions initial tree abundance and volume and harvest years The rows below the header contain the data from the simulation experiment The headings can be rewritten for increased clarity based on the following recommendations or on user preference run number Run Logging Logging on off minimum diameter Minimum Diameter cm retention rate Retention Rate 96 minimum density Minimum Density 100ha cutting cycle Cutting Cycle yr step Time yr count trees Trees count trees with diameter gt 20
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38. 8 Estimating the number of trees and forest area necessary to supply internationally traded volumes of big leaf mahogany Swietenia macrophylla in Amazonia Environmental Conservation 35 26 35 Grogan J Jennings SB Landis RM Schulze M Baima AMV Lopes JCA Norghauer JM Oliveira LR Pantoja F Pinto D Silva JNM Vidal E amp Zimmerman BL 2008 What loggers leave behind impacts on big leaf mahogany Swietenia macrophylla commercial populations and potential for post logging recovery in the Brazilian Amazon Forest Ecology and Management 255 269 281 Grogan J amp Galv o J 2006 Factors limiting post logging seedling regeneration by big leaf mahogany Swietenia macrophylla in southeastern Amazonia Brazil and implications for sustainable management Biotropica 38 219 228 Grogan J amp Galv o J 2006 Physiographic and floristic gradients across topography in transitional seasonally dry evergreen forests of southeastern Amazonia Brazil Acta Amazonica 36 483 496 Grogan J 2005 Mogno Swietenia macrophylla Meliaceae In Shanley P amp Medina G eds Frutiferas e Plantas teis na Vida Amaz nica pp 115 122 Mulheres da Mata Imazon Bel m Par Brazil 45 Free Landis amp Grogan Mahogany Growth amp Yield Grogan J Landis RM Ashton MS amp Galvao J 2005 Growth response by big leaf mahogany Swietenia macrophylla advance seedling regeneration to overhead canopy release in southeast Par Brazil Forest
39. A 4 eozage yo Red e s3eg fi SL 7 eeaV uoaed yes eur0Zz 27ed AS SuoTzZeTndog SWHUW HOLVd LINVAYG SILAS eoze yojed 4 ezTS yored 31 enz4 SIOII yes 4gequnu odez uou SATYATSOd e oq snu eodvV uo3ed bess u z sn 0 gt PEAY YO Red J 9nza3 sdaodd 3988 nzqa SIOII eas obessou 4gesn es ej SWeEN OTTA AS09 amp a1equeu jt Jequnu odgez uou SATATSOd e q snu qubr Hnu qrs J4equnu oz z uou sATATSOd e oq asnu y44 PpTM 7 TS bess u 1z sn 0 gt qub5r H qrtsS J obessow zoesn 0 gt YAPTM E4TS J ASO uoraerndogd d3 sn suorqeTndod 37 nzqa S I0II Yas perjrioeds eq asnu oueN e4nqr2433V WVIG V bess u 1i sn eueN e4nqr4g433V WVIG Aqduo jr nza S I0II Yes eTTF dus e eq asnu oueN e IJ4 ebessou dgesn es qej eueN e T4 dus eaequoeu jT dus uoraeTrTndoq zeSsn suoraeTIndod jJ 9TITJ 3X34 eq snu oueN 9I IJ ebessou 2gesn es ej SUWeEN OTTA 3X43 EAequow JT p x uotTye Tndog zaesn suoraer rndog jJ T T H f x F oqa w w w u oqa x w w u o3 w em w Io43euerp YATM 9e IJ ASO poprAodgd agesn e uo peseq uoranqridasrp e dn s3es Uerp pue Ax YATM eT rj dus peprAodgd Aesn e uo peseq uoranqrida3sip e dn sas wetp pue AX YATM eT IJ 3X43 peprAodgd Aesn e uo peseq uoranqridga3sip e dn sa sS 8002 Te 39e uebozg5 uozeuy 3seM edgovV uo peseq dn r00c uebozg5 ears pIierg 12d eug
40. As 39s OT snunrpead 3ee s snripedg ur seuoaed xse 0 lt snrpezag 39e89AS JT pez zoTood q s n eeouequnasrp 3es OT snunriped asrp sntpez ut s uoqed xse Z sntperz joems y Td eoage 3998AS YOST OT Snrped asip snripezag 43eeAs T td eeae asrp 32bs snrpezg 43sIip eT epque eud e ewweb wopuer eoage j3srp aT prsur qaTInq ST 30ds3ee 4s ou3 VE760SSS00 O epquet 49T x93euerp erodgeuuoo y uey AebrAe T seer Oq ureqad3 d sorasrqeas arsu a 9ouepunqyv Terodas uuroo 41eo3euerp uo QZ ueua I 6IeT s zq Oq Ureqad3a d sorqasrqaeas Aa31sueg eouepunqv TeIOL x DBIOA JUTAd aTTIZ uoraeuzojgur edou AOF TenueW I sN oyu ees oseorI d 2 buruuna Aq zo uorqeTnurs queaddgno y FO saeedez2 suorqeTnurs und e burs buruuna Aq sT op ued nox 3ur4d T1IJ 1ueurdeodxo ooedsguguorAeueg SUOTJETNUTS TOWU 39npuoo eseo d sa nsed s ua qeDprITe A OL uorae inurs e burs e FO sarns r y saueseudez2 aeuuns HbuTMOTTOF eurn pago auragd eT i3 uu 3UT4d e r3 szeok sxor3 poeuoeeuN ourn sueo A eurn 3TWTT eurrn pz0M aquragd erTr3i seToAo T atoAo bura3no sxor3 2z0013 ssaetToAD yseazeH FO Aequnn axea3 boT burb50T1 p Iom qyutad a tts eu T e ze ars uorsrioeud eeav ears 4xeq dod eueN 9ea31S pz0M aurad erir3 suora3erndogq 3xe43 dod 43es eueN e ir4 3xea34 dod yes suoraer ndog zesn wey yesez ATT
41. Ecology and Management 204 399 412 Grogan J amp Barreto P 2005 Big leaf mahogany on CITES Appendix II big challenge big opportunity Conservation Biology 19 973 976 Grogan J Vidal E amp Schulze M 2005 Apoio cient fico para os padr es de manejo de madeira na floresta amaz nica a quest o da sustentabilidade Ci ncia amp Ambiente 32 103 117 Grogan J Ashton MS amp Galv o J 2003 Big leaf mahogany Swietenia macrophylla seedling survival and growth across a topographic gradient in southeast Par Brazil Forest Ecology and Management 186 311 326 Grogan J Galv o J Sim es L amp Ver ssimo A 2003 Regeneration of big leaf mahogany in closed and logged forests of southeastern Par Brazil In Lugo A Figueroa Col n JC amp Alay n M eds Big Leaf Mahogany Genetics Ecology and Management pp 193 208 Springer Verlag New York NY USA Grogan J 2002 Some simple management guidelines could help the sustainable management of bigleaf mahogany in the neotropics Tropical Forest Update ITTO Newsletter 12 4 22 23 Grogan J Barreto P amp Ver ssimo A 2002 Mogno na Amaz nia Brasileira Ecologia e Perspectivas de Manejo Mahogany in the Brazilian Amazon Ecology and Perspectives on Management IMAZON Bel m PA Brazil 58 pp Grogan J 2001 Bigleaf mahogany Swietenia macrophylla King In southeast Par Brazil a life history study with management guidelines for sustained production from natur
42. N aA seuoqed 0 891 X P O09T lt u 6 9EE X u B TZE Suorsueurq yo ed u 8 89 X u 06 LIZE Ey 90 9801 STHueqosy ey 90 v801 er5bue3oeuN fey GZO0T ATepunog euscor aded AS SNOISNSNWIG SdVOSGNV I Tepow y Aq pesxoeda3 JOU ede sobpo AsAO pesagodsTip spoees sogenbs ug x WOT eae soyojed sul XOQq UTYUATM peur eu TOA uns ey go 3STI V Seun OA 9U3 JO 3STT V Soun OA 9U3 JO STT V y xXoe13 O i1exor3 V 1z qa uerp bur pees oum oos FO uorqagodoad eui Jo z qumu oebegoAe e our jo azequnu unurxeu ur 0 e go w snrpe2g eur e go AATTTQeqoid eum e go AATTTQeqoird eum 4stp u ozts deb eur uotyzzo0doid enuue aug paooe42 Of OTQeTAeA v paooe42 Of OTQeTAeA v paooe42 Of OTQeTAeA v paooe42 Of OTQeTAeA v buraeorpur uee ooq v SLNVILSNOO IHdOW ods poo jo urT STUL zna epoo jo eurT STUL em em em en en em em em em em en en em en em em em em LL LL w w em en em em em en em em em en em em em en em en en on eun oA 4seA4geu enuue eun oA pebboT uno sun TOA pebboT 704 TOYOTA Wsearey 4sr l uerp pees qoad Auns 341nagg 4ged speoes 41rn4Jj unu x eu Sntpeir pses Spoes ou orp qoad burpuejs erp qoad jesej3ep oouequnaisrp astp doid eunioA uuoo 0A Kqarsu p umuoo 04 AjyTsuep 3034 04 e rxze qrs SIOII sTeqoT5 992134 s 1 peeuq srb suorsuea3xe Sd IHVIHNVA ANW OOT OOT x TI Z X e Z T Sseuoaed gor x 3ed 6 LOT X P S lt u 8
43. S 1s the shortcut for the Setup button D is the shortcut for the Defaults button etc A button shortcut will appear black when enabled and gray when disabled To enable shortcuts click anywhere in the white background of the model 3 4 VENE C E I All Definitions Export Results interface Additional questions can be directed to the authors listed at the end of the Manual page 47 11 Free Landis amp Grogan Mahogany Growth amp Yield 5 A BRIEF GUIDE The following guide describes the most basic method for simulating a pre defined big leaf mahogany population Step 1 Designate Initial Population to Simulate Select either a pre defined example population or upload your own data using one of the USER DATA UPLOAD options section 9 Step 2 Set Simulation Time Limit A simulation will end when the time limit 1s reached or when all the trees are harvested or die Adjust the time limit by using your computer cursor to slide the red bar horizontally across the dark green slider Movements to the right increase the parameter values while movements to the left decrease the To simulate the population with a harvest regime select logging on otherwise select logging off If logging Set a minimum diameter cutting limit default 60 cm diameter Set a commercial tree retention rate default 20 commercial retention Set a minimum post harvest commercial popula
44. Spees jo dequnu y uruz qa p OF aqaueasuoo qTnaz Spees ayy Aq perridrarnu ST 31n42j FO ToOqunu suL sen eA epqueT pue eudie eua bursn p zra q uez1ed uor4nqridgasrp euueb e uo p seq 4TNAF jo ASqunu y s qaer noreo uor3ounj STYL LINA JO AHaWON SHLV IQO IVO w w o w em en em w em en pue 3Tnzgg unu oT eo qoad 4341n323j gt I a3 o j uopue42 JT sppo 4tnaz dxo T sppo arnag dxe qoad 41n433j joes s 0 eaea uaMo25 0 4ASTT xeu x G6 z 96L z eaea uaModg5 0S ie3euerp 0 4STT xeu x 6L01 0 LLTTI O adea3euerp ET 9 sppo a3rin323j a3eI 9nza eeonpoaded ua 3r seer yse qoad 4341indgj oT 9o oF UOr34ounj 4ZINAF eua OF uo seob T ngssooons sr KarTrqeqo4ad FI uoraeudogjsueg43 a3r50T sy bursn AytTtqeqozd o4 peadeAuoo pue p qeTnoTeo st qoagdg jo sppo b5oT eurn seedg43 bur pees ou STU3 Op aeATAONpOoAdeA se payrew soozg3 TUO ONILINYA AO AJLIUIIS8VGHOUHd SALVINOTWO en w w w w w w w w w w w sTrea q S IL eonpoideu w w w pu Spoos osagodsrp qoaud 41in4gj oT eo Soo21g34 oonpoude4g oqa Spees s sz dsrp pue sp s jo zgequnu 4TNAF jo ASqunu y s qeTInorlIeo burarnajg 9974 e FO AQATTTqeqorzd eua seaer noreo dAdn qgquooygd NOT LONGOYddY ew oa OD en w w SUTTINO Seer eonpoiudew em w w pu gaoueqinastp uar 4 seuoaed qunoo eode deb T 9e3043 Was zZ pea zoTood yes enzg43 e30ds3ee
45. T V saeo Aqatyyz I A OJOZ Oq 39 AAaYoOTRZ 9 O O Ysaazrey y FO NTLA TerqaTUur SUL e900Z o AT 5 pue uebozg5 sbur pees zeak 4ysAtTF uoo q oq burArAU2ns spees FO uorajaagododd eur S00Z Il 39e ueborzy arnag aged spees jo dgequnu obegoA our TepowW SrpueT q900Z O ATe5 pue uebo415 seuoaed zge Gg Sntpezr u z8 c G zu 00716 Mopeus pees eu T6 0 e FO snipeza ur suae p 1o3gj pees 0G uae p 41o3gj poss q uop 0G b5burpees e430j9q STP OF S907 PAETTTYX jo uoraaodoad say Tepow SrpueT DBurpueas ureuoa2 0G sdeb 9 j zqa oe43 e20 0G burpueas erp oq S 1I PAaATTTY jo uoraagodoad eur q900Z O A 5 pue ueboz2g5 zeek uoee pequnasrp 9Zz 00001 OOT x Seuoaed unod AT snorA SLNVLSNOO IHGOW STIVgHOTIO dn SIAS STUL STUL STUL sa s sa s sa s SLAS 9913 0 0 ead 4 Seez3 Aso dn3es Aso uoraerndog d3 sn seez3 dus dn3es dus uoraerndog d3 sn seeza3 p x dn3es pAx uoraerndog d3 sn em em en em em s za 1aoSe dna s uozeuy 3s9M 9JOV Sseeag3 scor ezaeu dn3es eugcor Ied FS seeag3 voz eaeu dn3es eupoz sized HS w em em em en em w suorqaerndod suorqaerndod suorqaerndod suorqaerndod suorqaerndod suorqaerndod s xza dna FT FT Jt BT JT Sr os our 3no s ar dna s w w w w w em soayo zed soyojzed dny o3 w w w pu u 1zB5 AOTOOd Was sTej
46. USER MANUAL for the BIG LEAF MAHOGANY GROWTH amp YIELD MODEL CHRISTOPHER FREE R MATTHEW LANDIS JAMES GROGAN Copyright O 2011 by the Authors Support for model development and publication provided by USDA Forest Service International Institute of Tropical Forestry ITTO CITES Program for Implementing CITES Listings of Tropical Timber Species ies On the cover A big leaf mahogany population 204 hectares in southeast Para after 70 years of simulation Dark circles represent mahogany trees sized according to diameter The red squares represent disturbances with the darker red portions representing the zone of recruitment Seasonal streams are shown in blue and the site boundary is shown in white Suo128s aui 11D 40 aQ 11V SS8ug xoq uoijluljap SIF ul S ND 0 uo1128s uoo oq 4x u uOiinQ uq SSaJd SNOLLINIJ3Q ka e mE dus eyep 3341 02 voozwvid ALIALLINGOUd 1S3Au VH O _ saad pab5o 2101 OST 514 aw a j 22 Ew aunoa er2aunuo EYOOT Ajsuag esaWWO gt EYOOT Asuag 80L NOILV1NdOd LNIYYNID a a Aysuag ep2aunuo Bu001 BIOL NOILV1NdOd 0 YVIA Se G sm j res s lm SONILL3IS BAON G snonunuo gt paads ewou gt Ppv apa upa seinpa2ojd uomneuuoju Model Schematic The model interface as it appears when installed on your computer Table of Contents Model Sc
47. able 4 HELP BUTTONS Pressing HELP buttons located on the right side of each model interface section allows you to see definitions of model features in the DEFINITIONS box see below Each model section can be queried in this way To see definitions of all model features without pressing each button press the All Definitions button located below the DEFINITIONS box In addition definitions are listed in APPENDIX B MODEL DETAILS amp DEFINITIONS of this Manual You can also look for help by selecting Help in the NetLogo menu bar The Search option can direct you to specific menu items or help topics The Look Up In Dictionary F1 option opens a web browser with the dictionary entry for the selected code The NetLogo User Manual and NetLogo Dictionary links will open the manual and dictionary in a web browser The NetLogo Users Group option will link you to the NetLogo Users Group also in a web browser DEFINITIONS This is the DEFINITIONS box as it appears on the Press the button next to each section to v model interface Feature definitions can be viewed by features in this definition box Press All De of all the sections using the blue bar to scroll across the text content All definitions can be accessed by pressing A on the keyboard This is the shortcut for the All Definitions button Button shortcuts are displayed in the upper right corners of the buttons E is the shortcut for the Export Results button
