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User Manual 2.1 - Institute of Marine and Coastal Sciences

1. Model Schematic The model interface as it appears when installed on your computer Table of Contents Model Schematic The model interface as it appears when installed on your computer 3 TL MODELETNTRODUC TION tinae idee Ee Ire Ede aeo E ove e EES 5 2 MANUAL GUIDE eeesesttotecceuto oido u eel ae eee uet cosa c euta evo ia oeste hae Pee Ara sous uto e eo ce Dessus o etae uoa pes 6 gt MODEL INSTADBEATION 2 2 EURISIEER E Ceu ede ed cioe e eine ie eene 7 SL AMVeb IBStal ldHOTE oio io te eece a tan aet Ande tide tpm e dde eM nla d M eU MEUM 7 SWR 8 Ae HREP BU EONS roria sites cbse sccceecceumzasce acc tesceexsetaedeedeons exvenaheacadhepscexeetesteediw nes 10 SA BREE COINS 11 0 MODELSETITINGS rc Tc 13 6 1 Setup amp Resize Initial Population eter eret e Eoo ne eva reo og ena een v loo 13 6 2 Setup amp Run Simulations airesin erenneren aa AA Ee AREE a ie r EAA AATA 14 T JO0OGGING PARAMPELDERS tix eie teria tans cyettadetvstansantectescstanscnexteleriec 15 S SIMULATION RESUNLLS iecit tees ER neca aHa eco eoi o Pe ERE RE ERE neca a aes cet erit Pe EE RE EE S ess 16 ool PODU On MONOT es cept ons etos metbadsic treu N E o ue aerated 16 5 2 Populauoh POIDS sicot iode o eee do Ooh adc n Ede ev dodici esset dui iios ett 17 5 2 Harvest Productivity MIORIDOES uie eoe oe eroi elu tole d paced di n tutu e ppt ad 17 9 USER DATA UP
2. 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 1s 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 14 Free Landis amp Grogan Mahogany Growth amp Yield The Run 1 Year button runs the model for a single year The Run X Years button runs the model until the time limit is reached or until all trees are harvested or die The Defaults button returns all variables to default conditions Populations SE Para 204 ha Logging On Patch Area 2 75 pixels Time 100 years 7 LOGGING PARAMETERS The default harvest parameters are set according to current Brazilian forest management regulations for mahogany These regulations mandate a minimum diameter cutting limit of gt 60 cm the retention of gt 20 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 LOGGING PARAMETERS Harvest par
3. 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 45 Free Landis amp Grogan Mahogany Growth amp Yield 16 REFERENCES amp SUGGESTED READING Electronic copies of journal references are available upon request to jgrogan swietking org or jgrogan crocker com 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 and Management 255 340 345 Blundell AG amp Gullison RE 2003 Poor regulatory capacity limits the ability of science to influence the management of mahogany Forest Policy and Economics 5 395 405 Blundell AG amp Rodan BD 2003 Mahogany and CITES moving beyond the veneer of legality Oryx 37 85 90 Blundell AG 2004 A review of the CITES listing of big leaf mahogany Oryx 38 1 7 Blundell AG amp Mascia MB 2005 Discrepancies in reported levels of international wildlife trade Conservation Biology 19 2020 2025 Blundell AG 2007 Implementing CITES regulations f
4. The area in hectares or ha of the field site 1s also MODEL sili NCS displayed in this section Site Area ha we SNL 212 8 fies mm eee e gl 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 Brazil 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 13 Free Landis amp Grogan Mahogany Growth amp Yield EXAMPLE POPULATIONS SE Para 204ha 204 ha field site with 158 trees SE Para 1035ha 1035 ha field site with 745 trees Acre West Amazon 685 ha field site with 81 trees SE Para 204ha and SE Para 1035ha present spatial diameter data for mahogany populations in southeast Para Brazil The forest management and long term research site called Marajoara is located 34 km northwest of Reden o 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
5. 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 2 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 model applet html The online model is identical to the computer model except that it cannot 1 upload user data files 2 export simulation Free Landis amp Grogan Mahogany Growth amp Yield results 3 run BehaviorSpace experiments 4 follow instructions from the Command Line or 5 resize the landscape elegantly The online version of the model cannot upload user data or export simulations because of the limitations of our web server 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 kept on the model interface It does not support any NetLogo services occurring outside the 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
6. 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 year 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 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 thorou
7. options Follow the unzip instructions for your software and extract the Model folder anywhere on your computer Step 3 View the Model Folder Contents If you successfully unzip the 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 seven elements 1 Growth amp Yield Model file 4 NetLogo folder 7 Results folder 2 Installation Guide file 5 Data folder 3 User Manual file 6 User 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 Installation Guide file gives instructions on installing the NetLogo software and the Growth amp Yield Model It is identical to MODEL INSTALLATION in the User Manual section 3 The User Manual file 1s the User Manual for the Big Leaf Mahogany Growth amp Yield Model Free Landis amp Grogan Mahogany Growth amp Yield The NetLogo folder contains the NetLogo 5 0 3 installer necessary for your operating systems This folder also contains the NetLogo 5 0 3 User Manual written by the NetLogo design team 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 The User folder contains example user upload files These files