48. ading your own data section 9 The Results folder 1s the default destination for certain BehaviorSpace simulation results and a recommended destination for all other results exports The NetLogo folder contains the NetLogo 4 1 2 installers necessary for setting up the growth amp yield model on your computer This folder also contains the NetLogo 4 1 2 User Manual written by the NetLogo design team Step 3 Choose a NetLogo 4 1 2 Installer Double click on the NetLogo folder to view its contents If you are using a Windows computer double click the Windows folder and then double click the NetLogo4 1 2Installer exe installer file If you are using a Mac OS X computer double click the MAC OS X folder and then double click the NetLogo 4 1 2 dmg installer file The installer file will open when double clicked Follow the installation instructions to install NetLogo software on your computer INSTALL NETLOGO ON YOUR COMPUTER AND NOT ON THE GROWTH amp YIELD MODEL CD ROM If you would prefer to download the NetLogo software from the NetLogo website download NetLogo 4 1 2 here http ccl northwestern edu netlogo 4 1 2 DO NOT USE ANY OTHER VERSION OF NETLOGO THE MODEL ONLY WORKS IN NETLOGO 4 1 2 Refer to the NetLogo User Manual if you require additional assistance Step 4 Move Model Files to Computer If you have successfully installed the NetLogo 4 1 2 software you are ready to open the Growth amp Yield Model file We recommend
49. af Mahogany Growth amp Yield Model CD ROM and how to run the model using this software Step I Insert CD into CD Drive Insert the Big Leaf Mahogany Growth amp Yield Model CD ROM into your computer CD drive If the computer does not open the CD folder within a few minutes access the CD folder from My Computer on a Windows computer or from the Desktop on a Mac OS X computer Step 2 View CD Contents If you successfully open the CD folder you will see the Model folder This folder contains all the files necessary to install the NetLogo software and run the growth amp yield model Double click the Model folder to view its contents It contains six elements 1 Growth amp Yield Model file 4 User folder 2 User Manual file 5 Results folder 3 Data folder 6 NetLogo folder Free Landis amp Grogan Mahogany Growth amp Yield The Growth amp Yield Model file is the NetLogo file nlogo containing the growth amp yield model This file will only run after installing the NetLogo software The User Manual file is a copy of this User Manual In PDF format The Data folder contains all the data files necessary to run the growth amp yield model Changes to these files may render the model inoperable DO NOT CHANGE THEM The User folder contains example user upload files These files should be viewed as templates when uploading your own data into the model framework You will also place your data files in this folder when uplo
50. ail Chris Free cfree swietking org If you are unable to email questions can be directed to James Grogan 44 Cave Hill Rd Apt 2 Leverett MA 01054 USA Tel 1 413 548 8180 More information on our research can be found on our website or in the publications above http www swietking org 47 Free Landis amp Grogan Mahogany Growth amp Yield APPENDIX A DATA SOURCES This research program s principal study site Marajoara is a forest industry owned management area in southeast Para Brazil 7 50 S 50 16 W The site was selectively logged for mahogany between 1992 1994 Model demographic parameters are derived from a sample mahogany population consisting of 358 surviving trees gt 10 cm diameter In an area of 2050 ha These trees were censused annually for survival stem diameter growth and fruit production from 1997 2010 Other phases of mahogany s life cycle including temporal and spatial patterns of seed dispersal seed germination and seedling establishment rates were quantified In observational and experimental studies at Marajoara Fruit production data are supplemented by observations of 325 mahogany trees at three additional sites in southeast Para and at the Acre West Amazon site Because few large gt 100 cm diameter adult trees survived logging at Marajoara or were available for observation at the other study sites fruit production data are supplemented with data from Gullison ef al 1996 The example pop
51. al forests PhD dissertation Yale University New Haven CT Gullison RE Panfil SN Strouse JJ amp Hubbell SP 1996 Ecology and management of mahogany Swietenia macrophylla King in the Chimanes Forest Beni Bolivia Botanical Journal of the Linnean Society 122 9 34 Jennings S amp Baima AMV 2005 The influence of population and forest structure on fruit production in mahogany Swietenia macrophylla King and their consequences for sustainable management International Forestry Journal 7 363 369 Kelty MJ C mara Cabrales L amp Grogan J 2011 Red oak in southern New England and big leaf mahogany in the Yucatan Peninsula can mixed species forests be sustainably managed for single species production Journal of Sustainable Forestry Lemes MR Dick CW Navarro C Lowe AJ Cavers S amp Gribel R 2010 Chloroplast DNA Microsatellites Reveal Contrasting Phylogeographic Structure in Mahogany Swietenia macrophylla King Meliaceae from Amazonia and Central America Tropical Plant Biology 3 40 49 Lemes MR Grattapaglia D Grogan J Proctor J amp Gribel R 2007 Flexible mating system in a logged population of mahogany Swietenia macrophylla King Meliaceae implications for the management of a threatened neotropical tree species Plant Ecology 192 169 180 Lemes MR Gribel R Procter J amp Grattapaglia D 2003 Population genetic structure of mahogany Swietenia macrophylla King Meliaceae across the Brazilian Amazon based
52. annual harvest volume total volume of logged trees annual harvest number lists number of logged trees in each harvest annual harvest volume lists volume of logged trees I each harvest If you would like to remove a reporter from this list simply delete it from the box If you would like to add or modify a reporter refer to the sections below sections 12 1 amp 12 2 Note a method for reporting harvest number and volume values in individual columns is detailed in section 12 2 The reporters will be measured every year time step if the Measure runs at every step option is selected This would generate an unnecessary amount of data so the default setting leaves this option unchecked If you would like to track every year of every simulation select this option Experiment Run Settings The Setup commands and Go commands fields correspond to the commands in the model procedure responsible for setting and running the model DO NOT CHANGE THESE FIELDS The Stop condition and Time limit fields are left purposefully empty because both stop conditions and time limits are already built into the model It would be redundant to specify them again here DO NOT ENTER ANY VALUES OR COMMANDS IN THESE FIELDS The Final commands field can be used to export the model landscape plots and world at the end of each model run The export view command exports the model landscape to an external 3l Free Landis amp Grogan Mahogany Growth amp Yield ima
53. arings initiated at Marajoara In 1995 These data present optimistic estimates of juvenile performance due to manual removal of competing vines and secondary vegetation during the experiments initial three years 42 Free Landis amp Grogan Mahogany Growth amp Yield Second population outcomes are highly sensitive to disturbance and the model s disturbance function is derived from data collected during a single year at Marajoara Because disturbance regimes vary widely across time and space this data only partially represents the temporal and spatial extent of gap forming disturbance events necessary for mahogany regeneration and recruitment to adult size Finally the model does not formally incorporate density dependent population regulation which may allow overestimation of population growth amp yield Steniscadia poliophaea a nocturnal specialist moth preys more regularly and intensely upon mahogany seedlings in close proximity to large fruiting trees or groups of clumped adults The population level influence of this density dependent seedling predator could be strong if population growth Is sensitive to observed reductions in seedling survival and growth As well impacts on population growth of the mahogany shootborer Hypsipyla grandella cannot be directly accounted for in the model due to lack of data addressing this issue Density dependent seedling mortality has been shown to reduce population growth rates In other neotropi
54. blishing the initial population on the landscape These steps happen in discrete sections of code known as procedures bounded by the keywords to and end Each step is explained thoroughly in the model code The third and final section of code RUN MODEL successively grows kills disturbs and reproduces trees on the landscape This section also contains the code for exporting data and resetting the trees and landscape for the next year of simulation These steps are also contained within procedures and each procedure ts extensively commented in the model code Procedures In the Procedures tab of the NetLogo interface use the Procedures menu to view a list of model procedures and zoom to a specific procedure Procedures are color coded according to the following scheme keywords are green constants are orange comments are built in NetLogo commands are blue primitive reporters are purple and everything else 1s black Modifying Global Variables It is possible to modify the growth amp yield model using alternative data to calculate alternative regressions but explaining this process is beyond the scope of this User Manual If you intend to modify model functions we recommend that you modify only global variables model constants Global variables are set in the first section of code and are briefly summarized below Variable Value Definition prop dist 0 026 the proportion of the landscape disturbed each year seed radius 5 382
55. cal trees 14 FUTURE MODIFICATIONS We are interested in using the recently published R Extension for NetLogo Thiele amp Grimm in press http netlogo r ext berlios de to increase the robustness of the model regressions the potential for 1n model data analysis and the functionality of the Export Results command We also plan to make the model run faster by improving the processing efficiency of the disturbance and reproduction functions Similarly we plan to include more built in example populations and to streamline the user data upload process The online version of the model will be continually updated as the computer version of the model becomes more compatible with the web server and applet export services Future versions of the model may also be improved according to user feedback and recommendations Please take the user survey listed on our website http www swietking org 43 Free Landis amp Grogan Mahogany Growth amp Yield 15 ACKNOWLEDGEMENTS Principal funding support for this long term research program has been provided by the USDA Forest Service s International Institute of Tropical Forestry and by the ITTO CITES Program for Implementing CITES Listings of Tropical Timber Species see page 2 At IITF Ariel Lugo s vision and commitment to this research program made it possible This research has additionally been supported by a broad spectrum of public and private sources including the USDA Forest Service
56. cedure Code This section provides insight into both modifying and understanding the underlying model code A fully annotated version of the model code is available in APPENDIX D MODEL CODE page 57 and in the Procedures tab of the NetLogo interface A close review of the code will help you better understand how the model works NetLogo Resources section 12 4 provides additional information towards understanding the code 40 Free Landis amp Grogan Mahogany Growth amp Yield Procedure Summary The gray text preceded by repeat semi colons represents comments provided to guide you through the model code This text is not read by the computer and 1s included only to explain the functional model code The head of the model code provides basic information about the model the title the authors the funders the landscape dimensions etc The first section of real code EXTENSIONS BREEDS AND VARIABLES identifies code extensions and variables used throughout the model Code extensions activate code types not included in the default language as well as variables used throughout the model to modify trees and the landscape Global variables are constant values used to make these modifications these are the only variables we suggest that you modify as explained below MODEL SETUP the second section of code sets up the model by checking for errors setting variable values drawing the landscape setting the plots and monitors and esta
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58. cial diam Black initial size distribution red current size distribution Vertical gray lines harvest years Black total tree abundance red commercial tree abundance HARVEST PRODUCTIVITY Logged Volume The volume of trees logged in the most recent harvest m Total Logged Volume The volume of trees logged in all previous harvests m Total Logged Trees The number of trees logged in all previous harvests DATA UPLOAD File Name Name of user data file with diameter and or XY data DIAM Attribute Name Site Width Site Height Patch Area Resize DEFINITIONS All Definitions Export Results Name of the diameter attribute in the user shapefile The width X of the user field site meters The height Y of the user field site meters The size of the patches on the landscape pixels Resizes the landscape based on the Patch Area listed Displays the definition function of all features on the interface Exports simulation results to a user named and located file Commercial sized trees or commercial trees are trees whose diameters are larger than the minimum diameter cutting limit or minimum diameter Note that in both Diameter Distribution and Tree Abundance plots no trees lt 20 cm diameter are shown COMMAND CENTER Command Center Ww Clear observer show count trees observer 118 observer show count trees with diameter gt 60 observer 15 observer show sum volume of tree
59. d as a text txt file In Excel or a similar spreadsheet program choose File gt Save As and select Text tab delimited from the Save As options Include the tvt extension in the file name The head of the new text file should look like this WITHOUT COLUMNS HEADERS X Coordinates Y Coordinates Diameters Y v v 579775 8 9136498 4 fled 579744 8 9136561 6 79 4 568177 6 9135822 6 66 1 536265 1 9135778 8 oB 4 Trees 550300 9 9135752 5 45 5 568317 3 91356986 3 64 7 536343 1 9135666 1 72 5 5oB4B86 1 9135441 5 79 Read 7 Q1 FR4 F 44 2 Place the new text file in the Model gt User folder Remember the name of the new text file 19 Free Landis amp Grogan Mahogany Growth amp Yield Step 3 NetLogo File Parameters The final steps towards uploading your data into the model are completed in the DATA UPLOAD portion of the model interface These parameters specify the name of the user data file the dimensions of the user field site and the resolution of the resulting landscape DATA UPLOAD mara 204 tree data xt 204 tree mara 204 tree data xt za ca am Type the name of the text file from Step 2 containing spatial and diameter data located in the User folder into the File Name input box Be sure to include the txt file extension when typing the name Leave the DIAM Attribute Name input blank This input is only necessary for data uploaded from a user shapefile section 9 2 Input here will
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62. e mara 204 tree data csv CSV zm zz co Leave the DIAM Attribute Name input blank This input is only necessary for data uploaded from a user shapefile section 9 2 Input here will interfere with the present upload Type the width X in meters of your site into the Site Width input box and the height Y in meters of your site into the Site Height input box If your site 1s not rectangular estimate the width and height of the smallest bounding rectangle examples shown above Again the width and height of your site must be in meters m Type the value 1 00 into the Patch Area input box Patch Area determines the size of landscape patches in pixels and therefore determines the size of the landscape A Patch Area of 1 00 is purposefully small and should draw a landscape contained by the available space on the model interface Step 4 Resize Site Drawing After File Name Site Width Site Height and Patch Area have been specified press the Setup button under MODEL SETTINGS to draw your site on the model interface The site should be drawn using a Patch Area of 1 00 pixel but a larger or smaller Patch Area may be preferred depending on the dimensions of your site If the site 1s drawn too small for the available space increase the Patch Area by entering 2 00 and press the Resize button If the site 1s drawn too large for the available space decrease the Patch Area by entering 0 50 and press the Resize button Continue to mak
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64. e the data file name if running a user population 2 the area of the field site in hectares 3 whether logging was turned on or off and 4 the number of harvest cycles the simulation time limit in years and the actual time run in years The second section of the Results file reminds the user that additional simulations are necessary to validate the results of a single simulation This can be achieved by repeating the same single run simulation or by running a BehaviorSpace experiment section 11 as described below The lines following these reminders define 7otal Abundance Density and Commercial Abundance Density as referred to in the Results file statistics In all cases Total Abundance Density refers to trees gt 20 cm diameter Commercial Abundance Density refers to trees gt the minimum diameter cutting limit designated on the model interface The next section LOGGING PARAMETERS only appears if logging was turned on during the simulation and reports the logging parameter values used during the simulation If the logging parameters are changed mid simulation only the end parameter values will be displayed YEAR 0 STATISTICS and YEAR XXX STATISTICS report the total abundance and density and commercial abundance density and volume of trees in the initial and final years of the simulation The year value in the YEAR XXX STATISTICS heading will be the final year of simulation that 1s a simulation lasting 100 years will read YEAR
65. e adjustments by increasing or decreasing the Patch Area until you are satisfied with the size of your site on the model interface Step 5 Trouble Shooting If you require quick assistance press the button for a summary of the DATA UPLOAD features or refer to this manual See Error Messages Trouble Shooting section 9 4 below for a discussion of error messages you may encounter when uploading your data into the model 24 Free Landis amp Grogan Mahogany Growth amp Yield 9 4 Error Messages amp Trouble Shooting If an error occurs while uploading your data the model will stop the uploading process and present a message explaining the cause of the error The following is a list of potential error messages and possible solutions A Population must be selected You selected the blank population option Please select an actual population to simulate An Example Population must be selected You selected the Example Population heading Please select an actual example population to simulate A User Population must be selected You selected the User Population heading Please select an actual user population to simulate A File Name must be specified You selected a User Population but did not specify a user data file Please provide the name of the user data file or choose an example population File Name must be a txt file You selected the User Population xyd option which requires a user text file but the file sp
66. e results are not stored in memory or elegantly summarized for the user simulation end results can be permanently stored and easily reviewed by pressing the Export Results button The resulting file summarizes a given simulation by showing the model settings harvest parameters and initial population final population and harvest statistics simulation results must be saved as a text txt file These files can be named and placed anywhere on your computer It may be useful to name your file based on the simulated parameters for example Marajoara 60cm 20rr 5md 30yr 1 indicates the population simulated while cm rr md and yr indicate the simulated minimum diameter cutting limit retention rate minimum density and cutting cycle respectively and indicates the simulation number Results text files can be opened with Notepad on Windows and TextEdit on Mac OS X If you are missing either of these programs they come preinstalled on your computer free alternatives are available online For Windows users Another Notepad is a simple and free text editor http www pc shareware com anotepad htm For Mac users Plain Text Editor is also a simple and free text editor http www macupdate com app mac 8724 plain text editor 26 Free Landis amp Grogan Mahogany Growth amp Yield SIMULATION RESULTS the head of the Results file summarizes the model settings used in the completed simulation This section lists 1 the name of the field sit
67. ecified in File Name does not have a txt extension Please ensure the file 1s a text file and has the text file extension txt File Name must be a shp file You selected the User Population shp option which requires a user shapefile but the file specified in File Name does not have a shp extension Please ensure the file 1s a shapefile and has the shapefile extension shp A DIAM Attribute Name must be specified You selected the User Population shp option which requires a DIAM Attribute Name but the DIAM Attribute Name field is empty Please provide the name of the shapefile diameter attribute 1n this field File Name must be a csv file You selected the User Population csv option which requires a user csv file but the file specified in File Name does not have a csv extension Please ensure the file 1s a csv file and has the csv file extension csv Site Width must be a positive non zero number You provided a non zero negative or zero site width Please provide a positive site width measured in meters m Site Height must be a positive non zero number You provided a non zero negative or Zero site height Please provide a positive site height measured in meters m Patch Area must be a positive non zero number You provided a non zero negative or Zero patch area Please provide a positive patch area measured in meters m The site cannot be set up Please review the file formatting placement guide
68. elopment In southeast Para Jurandir Galvao was instrumental in setting up field studies and training field assistants for long term studies Mark Cochrane provided the original geospatial data that mapping studies were built upon In Acre nothing would have been possible without Frank Pantoja s unflagging commitment and determination In the field we thank Miguel Alves de Jesus Valdemir Ribeiro da Cruz Maria Nascimento Rodrigues Amildo Alves de Jesus Ruberval Rodrigues Vitorino Manoel Rodrigues Vitorino and Antonio Barbosa Lopes for their dedication re censusing trees and experiments Additional contributions in the field were made by Denis Valle Marcelo Galdino Simone Bauch and field assistants too numerous to list here Ted Gullison kindly provided supporting data from field sites in Bolivia 44 Free Landis amp Grogan Mahogany Growth amp Yield 16 REFERENCES amp SUGGESTED READING Electronic copies of journal references are available upon request to jgrogan crocker com or james grogan a yale edu Andr T Lemes MR Grogan J amp Gribel R 2008 Post logging loss of genetic diversity in a mahogany Swietenia macrophylla King population in Brazilian Amazonia Forest Ecology amp Management 255 340 345 Cornelius JP 2001 The effectiveness of pruning in mitigating Hypsipyla grandella attack on young mahogany Swietenia macrophylla King trees Forest Ecology and Management 148 287 289 Cornelius JP Navarro CM Wigh
69. ement practices The Big Leaf Mahogany Growth amp Yield Model presented here projects population recovery and timber production from simulated harvests of mahogany in the Brazilian Amazon The model offers forest managers a computer based tool for assessing the impact of current management practices on both pre installed example mahogany populations and on user entered populations The growth amp yield model uses the NetLogo 4 1 2 Wilensky 1999 platform and can be installed on computers using Windows or Mac OS X operating systems The growth amp yield model functions algorithms are derived from demographic data collected annually during 1995 2009 for nearly 600 mahogany trees and many thousands of seedlings saplings and poles at multiple field sites In southeast Par and Acre Model simulations can be run with or without harvesting Under logging scenarios the model harvests kills trees at specified intervals During intervals between harvests surviving individuals grow reproduce and die at rates observed in field studies Harvest simulations are based on current legal management practices 60 cm minimum diameter cutting limit 20 commercial sized tree retention rate minimum 5 commercial sized trees 100 ha retention density 30 year cutting cycle Forest managers can input mahogany population data from field inventories In order to project recovery and production outcomes following multiple harvests at legal management sites Harves
70. ents This design can be implemented with all four harvest parameters to simulate the outcomes of multiple harvest regimes Although it generates many runs and therefore requires a lot of processing time it collects the results In a single spreadsheet for quick analysis Adding New Reporters The built in experiments can also be personalized by adding new reporters or stop conditions to the experiment settings New reporters can be added from those listed in Command Line Code section 12 1 although reporters requiring bold italicized commands will not generate meaningful data since BehaviorSpace reporters are measured at the end of each run Copy and paste the Command Line reporters exclude show from the reporter into the BehaviorSpace reporter settings For example rather than pasting show median diameter of 39 Free Landis amp Grogan Mahogany Growth amp Yield trees with diameter lt 20 only paste median diameter of trees with diameter lt 20 These reporters will provide even more information when running the experiments Harvest List Reporters The annual harvest number and annual harvest volume reporters prints a list of harvest values in two columns as item item n2 item 45 item 4 where each item represents the harvest value for harvest number x If you prefer that each item receive its own column you must replace the annual harvest volume reporter for example with the following reporters item 0
71. ents Step 1 Define Model Parameters BehaviorSpace experiments will systematically vary the harvest parameters but you must define the other model settings before running an experiment Define Populations Logging and Time on the model interface according to the directions above section 6 2 If you intend to simulate one or more harvest regimes be sure that the Logging switch is turned on Step 2 Open BehaviorSpace Open the BehaviorSpace tool by selecting Tools gt BehaviorSpace in the NetLogo menu The BehaviorSpace window will open in the center of your screen aA BehaviorSpace Experiments Population Growth No Logging 100 runs Population Growth amp Productivity Standard Logging 100 runs Population Growth amp Productivity Diameter Experiment 600 runs Population Growth amp Productivity Retention Experiment 600 runs Population Growth amp Productivity Density Experiment 1500 runs Population Growth amp Productivity Cutting Cycle Experiment 400 runs Population Growth amp Productivity Custom Logging 100 runs New Edit Duplicate Delete New J Edit Duplicate Delete Seven built in experiments are listed in this window Resize the window to view the full experiment names by grabbing the triangle in the bottom right corner The function of each experiment is summarized below The buttons in the BehaviorSpace window behave as follows New creates a new BehaviorSpace
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73. f parameter values change the start increment and end values according to preference 30 Free Landis amp Grogan Mahogany Growth amp Yield Alternatively values to be tested can be listed using the following syntax harvest parameter value value value For example minimum diameter 50 55 60 75 80 would simulate the non incremental minimum diameters of 50 55 60 75 and 80 cm MAKE SURE YOU USE THE BRACKETS EXACTLY AS SPECIFIED The Repetitions field specifies the number of simulations performed for each harvest parameter value The Population Growth amp Productivity Diameter Experiment simulates six minimum diameter values 40 50 60 70 80 and 90 cm each 100 times for a total of 600 simulations Type a new number into the Repetitions field to increase or decrease the simulation sample size Experiment Reporters The Measure runs using these reporters field designates the reporters or measurements used to evaluate the simulated population The reporters for the Diameter Experiment are repeated in all other experiments except Population Growth No Logging which does not require harvest reporters as measures of population growth and harvest productivity count trees total tree abundance count trees with diameter gt 20 abundance of trees gt 20 cm diameter count trees with diameter gt minimum diameter abundance of commercial sized trees sum annual harvest number total number of logged trees sum
74. f values The model has um inis sliders for Time and LOGGING PARAMETERS Plot A Output Switch A switch allows a variable to be turned on off The Logging switch os turns the logging function on off before simulation Chooser A chooser allows a user to choose among variable values The Populations chooser allows the user to select between three example populations and three user defined population options Input An input box allows the user to type in a value for a variable There are two types of inputs number and text The Site Width Site Height and Patch Area input boxes accept number inputs The File Name and DIAM Attribute Name input boxes accept text inputs Monitor A monitor displays the value of a built in expression The Area Population and Harvest Productivity monitors report the area of the field site the density volume of trees in the initial and current populations and the number volume of trees logged during harvests Plot A plot provides a real time graph of model results The Diameter Distribution plot tracks the size distribution of the population and the Tree Abundance plot tracks tree abundance Output An output provides a text window on the model interface The Definitions output provides definitions of the interface features when the Help buttons are pressed Note A note provides text labels for each section of features MODEL SETTINGS LOGGING PARAMETERS YEAR 0 POPULATION etc are all pro
75. files These files should be viewed as templates when uploading your own data into the model framework You will also place your data files in this folder when uploading your own data section 9 The Results folder 1s the default destination for certain BehaviorSpace simulation results and a recommended destination for all other results exports The NetLogo folder contains the NetLogo 4 1 2 installers necessary for setting up the growth amp yield model on your computer This folder also contains the NetLogo 4 1 2 User Manual written by the NetLogo design team Step 4 Choose a NetLogo 4 1 2 Installer Double click on the NetLogo folder to view its contents If you are using a Windows computer double click the Windows folder and then double click the NetLogod4 I 2Installer exe installer file If you are using a Mac OS X computer double click the MAC OS X folder and then double click the NetLogo 4 1 2 dmg installer file The installer file will open when double clicked Follow the installation instructions to install NetLogo software on your computer If you would prefer to download the NetLogo software from the NetLogo website download NetLogo 4 1 2 here http ccl northwestern edu netlogo 4 1 2 DO NOT USE ANY OTHER VERSION OF NETLOGO THE MODEL ONLY WORKS IN NETLOGO 4 1 2 Refer to the NetLogo User Manual if you require additional assistance Step 5 Open Model NetLogo File If you have successfully installed the NetLogo 4 1 2
76. following e0 0 467 el 0 247 e2 0 111 e3 o 1 where o N 0 0 48 The residuals are recalculated each time step because as a year passes the residual of the previous year becomes the residual of two years before The residuals are therefore recalculated as e3 e2 e2 el el e0 and e0 the value of the above equation calculated with the new residual values The growth rate or diameter increment of each tree 1s then calculated using the following equation growth rate cm yr 0 36 diameter 0 011 0 0127 max 0 diameter 30 e0 2 where the max 0 diameter 30 evaluates to zero when a tree is lt 30 cm diameter and evaluates to diameter 30 when a tree is gt 30 cm diameter The resulting diameter increment is added to the current diameter to calculate the new tree diameter A diameter increment lt 0 1s reclassed as 0 given the impossibility of negative growth 53 Free Landis amp Grogan Mahogany Growth amp Yield Logging Function The logging function removes eligible trees from the population at the beginning of the simulation and during the subsequent harvest years as determined by the cutting cycle parameter The function removes the maximum possible number of trees larger than minimum commercial size without violating either the retention rate or post harvest density requirements Half of logged trees are allowed to disperse seeds prior to death and all logged trees
77. ge file The export plot and export all plots commands export either a specific plot or all plots to an external csv file The export world command exports the values of all variables both built in and user defined including all observer turtle and patch variables and the plot contents The commands for exporting each feature are listed below export view word Results view date and time jpg export plot Tree Abundance word Results Tree Abundance date and time csv export all plots word Results plots date and time csv export world word Results world date and time csv The exported files are all written to the Model gt Results folder Each file type 1s saved with a common identifier 1 e view plots world but the date and time extension varies between runs in order to prevent file overwriting The view image can be saved with any image extension jpg png bmp tif etc but the plots and world files must be saved with the csv extension Step 5 Run BehaviorSpace Experiment Run the chosen experiment by selecting the experiment in the BehaviorSpace window and pressing the Run button The Run Options window shown on the next page will open in the center of your screen Check the Table output option and leave the Spreadsheet output option unchecked Enter 2 into the Simultaneous runs in parallel field The Table output option creates a more analysis friendly output and the
78. growth rate of tree 17 show median growth rate of trees show diameter of trees with max growth rate show who of trees with max growth rate show who of trees with min basal area show who of trees with dbh gt median dbh of trees show length cur logged volume Last Harvest Total Logged Volume m show sum cur logged volume Last Harvest Largest Logged Tree Volume m show max cur logged volume All Harvests Number of Logged Trees show length tot logged volume All Harvests Total Logged Volume m show sum tot logged volume All Harvests Largest Logged Tree Volume m show max tot logged volume Number of Trees Logged in Harvest Number X show item X 1 annual harvest number Volume of Trees Logged in Harvest Number X show item X 1 annual harvest volume tot logged volume a list of the volum es of trees logged during all previous harvests cur logged volume a list of the volumes of trees logged during the most recent harvests annual harvest number a list of the number of trees logged during each harvest year annual harvest volume a list of the volume of trees logged during each harvest year Mortality Statistics Kill trees Specific Tree Mortality Probability show mort rate of tree 17 Median Tree Mortality Probability show median mort rate of trees Live Tree Mortality Probabilities show mort rate of trees with alive true Dead Tree Abundance show count trees with alive
79. hanges in tree size class distribution and abundance over time These plots are updated each year according to simulation results The Diameter Distribution plot shows the initial size class distribution in black and the current year size class distribution in red The vertical gray line divides non commercial and commercial trees The Tree Abundance plot shows the abundance of all trees gt 20 cm diameter in black and the abundance of commercial sized trees in red The vertical gray lines indicate the harvest years that 1s 31 61 and 91 years in the example shown Harvest Productivity monitors report the volume of trees logged in the most recent harvest as well as the number and volume of trees logged in all previous harvests Monitors are updated after each logging event Logged Volume reports the volume m of trees logged in the most recent harvest Total Logged Volume reports the volume m of trees logged in all previous harvests Total Logged Trees reports the number of trees logged in all previous harvests Step 7 Export Simulation Results E Export the simulation results to a text txt file on your computer Export Results Results describe initial and final populations and harvest productivity 13 Free Landis amp Grogan Mahogany Growth amp Yield 6 MODEL SETTINGS The MODEL SETTINGS parameters determine 1 which population is simulated during model runs 2 whether logging is performed and 3 how long the simulation
80. hematic 1 2 3 10 11 12 Model Introduction Manual Guide Model Installation 3 1 CD Installation 3 2 Web Installation 3 3 Online Model Help Buttons A Brief Guide Model Settings 6 1 Setup amp Resize Initial Population 6 2 Setup amp Run Simulations Logging Parameters Simulation Results 8 1 Population Monitors 8 2 Population Plots 8 3 Harvest Productivity Monitors User Data Upload 9 1 Spatial Diameter Data User Spreadsheet 9 2 Spatial Diameter Data User Shapefile 9 3 Non Spatial Diameter Data User Spreadsheet 9 4 Error Messages amp Trouble Shooting 9 5 User Data Upload Examples Export Simulation Results Simulation Experiments BehaviorSpace Advanced Users amp NetLogo Resources 12 1 Command Line Code 12 2 Modifying BehaviorSpace Experiments 12 3 Model Procedure Code 12 4 NetLogo Resources Limitations amp Considerations Future Modifications Acknowledgements References amp Suggested Reading Contact Us Appendix A Data Sources Appendix B Model Details amp Definitions Appendix C Model Functions Appendix D Model Code Free Landis amp Grogan Mahogany Growth amp Yield 1 MODEL INTRODUCTION In recent decades big leaf mahogany Swietenia macrophylla has been intensively harvested across its natural range In tropical South America Future timber production from natural forests will depend on protection and stewardship of surviving commercial populations through sustainable manag
81. iew updates yields faster model runs Settings Determines the size shape and resolution of the landscape and sets the time unit MODEL CONTROLS MODEL CONTROLS Setup Establishes initial population on landscape Defaults Resets harvest and other parameters to default conditions Populations Lists selection of example and user defined initial populations Site Area Area of selected site in hectares ha Logging Determines whether logging is on off during the simulation s Time Number of years the model will simulate Run 1 Year Runs the model for one year Run X Years Runs the model until time limit or all trees are harvested or die Help button returns definitions for a given model section LOGGING PARAMETERS Minimum Diameter The minimum diameter of commercial trees cm Retention Rate The retention rate of commercial sized trees 90 Minimum Density The minimum post harvest density of commercial size trees trees 100 ha Cutting Cycle The number of years between harvests 50 Free Landis amp Grogan Mahogany Growth amp Yield YEAR 0 CURRENT POPULATION Total Density Commercial Density Commercial Volume Diameter Distribution Tree Abundance The density of trees gt 20 cm diameter in the field site trees 100 ha The density of commercial sized trees in the field site trees 100 ha The volume of timber in the commercial population m Bar columns 10 cm diam increments gray line commer
82. ime where the Behavior axis describes each metric The metrics are color coded according to the legend on the right The output window below the graph tracks the experiment progress The window reports the number of completed runs and the number of completed steps where each step represents a year The total elapsed time is also reported The experiments take some time to run so please be patient The pace of the experiment can be accelerated by sliding the blue circle to the right from normal speed to faster speed Turning off the visuals will also reduce processing time uncheck Update view and Update plots and monitors to further accelerate the experiment run time Pressing Abort will end the BehaviorSpace experiment It is not possible to resume an aborted experiment To continue a BehaviorSpace experiment after pressing Abort you will need to start again from the beginning 33 Free Landis amp Grogan Mahogany Growth amp Yield Step 7 Format Data Output The Running Experiment window will close when the experiment 1s completed returning the BehaviorSpace window to the center of the screen Close the window and browse to the experiment results file The head of the experiment results file should look like this gt A B E D 1 BehaviorSpace results NetLogo 4 1 1 2 Jimmy Model 3 1 nlogo 3 Population Growth amp Productivity Standard Logging 4 12 26 2010 09 25 53 079 0500 5 min pxcor max pxcor min pycor max pycor 6 6
83. interfere with the present upload Type the width X in meters of your site into the Site Width input box and the height Y in meters of your site into the Site Height input box If your site 1s not rectangular estimate the width and height of the smallest bounding rectangle examples shown below Again the width and height of your site must be in meters m Width p 20 Height Free Landis amp Grogan Mahogany Growth amp Yield Type the value 1 00 into the Patch Area input box Patch Area determines the size of landscape patches in pixels and therefore determines the size of the landscape A Patch Area of 1 00 1s purposefully small and should draw a landscape contained by the available space on the model interface Step 4 Resize Site Drawing After File Name Site Width Site Height and Patch Area have been specified press the Setup button under MODEL SETTINGS to draw your site on the model interface If the site dimensions are incorrect ensure that the file 1s formatted correctly columns X coordinate Y coordinate diameter If you receive an error message refer to Error Messages Trouble Shooting section 9 4 below The site should be drawn using a Patch Area of 1 00 pixel but a larger or smaller Patch Area may be preferred depending on the dimensions of your site If the site is drawn too small for the available space increase the Patch Area by entering 2 00 and press the Resize button If the site is draw
84. ions In Harvest List Reporters of BehaviorSpace Experiments section 12 2 to report the harvest list values in individual columns as opposed to single column list Label these new columns accordingly The analysis of the experiment data should be performed according to your familiarity with statistics A thorough review of statistical analysis 1s beyond the scope of this User Manual however simple statistics such as average and standard deviation should suffice most of the time For example a comparison of the average final commercial density to the initial commercial density is a simple but powerful statistical method similarly calculating the average logged volume from each harvest year provides a simple but powerful summary of harvest productivity over time under different harvest regimes A standard deviation of these averages would provide an estimate of confidence The BehaviorSpace experiments provide a large sample size and these simple statistics can convey much information about population growth and harvest productivity 12 ADVANCED USERS amp NETLOGO RESOURCES 12 1 Command Line Code The following section provides an introduction to using the Command Center to query the landscape for information not displayed In the population monitors or plots or harvest monitors Commands are entered in the command line window the small window labeled observer shown on the next page The results of the commands are printed in the large
85. is RM amp Vidal E 2008 How rare is too rare to harvest Management challenges posed by low density timber species in the Brazilian Amazon Forest Ecology and Management 256 1443 1457 Schulze M Vidal E Grogan J Zweede J amp Zarin D 2005 Madeiras nobres em perigo pr ticas e leis atuais de manejo florestal n o garantem a explora o sustent vel Ci ncia Hoje 214 66 69 Snook LK C mara Cabrales L amp Kelty MJ 2005 Six years of fruit production by mahogany trees Swietenia macrophylla King patterns of variation and implications for sustainability Forest Ecology and Management 206 221 235 Snook LK amp Negreros Castillo P 2004 Regenerating mahogany Swietenia macrophylla King on clearings in Mexico s Maya forest the effects of clearing method and cleaning on seedling survival and growth Forest Ecology and Management 189 143 160 Thiele JC amp Grimm V in press NetLogo meets R Linking agent based models with a toolbox for their analysis Environmental Modelling and Software Verwer C Pefia Claros M van der Staak D Ohlson Kiehn K amp Sterck FJ 2008 Silviculture enhances the recovery of overexploited mahogany Swietenia macrophylla Journal of Applied Ecology 45 1770 1779 Wilensky U 1999 NetLogo http ccl northwestern edu netlogo Center for Connected Learning and Computer Based Modeling Northwestern University Evanston IL USA 17 CONTACT US If you have questions about the model please em
86. is run The MODEL SETTINGS buttons set up the initial population re set parameters to default conditions and begin model simulations The area in hectares or ha of the field site 1s also MODEL SETTINGS displayed in this section S D Site Area ha Setup Defaults SE Par 204ha y 212 8 1 R Run 1 Year Run X Years ey 6 1 Setup amp Resize Initial Population The Setup button establishes the initial population on the model landscape shown across the center of the model interface The population displayed on the landscape is selected from the Populations menu which lists three pre defined example populations and three user defined population upload options The example populations are based on mahogany population and spatial data from study sites in southeast Par and Acre The user populations represent the three methods for uploading user data into the model The six population options are summarized below User populations are discussed in greater depth in USER DATA UPLOAD section 9 EXAMPLE POPULATIONS SE Par 204 ha 204 ha field site with 143 trees SE Par 1035 ha 1035 ha field site with 745 trees Acre West Amazon 685 ha field site with 81 trees SE Par 204 ha and SE Par 1035 ha present spatial and diameter data for mahogany populations in southeast Par Brazil The forest management and long term research site called Marajoara is located 34 km northwest of Reden o
87. lines You most likely received this error because the data file is formatted incorrectly or is not located in the Model gt User folder The data file should be placed in the User folder and should not have 25 Free Landis amp Grogan Mahogany Growth amp Yield any headers commas spaces or other symbols Review this manual to ensure proper formatting 9 5 User Data Upload Examples There are example user files in the Model gt User folder to help illustrate the user data upload process The folder contains the files necessary to set up the SE Par 204ha population using each of the three user data upload methodologies The files and inputs required for each methodology are listed below If you have any questions about formatting look to these files as templates If you have questions about the inputs look to the information below and the DATA UPLOAD figures presented above sections 9 1 9 2 amp 9 3 Data DIAM Site Site Patch Upload Type File Name Attribute Name Width Height Area Spatial TXT File mara 204 tree data txt 1216 1 1712 4 1 0 Spatial SHP File mara 204 tree data shp DIAM2004 1216 1 1712 4 1 0 2 i dd mara 204 tree data csv 1216 1 17124 1 0 The dbf file 1s associated with this shapefile and 1s necessary for data upload using this method 10 EXPORT SIMULATION RESULTS Export Results i The monitors plots and landscape features provide a means for observing simulation results in real time but thes
88. n too large for the available space decrease the Patch Area by entering 0 50 and press the Resize button Continue to make adjustments by increasing or decreasing the Patch Area until you are satisfied with the size of your site projected onto the model interface Step 5 Trouble Shooting If you require quick assistance press the button for a summary of the DATA UPLOAD features or refer to this manual See Error Messages Trouble Shooting section 9 4 below for a discussion of error messages you may encounter when uploading your data into the model 9 2 Spatial Diameter Data User Shapefile This section describes the procedures necessary to upload your data from a GIS shapefile A shapefile 1s a file type produced by GIS software to store location and attribute data This user data upload feature will not support any other geospatial file format Step 1 Place Shapefile in User Folder Place the shapefile containing spatial diameter data of your tree population in the Model gt User folder Place the dbf file dbf associated with the shapefile here as well the prj sbn sbx shx and xml files are not necessary Remember the name of the overarching shapefile shp Step 2 NetLogo File Parameters Parameters in the DATA UPLOAD portion of the model interface specify the name of the user data file the name of the diameter attribute the dimensions of the field site and the resolution of the landscape shown on the next page T
89. nd diameter increment of trees marked as reproductive all non seedling trees and 50 of dead trees using the following equation log odds fruiting 6 13 diameter 0 1177 0 1079 max 0 diameter 50 T growth rate 2 796 2 957 max 0 growth rate 0 75 which 1s subsequently used to calculate the fruiting probability using the logit transformation fruiting probability exp log odds 1 exp log odds 8 If fruiting occurs fruit production is estimated as a function of current year stem diameter and diameter increment in a generalized linear model with a gamma error term The gamma distribution function is parameterized with the scale and shape factors alpha a and lambda A The a value is a constant 1 22 while the A value is calculated as a function of the mean number of fruit and the variance of this mean The mean number of fruit and variance of the mean for a tree of any given diameter are calculated as follows mean fruit exp 0 2933 0 03153552 diameter 9 0 00025 diameter 2 1 514 10 6 diameter 3 variance fruit 0 822 mean fruit 2 10 These values are subsequently used in the calculation of A which in conjunction with a is used to calculate the gamma distribution describing the distribution of fruit production values for a single tree These two equations are as follows lambda 1 variance fruit mean fruit 11 number of fruit produced
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91. ogo landscape The landscape is contained within a box where each cell represents a 10 m x 10 m 100 m patch on the landscape disturbances and seeds dispersed over a landscape edge are not returned to the other side Because the model is spatial the arrangement of trees on the landscape is significant in determining simulation outcomes At each time step one year the following demographic parameters are estimated for each tree based on regression equations derived from field census data 1 diameter increment cm yr 2 mortality probability 3 probability of fruit production and 4 number of fruit produced The model simulates logging growth mortality disturbance and reproduction each year with these parameters until the time limit is exceeded or all trees are harvested or die Growth Function The growth function incorporates growth autocorrelation the tendency of fast growing trees to remain fast growing in order to account for past growth history Diameter increment is estimated as a function of stem diameter using generalized least squares to incorporate an autoregressive error term accounting for growth autocorrelation over the preceding three years The trees begin the simulation with no growth history so three residuals e 1 year previous e2 2 years previous and e3 3 years previous are assigned an identical random number drawn from the distribution N 0 0 48 The present year residual e0 is calculated as the
92. on variation at microsatellite loci implications for conservation Molecular Ecology 12 2875 2883 Lopes JCA Jennings SB amp Matni NM 2008 Planting mahogany in canopy gaps created by commercial harvesting Forest Ecology and Management 255 300 307 Mayhew JE amp Newton AC 1998 The Silviculture of Mahogany CABI Publishing New York NY USA 46 Free Landis amp Grogan Mahogany Growth amp Yield Negreros Castillo P Snook LK amp Mize CW 2003 Regenerating mahogany Swietenia macrophylla from seed in Quintana Roo Mexico the effects of sowing method and clearing treatment Forest Ecology and Management 183 351 362 Norghauer JM Nock C amp Grogan J in review The importance of tree size and fecundity for seed dispersal of a threatened Neotropical timber tree big leaf mahogany Swietenia macrophylla PLoS ONE Biology Norghauer JM Malcolm JR amp Zimmerman BL 2008 Canopy cover mediates interactions between a specialist caterpillar and seedlings of a neotropical tree Journal of Ecology 96 103 113 Norghauer JM Grogan J Malcolm JR amp Felfili JM 2010 Long distance seed dispersal helps big leaf mahogany seedlings escape defoliation by a specialist caterpillar Oecologia 162 405 412 Schulze M 2008 Technical and financial analysis of enrichment planting in logging gaps as a potential component of forest management in eastern Amazonia Forest Ecology and Management 255 866 879 Schulze M Grogan J Land
93. ormation into the model Create a spreadsheet to organize the data into a single column tree diameter cm DO NOT GIVE THE COLUMN A HEADER The head of your file should look like this Diameters v A B 71 3 79 4 66 1 80 4 45 5 64 7 72 5 79 At 0 Trees Do qon awl Diameters must be measured In centimeters cm Tree diameter measurements should be taken at 1 3 m above the forest floor or at least 30 cm above the reach of the tallest buttress Step 2 Save As CSV File The modal software cannot read data from Excel xls or similar files so the data must be saved as a comma separated value csv file Choose File gt Save As and select CSV comma delimited from the Save As options INCLUDE THE CSV EXTENSION IN THE FILE NAME Place the new csv file in the Model gt User folder Remember the name of the csv file Step 3 NetLogo File Parameters The final steps towards uploading your data into the model are completed in the DATA UPLOAD portion of the model interface These parameters specify the name of the user data file the dimensions of the user field site and the resolution of the resulting landscape Type the name of the csv file from Step 2 containing diameter data located In the User folder into the File Name input box Be sure to include the csv file extension when typing the name 23 Free Landis amp Grogan Mahogany Growth amp Yield DATA UPLOAD mara 204 tree data csv 204 tre
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95. parameters because it 1s designed to monitor populations under current legal management practices for mahogany a0 Experiment Experiment name Population Growth amp Productivity Diameter Experiment Vary variables as follows note brackets and quotation marks Logging true minimum diameter 40 10 90 Either list values to use for example l my slider 12 7 8 or specify start increment and end for example my slider 0 1 10 note additional brackets to go from 0 1 at a time to 10 You may also vary max pxcor min pxcor max pycor min pycor random seed Repetitions 100 run each combination this many times Measure runs using these reporters count trees with diameter gt 20 count trees with diameter gt minimum diameter sum annual harvest number Y one reporter per line you may not split a reporter across multiple lines __ Measure runs at every step ifunchecked runs are measured only when they are over Setup commands Go commands setup run model Stop condition Final commands the run stops if this reporter becomes true run at the end of each run stop after this many steps 0 no limit Cancel C OK The other four Population Growth amp Productivity experiments Diameter Retention Density Cutting Cycle vary each harvest parameter according to the syntax described above harvest parameter start increment end To examine a different range or resolution o
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97. r output window labeled Command Center 35 Free Landis amp Grogan Mahogany Growth amp Yield Command Center W Clear observer show count trees observer 143 observer show count trees with diameter gt 60 observer 8 observer show sum volume of trees with diameter gt 69 v Copy and paste any of the italicized commands listed below into the command line window Press Return Enter to run the command ALWAYS LEAVE THE COMMAND LINE IN OBSERVER MODE DO NOT SUBMIT COMMANDS IN TURTLES PATCHES OR LINKS MODES You can access previous commands using the history popup menu the small downward pointing triangle to the right of the command line window Press the triangle to see a menu of previously entered commands Alternatively you can access previous commands with the UP and DOWN keys on the computer keyboard as long as the cursor is in the command line window Pressing the Clear button in the upper right corner of the Command Center window will erase the contents of the output window Additionally the Command Center can be resized by grabbing and moving the gray bar at the top of the Command Center window The following is a list of commands that may be useful to your analysis For sections with bold italicized commands 1 e grow trees kill trees log trees etc you must enter the bold italicized command before entering the other commands The commands can be modified using the statements at the bottom of the s
98. ramming complications BehaviorSpace experiments and Command Line queries can only be accommodated by installing and running NetLogo on your computer The online applet only runs the features maintained on the model interface It does not support any NetLogo features occurring outside this interface The interface landscape can be resized in the online version of the model but this feature is more difficult to manipulate online than on your computer The online model will not resize the landscape to a new Patch Area if the blinking mouse cursor is still in the Patch Area input Click anywhere within the online interface to remove the blinking mouse cursor from the input clicking in another input is an effective strategy and click Resize to resize the model landscape These issues will be resolved if possible Please sign up to receive updates on the model and our research on our website http www swietking org Java Versions The Big Leaf Mahogany Growth amp Yield Model applet requires that your web browser support Java 5 or higher The correct version of Java can be obtained following these directions e Windows users Vista XP or 2000 can download the Java browser plug in from here http www java com en download windows_manual jsp Mac OS X users require version 10 4 or higher No plug in is necessary Linux and Unix system users need the Sun Java Runtime Environment Version 5 or higher This is available for download here http
99. re dbh or diameter at breast height 1 3 m 1s calculated from diameter as follows dbh cm diameter 0 2842709 1 1003362 6 The radius of the disturbance area is calculated using the equation for the area of a circle a nr The zone of recruitment that is the area of the disturbance available for seedling recruitment 1s estimated to be 10 m shorter 1n radius than the radius of the disturbance area The resulting disturbance and zone of recruitment areas are constructed on the landscape using the tree as the center of the each circular area 54 Free Landis amp Grogan Mahogany Growth amp Yield Disturbance Function Canopy disturbances and the associated zones of recruitment are added to the landscape until 0 026 of the landscape is disturbed including disturbances from fallen trees Disturbance sizes are drawn from a gamma distribution fit to an observed size distribution of gap forming canopy disturbances n 87 shape 0 6127 scale 0 0056 The radius of the zone of recruitment is 10 m less than the radius of the disturbance therefore a disturbance with a radius gt 10 m is necessary to for recruitment The zones of recruitment represent the only viable areas for recruitment on the landscape as recruitment does not occur in the forest understory or on the outer edge of canopy disturbances Reproduction Function Fruiting probability is estimated as a binary logistic regression of the current year stem diameter a
100. rea and press the Resize button Continue to make adjustments by increasing or decreasing the Patch Area until you are satisfied with the size of your site on the interface See section 9 1 Step 4 for more details 6 2 Setup amp Run Simulations The Logging and Time parameters determine how the model will simulate the initial population The Logging switch determines whether the population is simulated with or without logging select On to run simulations with logging Select Off to run simulations without logging The Time slider determines how long the simulation will run The model will simulate the growth and harvest of the initial population until the time limit is reached or until all trees are harvested or die whichever happens first Population growth and harvests can be simulated up to 150 years Changes to the simulation length can be made in 5 year increments The Run 1 Year button runs the model for a single year The Run X Years button runs the model until the time limit 1s reached or until all trees are harvested or die whichever happens first The Defaults button returns all variables to default conditions Populations SE Par 1 204 ha Logging On Patch Area 2 75 pixels Time 100 years 7 LOGGING PARAMETERS The default harvest parameters are set according to the current Brazilian forest management regulations for mahogany These regulations mandate a minimum diameter cutting limit of gt 60 cm the retention of gt 2
101. roductivity of the initial population under these guidelines Step 4 Examine amp Modify a BehaviorSpace Experiment Select the chosen baseline experiment in the BehaviorSpace window by pressing the name of the experiment The name should now be highlighted in blue Press Edit to edit the details of the experiment The Experiment window shown on the next page will open in the center of your screen Resize the window as needed by grabbing the triangle in the bottom right corner The window displayed on the next page describes the Population Growth amp Productivity Diameter Experiment as listed in the Experiment name field at the top of the window Experiment Variables The second field lists the variables to be examined during the BehaviorSpace simulation In this experiment logging is turned permanently on logging true and the minimum diameter is varied from 40 cm to 90 cm by increments of 10 cm 1 e 40 50 60 70 80 90 cm All other harvest parameters and model settings will remain constant based on the current interface settings The variables section has a similar structure In each experiment Population Growth No Logging is the only experiment with logging turned off because it 1s designed to monitor populations under natural conditions Population Growth amp Productivity Standard Logging 29 Free Landis amp Grogan Mahogany Growth amp Yield unlike the other experiments permanently sets the four harvest
102. ru oua s qerTnoTeo 4astT A uru uru A 3er Oon A 9ejeurpdgooo x unurxeu y sea3einoieo 34ST X Xeu Xe Ux JOT On A qeurpaooo x UnurUuru oua s qeTnoTeo AST T X uru urux JOT 9 TjJ ayy sesor o 9SO D 9TI3 1STI U IDp ua UT s nTe A do3ouelrp ou3 sang 4sTl uerp pe xa TT1jJ a3ndj asrT uerp jos 1STT ua ur s qaeurp4aooo ou3 sang 4sTT A peedg e rj a3nd3j 4 STT as uerp A 4x 3eudo ur rqea eq asnu TTJ AST X ua UT s qaeurpaooo x y sang 3asrr x peedg oe rj a3ndj 4 STT X eas pue y oq Buruurb q y uo4gj eTTF eua speoy gpue je eTTF you erru qgduoid SWYN STIIA uq ur desn oua Aq peaeubrsop TTJ y suedo eueN e r4 7ESN pao 4 usedo aeTTI OTTF desn y worAF sago4euerp oua Hutz0j4s 403 3STI Sexew 3STT 3STT wetp T OTTj AZaesn ou3 worF sejeurpdooo ayy Hutz04s AOF STI e Sexew 3STT 4STT T OTTFJ Aasn y worAF sejeurpdiooo x y Hutz04Ss AOF ASTT e Sexew 4STT 3STI X 3er NOILWINdOd GAX NHS0 AdWOSANWI NO SHAUL SLES soo0i13 pAx dnyes 0 pue Son eA oo2d34 dn4jes J NVIG enieA A4a2edoud srb zajoewetp yes SO Q TJ289A 997 burureuod oua dn s3es our 3xou oup s1Ii qa uerp peaeroosse oua seer eua subrsse pue s qeurpaooo p asrr ua FO uoee qe ooJ4343 e SAazeAeTD pue e rrjedeus SID eua jo MOT uose spear opoo STYL w em em em w w w w w uorqaeooT I u qrt 100 uorqaeooT 0 u qr 102 A yes X q
103. s International Programs USAID Brazil the Charles A and Anne Morrow Lindbergh Foundation and the International Tropical Timber Organization s Fellowship Programme In Acre additional funding support was provided by the Brazilian Ministry of the Environment MMA and WWE Brazil In southeast Par generous logistical support has been provided by the Marajoara field site owners Sr Claudiomar Vicente Kehrnvald current and Sr Honorato Babinski previous Serraria Marajoara Ltda To both we extend our sincere thanks and gratitude Additional logistical support in this region was provided by Peracchi Ltda and Conservation International Brazil In Acre logistical support was provided by the State Government of Acre s Secretariat for Forestry amp Extractivism SEFE the Technology Foundation for the State of Acre FUNTAC and the forest products companies Acre Brasil Verde and Laminados Triunfo Ltda We thank the Brazilian Ministry of Science and Technology CNPq for permission to conduct fieldwork and the Instituto do Homem e Meio Ambiente da Amazonia IMAZON for providing institutional affiliation and collegial support especially Edson Vidal Paulo Barreto and Adalberto Verissimo We thank Marco Lentini and Johan Zweede at the Instituto Floresta Tropical IFT for institutional support and expertise and Mark Schulze for keeping field studies on course At Yale University Mark Ashton and F Herbert Bormann guided this program s dev
104. s with diameter gt 69 vii The Command Center allows commands to be issued directly without adding them to the model s procedures This is useful for extracting more specific information about the population than default outputs provide 51 Free Landis amp Grogan Mahogany Growth amp Yield observer This pop up menu specifies the Command Center mode It can be changed to turtles patches or links modes but should be left in observer mode Y Click on the History triangle to browse and select from previously typed commands W This button switches the Command Center window between vertical window and horizontal views Other resizing options include Drag the gray bar separating the window from the interface to a new position Or press the small gray arrows above the Clear button to hide the window or make it very large Clear Press this button to clear the contents of the Command Center window To clear the History pop up menu choose Clear History 1n the menu options 22 Free Landis amp Grogan Mahogany Growth amp Yield APPENDIX C MODEL FUNCTIONS This section provides an in depth review of how the model functions APPENDIX D MODEL CODE provides a similar review alongside the actual model code The fully annotated model code is also available in the Procedures tab of the NetLogo interface Initial Population The model begins with an initial population selected by the user and represented on the NetL
105. software on your computer you are ready to open the Growth amp Yield Model file Double click the Growth amp Yield Model file to begin using the growth amp yield model on your computer If you use Mac OS X a blank NetLogo file may open instead of the Growth amp Yield Model file This is a known Mac OS X NetLogo bug and may commonly occur on your computer It is easily resolved simply leave the blank NetLogo file open and double click the Growth amp Yield Model file again This will always open the Growth amp Yield Model file correctly 3 3 Online Model The online version of the Big Leaf Mahogany Growth amp Yield model can be accessed from the following website http www swietking org The online model is identical to the computer model except that it cannot 1 upload user data files 2 export simulation results 3 run BehaviorSpace experiments 4 accommodate Command Line queries and 5 resize the model landscape elegantly Free Landis amp Grogan Mahogany Growth amp Yield The online version of the model cannot upload user data or export simulations because of the limitations of our web server Additionally the online version of the model cannot display the stream and boundary data exhibited 1n the computer model because the NetLogo GIS extension is currently incompatible with the online applets Finally the online version of the model only simulates the SE Par 204 ha population because of unidentified prog
106. sy yo ued Fo z20ooxd xa3es dnjes edge son eA eo43434 burureued oup a3sr uerp pees y uozj seuoa3ed A 4opeuspees unu spees unu 41ooT j seezg34 4nodds 1z qa uerp e poubrsse pue yo zed y ut peoerid quopueza pa ynorzds za qau zed jo spees Aduns spees unu T o1e s ur uoa3ed 30ds34eeAs Mopeus p s uoeo OF MOPeYS p s y ur snrpea pees sntperz ut 2g 30dsje0ms ua3r soyojed yse souoqed jo zequnu y spees HuTATAANS Jo AZSequnu y sesAedstp JI9S eo4143 4uezuged q T pue Aopeus p s sqar ur s uoqed 4340ds4eeAs OY S TJTJU PT 99424 Yor snrpeaq pees snripedg ur s uoqed qunoo seuoaed A 4opeuspees unu T ounpeoo4gd sty op o4 pexse ode spoes burArAd4nS YTM Sood3 ATUO 0 lt spees Azauns ua r seer xse SdguS HSuHdsIG spees esiedsrip 0 en er GO OA OA OO OD w em O OR OR OR OD pue qoad aans y sSpoes unu 4100Tj Spees Auns yes 4rnagj ded spoes y 31ndgg unu spees unu T 3Tnagj unu xeu 3rngj unu 3es qarnajg unu xeu lt 31rn4ggj unu jr epque eud e ewweb wopuez j3rn4ggj unu jos 31Tnag ueeu 341indgg eouergeA T epquet 3 T Z 31na4gg ueeu y zz8 0 4AINAF OOUeTACA YOST zz8 0 T eudqze 3er g z q uerp x 9 OT vIS TI z 283eueTp x GzZ000 0 aea3euerp x ZSSESTIEO 0 62 0 qarnajg ue u T 4rnaggj unu oT O oqa Spees burATrAJns jo Zaequnu 72404 9u3 395 0 Ayt Ttqegqozd eArAudns bur pees pees oua Aq peonpedg st Aequnu styL peonpoud
107. t deageuerp YATM seed43 qunoo uorsrioedd Sseezu3 0 LOZ lt z qa uerp YATM seezg4 aunoo S89TLSTDEVIPS X T eun qoA uuoo 0o uorsroeud T A3Tsuep uuoo 0oA uorsrioeaud OOT e re qts x Aarsuep uuoo 0 A 20017 eu 00T Ss zqa T Aarsuep 303 04 uorsroead 00T eedae ears x a3rsuep 303 04A 20013 gu I lt Sxor3 pue enz3 burbb5oT jr S IL pebboT Fo umTOA PIM S IL pebboT jo zequnn puo S S AILH FO Aequnn PIs uSOILSILVLS LSZHAHNVH qUTId eTTF qUuTId eTTF quTId eTTF qUuTId eTTF quUTId eTTF ena3 9UnT TOA Teroz1 uuoo PIOM TSU QA TetorAewuUoD pz0M 90uepunqyv IOJeUUO PIOA TSU A 301L PIOM oouepunqv TeIOL PIOM sxor3 a YEA p3o 9UnT OA I IOZdeUuuOo puoA TSU QA IOJOeUUO puoA 9o0uepunqyv IOJeUUO PIOA TSU A 9 301L PIOM oouepunqv TeIOL PIOM uSOILSILVLS O HVHA burbb5oT jr 3ur3d e 13 3ur4dd eT r3 3ur3d eT13 3ur4dd eT r3 3ur43d eT13 3ur4dd eT r3 qUTId eTTF qUTId eT TF 3ur4dd eT r3 3ur43d e T13 3ur4dd eT r3 3ur4dd eT r3 3ur4dd eT r3 3ur13d e 13 NOILVIQNIS SIHL ONIYNG GQ4550 I dgWUIM SHAUL ON NO QAANANL LON SWM NOITDLONNA NI OT HHL eu OOT Seer TeTOASWUIOS See243 rerodeuuoo g szxeoA roAo buraano A 3TSsuep unururu aez uorqu q 41 uo z q uerp umururu sz To Oo bur33n5 PIM AKarsu
108. t parameters can be changed to view population and timber production outcomes under alternative management scenarios by adjusting one or more of the four management practices The model interface allows harvest simulations to be set up and run by clicking on a series of buttons as explained in the sections to follow For a given starting population and harvest scenario each run will yield a different outcome number of trees and commercial volume harvested surviving density etc This occurs because the model functions for survival growth and reproduction are recalculated each time step using a random error term leading to different long term outcomes For this reason average outcomes from multiple simulations will best represent long term population recovery and production rates for a given population and harvest scenario During each time step year of model simulation the following actions occur on the model interface 1 the time display advances 1 year 2 trees grow In size on the landscape trees are sized according to diameter 3 trees are logged and removed from the landscape at specified harvest intervals 4 trees die and are removed from the landscape 5 the landscape experiences disturbance red circles disturbance dark red zone of recruitment 6 trees reproduce and new seedlings are added to the landscape and 7 disturbances are removed from the landscape and the plots and monitors are updated Free Landis
109. that you copy the files from the CD onto your computer Copy the Models folder and paste it anywhere on your computer Double click the Growth amp Yield Model file to begin using the growth amp yield model on your computer If you use Mac OS X a blank NetLogo file may open instead of the Growth amp Yield Model file This is a known Mac OS X NetLogo bug and may commonly occur on your computer It is Free Landis amp Grogan Mahogany Growth amp Yield easily resolved simply leave the blank NetLogo file open and double click the Growth amp Yield Model file again This will always open the Growth amp Yield Model file correctly 3 2 Web Installation The following section explains how to install the NetLogo software from the Big Leaf Mahogany Growth amp Yield Model website and how to run the model using the software Step 1 Download Model Package from Website Please visit our website to download the most recent version of the growth amp yield model and to learn more about our research http www swietking org The model can be downloaded from THE MODEL page on the website or from the QUICK LINKS section on every page on the site the location of the download file 1s subject to change but will always be hosted somewhere on the site Download the zip file Model zip containing the files necessary to install the NetLogo software and run the model on your computer The model will be downloaded to your default download location
110. the radius of a 0 91 ha seed shadow in patches 1 patch 10 m max num fruit 750 the maximum number of fruit per tree seeds per fruit 42 4 the average number of viable seeds per fruit surv prob 0 085 the proportion of seeds surviving to become first year seedlings 41 Free Landis amp Grogan Mahogany Growth amp Yield To change the value of any of these constants simply replace the old value with a new one Remember to rename the new model when saving to avoid overwriting the original model OVERWRITING THE ORIGINAL MODEL WILL FORCE YOU TO REINSTALL THE MODEL The ability to redefine global variables is useful for personalizing the model constants to your field site For example if you think your site experiences more disturbance increase the proportion of landscape disturbance prop dist value Similarly if you think the trees in your site have a smaller maximum fruit output max num fruit or produce fewer viable seeds per fruit seeds per fruit you can reduce these values 12 4 NetLogo Resources NetLogo is a multi agent programmable modeling environment developed by Uri Wilensky at the Center for Connected Learning and Computer Based Modeling Wilensky 1999 If you are interested in learning more about the software please visit the NetLogo website http ccl northwestern edu netlogo index shtml The website includes resources for learning NetLogo including a User Manual online dictionary example models and publica
111. tion density default 5 trees 100 ha Set a cutting cycle length default 30 years Default harvest parameters can be restored using the Defaults button in the upper left hand corner of the model interface This button also restores default model settings Default conditions are reviewed below sections 6 2 amp 7 Step 4 Setup Initial Population ES Establish the initial population on the landscape The population will appear on the model interface in the landscape middle field The landscape population can be resized using the Patch Area input and the Resize button section 6 1 12 Free Landis amp Grogan Mahogany Growth amp Yield Step 5 Begin Simulations 1 Run the simulation for a single year This feature is useful when Run 1 Year carefully monitoring a simulation or when troubleshooting RI Run the simulation until the time limit is reached or until all trees are Run X Years l harvested or die if this occurs before reaching the time limit Step 6 Monitor Simulations Year 0 Population and Current Population monitors report total tree density trees gt 20 cm diameter 100 ha commercial sized tree density commercial trees 100 ha default value and commercial sized tree volume m during Year 0 and the Current simulation year Diameter Distribution Tree Abundance 50 250 5 c 9n g o u kig 0 0 1 _ Time yrs Size Class Current Population plots show c
112. tions The NetLogo Users Group an online community of NetLogo users 1s also available for help and advice http groups yahoo com group netlogo users The NetLogo software comes with a Models Library available in Files gt Models Library in the NetLogo menu These models can be used as examples or templates for learning the NetLogo language modifying the growth amp yield model or creating new NetLogo models NetLogo 4 1 2 the version used to run the Big Leaf Mahogany Growth amp Yield Model can be downloaded here http ccl northwestern edu netlogo 4 1 2 The most recent version of the software can be downloaded here http ccl northwestern edu netlogo download shtml 13 LIMITATIONS amp CONSIDERATIONS The Big Leaf Mahogany Growth amp Yield Model functions are derived from demographic data collected annually from 1995 2009 for nearly 600 mahogany trees and many thousands of seedlings saplings and poles at multiple field sites in southeast Para and Acre This comprehensive dataset allows for robust predictions of mahogany population growth amp yield outcomes over reasonable time periods Even so it Is important to acknowledge model limitations that constrain the accuracy and precision of projected outcomes First due to the scarcity of natural regeneration in gap environments simulated seedling sapling mortality and growth rates 1n large gaps are based on data from experimental outplantings across light gradients in large cle
113. tman KE amp Ward SE 2005 Is mahogany dysgenically selected Environmental Conservation 32 129 139 Brown N Jennings S amp Clements T 2003 The ecology silviculture and biogeography of mahogany Swietenia macrophylla a review of the evidence Perspectives in Plant Ecology Evolution and Systematics 6 37 49 Grogan J amp Schulze M in review The Impact of annual and seasonal rainfall patterns on growth and phenology of emergent tree species in southeastern Amazonia Brazil Biotropica Grogan J Pefia Claros M amp G nter S 2011 Managing natural populations of big leaf mahogany In G nter S Stimm B Weber M Mosandl R eds Silviculture in the Tropics Institute of Silviculture Technische Universitat M nchen Munich Germany Grogan J Blundell AG Landis RM Youatt A Gullison RE Martinez M Kometter RF Lentini M amp Rice RE 2010 Over harvesting driven by consumer demand leads to population decline big leaf mahogany in South America Conservation Letters 3 12 20 Grogan J Schulze M amp Galv o J 2010 Survival growth and reproduction by big leaf mahogany Swietenia macrophylla in open clearing vs forested conditions in Brazil New Forests 40 335 347 Grogan J amp Landis RM 2009 Growth history and crown vine coverage are principal factors influencing growth and mortality rates of big leaf mahogany Swietenia macrophylla in Brazil Journal of Applied Ecology 46 1283 1291 Grogan J amp Schulze M 200
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115. ulations discussed at greater length in section 6 1 were derived from a 100 area inventory of mahogany trees gt 20 cm diameter in a 204 ha subplot of the Marajoara field site a randomly stratified transect survey of mahogany trees gt 20 cm diameter in 1035 ha at Marajoara 10 of the total area and a 100 area inventory of mahogany trees gt 20 cm diameter in 685 ha at the Acre West Amazon site Due to selective logging prior to the study mortality and growth rates may reflect a small post logging increase Due to the scarcity of natural regeneration in gap environments simulated seedling sapling mortality and growth rates In large gaps are based on data from experimental outplantings across light gradients in large clearings initiated in 1995 These data present optimistic estimates of juvenile performance due to the manual removal of competing vines and secondary vegetation during the experiments initial three years Canopy disturbances are simulated based on an observed size distribution of gap forming canopy gaps during 1996 1997 at Marajoara 48 Free Landis amp Grogan Mahogany Growth amp Yield APPENDIX B MODEL DETAILS amp DEFINITIONS MODEL FEATURES be Button Button A button executes instructions when pressed Setup Defaults Run slider 1 Year Run X Years Resize All Definitions Export Results etc are Won Switch all buttons t Chooser ipt Slider A slider allows selection from a range o
116. ummary to more powerfully query the model results Population Statistics Total Tree Abundance Commercial Tree Abundance First Year Seedling Abundance Total Tree Volume m Maximum Tree Basal Area cm Median Small Tree Diameter cm Initial Population Abundance Initial Population Density Initial Commercial Abundance Initial Commercial Density Commercial Density trees 100ha show count trees show count trees with diameter gt 60 show count trees with seedling true show sum volume of trees show max basal area of trees show median diameter of trees with diameter lt 20 show y0 tot density site area 100 show y0 tot density show y0 comm density site area 100 show y0 comm density show count trees with diameter gt 60 site area 100 36 Field Site Statistics Field Site Area m Field Site Area ha Field Site Area km Field Site Width m Field Site Width km Field Site Height m Growth Statistics grow trees Specific Tree Growth Rate cm yr Median Tree Growth Rate cm yr Fastest Growing Tree Diameter cm Fastest Growing Tree tree 7 smallest Basal Area Tree tree 7 Large DBH Trees tree s Harvest Statistics log trees Last Harvest Number of Logged Trees Free Landis amp Grogan Mahogany Growth amp Yield Show site area 10000 show site area show site area 100 Show world width 10 Show world width 10 1000 show world height 10 show
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118. ved in the field site seed diam list a list of first year seedling diameters cm observed in the field The seedling diameter and disturbance size data distributions can be viewed in the Model gt Data folder The seedling diameter distribution file is called seedling data csv while the disturbance size distribution file 1s called gap data csv Export Data Export Landscape Image pg export view user new file Export Interface Image jpg export interface user new file Export Output Text txt export output user new file Export Single Plot Values csv export plot Tree Abundance user new file Export All Plot Values csv export all plots user new file Export All Variables csv export world user new file Name and place the exported file anywhere on your computer Include the file extension listed in the parenthesis following each export method Available Statements Math Statements lt gt lt gt Logic Statements true false Statistic Statements max min mean median modes with min with max Patch Variables disturbance sweetspot 38 Free Landis amp Grogan Mahogany Growth amp Yield Tree Variables who alive seedling reproduce diameter dbh basal area volume growth rate mort rate fruit prob num fruit surv seeds These statements can be substituted for similar statement types in the italicized commands provided above For example any statistical statement max min mean etc
119. vided to organize and structure the interface INTERFACE DEFINITIONS see schematic page 3 MODEL CONTROL BAR Interface Information Procedures W y V view updates 4 a abc Button T Settings Edit Delete Add normal speed continuous r The Interface tab displays model controls and simulations 49 Free Landis amp Grogan Mahogany Growth amp Yield The Information tab displays a basic information about the model The Procedures tab displays the workspace where the model code is stored and modified Edit This button 1s only active when a feature 1s selected on the interface Pressing the button allows the selected feature to be edited Use it to modify the range increment of a harvest parameter Delete This button is only active when a feature is selected on the interface Pressing the button will delete the selected feature Do not use this button All features are necessary to the model Add Button In combination these add buttons sliders switches choosers inputs monitors plots outputs or notes to the interface First press Add and then Button to choose a feature from the pop up menu normal speed This slider determines the speed of model runs Slide the round knob left for slower slide right for faster view updates Determines whether landscape updates are shown When checked you can view continuous updates or on ticks updates that 1s at the end of each year Unchecking v
120. volume during year 0 and the current simulation year respectively YEAR 0 POPULATION monitors are static while CURRENT POPULATION monitors are updated each year according to simulation results YEAR D POPULATION Total Density 100ha Commercial Density 100ha Commercial Volume m3 67 2 40 9 546 4 CURRENT POPULATION Total Density 100ha Commercial Density 100ha 27 3 5 6 87 5 16 Free Landis amp Grogan Mahogany Growth amp Yield Density monitors report tree density as the number of trees per 100 hectares Density can be converted to abundance using the following equation Abundance Density Area 100 where density trees 100 ha 1s either total or commercial density and area ha 1s the Site Area as reported in the upper right portion of the MODEL SETTINGS section of the model interface Volume monitors report volume in cubic meters m Volume is calculated from the diameter of each tree according to the equation Volume m 0 056 0 01421 Diameter 0 001036 Diameter 2 where tree diameters cm are measured 1 3 m above the forest floor or at least 30 cm above the reach of the tallest buttress Mayhew amp Newton 1998 p 117 8 2 Population Plots The CURRENT POPULATION plots show changes in tree size class distribution and abundance over time These plots are updated each year according to simulation results Diameter Distribution Tree Abundance 5D 250 g E 3
121. ype the name of the shapefile from Step 1 containing spatial and diameter data located in the User folder in the File Name input box Include the shp file extension when typing the name 21 Free Landis amp Grogan Mahogany Growth amp Yield Type the name of the attribute data column header in the shapefile containing the diameter data in the DIAM Attribute Name input box The diameters listed in the shapefile must be measured in centimeters cm Tree diameter measurements should be taken at 1 3 m above the forest floor or at least 30 cm above the reach of the tallest buttress DATA UPLOAD mara 204 tree data shp 204 tree data mara 204 tree data shp Type the width X in meters of your site into the Site Width input box and the height Y in meters of your site into the Site Height input box If your site is not rectangular estimate the width and height of the smallest bounding rectangle examples shown above Again the width and height of your site must be in meters m DIAM2004 004 Type the value 1 00 into the Patch Area input box Patch Area determines the size of landscape patches in pixels and therefore determines the size of the landscape A Patch Area of 1 00 is purposefully small and should draw a landscape contained by the available space on the model interface Step 3 Resize Site Drawing After File Name DIAM Attribute Name Site Width Site Height and Patch Area

User Manual 5.1

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