8. 0 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 1s harvest 1 item 1 1s harvest 2 item 3 is 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 cutting cycle 1 where the floor of a number of harvests is the largest integer less than or equal to the number Pre Post Harvest List Reporters The pre post cut number and pre post cut volume reporters print a list of harvest values in two columns as iteMpre h1 item post h1 item pre n2 Item post n2 where itemp u and iteMpost x represent a population statistic before and after harvest number x respectively If you prefer that each item receive its own column you must replace the pre post cut number reporter with the following reporters item 0 pre post cut number number of commercial trees before harvest 1 item I pre post cut number number of commercial trees after harvest 1 item 2 pre post cut number number of commercial trees before harvest 2 item X 1 2 pre post cut number number of commercial trees before harvest X item X 1 2 I pre post cut number number of commercial trees afte
9. 416 D nisch O Mont ia VR amp Bauch J 2003 Dendroecological investigations on Swietenia macrophylla King and Cedrela odorata L Meliaceae in the central Amazon Trees Berlin 17 244 250 D nisch O amp Puls J 2003 Changes in content of reserve materials in an evergreen a semi deciduous and a deciduous Meliaceae species from the Amazon Journal of Applied Botany 77 10 16 Fearnside PM 1997 Protection of mahogany a catalytic species in the destruction of rain forests in the American tropics Environmental Conservation 24 303 306 Fujii T Marsoem SN amp Fujiwara T 1998 Annual growth rings in mahogany Swietenia macrophylla growing in Java IAWA Journal 19 449 450 Garcia XC Negreros PC amp Rodriguez BS 1993 Regeneracion natural de caoba Swietenia macrophylla King bajo diferentes densidades de dosel Revista Ciencia Forestal en Mexico 18 25 43 Gerhardt K 1993 Tree seedling development in tropical dry abandoned pasture and secondary forest in Costa Rica Journal of Vegetation Science 4 95 102 Gerhardt K amp Fredriksson D 1995 Biomass allocation by broad leaf mahogany seedlings Swietenia macrophylla King in abandoned pasture and secondary dry forest in Guanacaste Costa Rica Biotropica 27 174 182 Gerhardt K 1996 Effects of root competition and canopy openness on survival and growth of tree seedlings in a tropical seasonal dry forest Forest Ecology and Management 82 33 48 Gerhardt K 1996
10. Area by entering 2 00 and press the Resize button If the site is 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 amp 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 is 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 is to structure your data so the computer can read the information 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 Y A B 71 3 79 4 66 1 80 4 45 5 64 7 72 5 79 A Y Trees 2 0 4 OY V1 We O Diameters must be measured in cent
11. 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 gt shown below The results of the commands are printed in the larger output window labeled Command Center Command Center W Clear observer show count trees observer 158 observer show count trees with diameter gt 60 observer 81 observer show sum stand volume of trees with diameter gt 60 v P 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 wit
12. Density 100ha Commercial Volume m3 65 7 39 7 423 8 CURRENT POPULATION Total Density 100ha Commercial Density 100ha Commercial Volume m3 44 1 7 4 65 1 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 Site 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 5 297672 0 1263387 Diameter 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 Kometter 2011 16 Free Landis amp Grogan Mahogany Growth amp Yield 8 2 Population Plots The CURRENT POPULATION plots show changes in tree size class distribution and population density over time These plots are updated each year according to simulation results Diameter Distribution Tree Density 34 80 ri pi Hm eo 9 uc u pe 0 0 Loo nA Lp 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 i
13. Time yr count trees Trees count trees with diameter gt 20 Trees 7 20 cm diameter count trees with diameter gt minimum diameter Commercial Trees sum annual harvest number Logged Trees 34 Free Landis amp Grogan Mahogany Growth amp Yield sum annual harvest volume Logged Tree Volume m annual harvest number Harvest Number List yr annual harvest volume Harvest Volume List m yr pre post cut number Pre Post Harvest Commercial Abundance pre post cut volume Pre Post Harvest Commercial Volume m If you would like to query the model for additional information please refer to Command Line and Modifying 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 is measured in hectares ha and density is 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 columns containing harvest lists and use the Find and Replace feature to remove the brackets from the cells Then use the Text to Columns feature with data delimited
14. 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 sp e 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 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 website 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
15. cut number new list contains live tree abundance pre amp post harvest e pre post cut volume new list contains live tree volume pre amp post harvest e harvest ticker removed removed because of new harvest method Tree Variables age specifies age of tree ages of initial trees are unknown e fall gap specifies whether a tree creates a treefall gap e sawn volume specifies sawn volume e e4 e10 specifies growth residuals from 4 to 10 years previous MODEL SETUP Helper Functions The new model has six helper functions to perform calculations repeated throughout the model These functions help protect against copy paste errors and simplify the model code The helper functions are summarized as follows Function Name Function Purpose Function Location calc e0 calculates eO residual setup tree values update residuals disperse seeds calc diam calculates diameter calculate diameter disperse seeds calc basal diam calculates basal diameter setup tree values calc basal area calculates basal area setup tree values calculate diameter disperse seeds calc stand volume calculates stand volume setup tree values calculate diameter disperse seeds calc sawn volume calculates sawn volume setup tree values calculate diameter disperse seeds Volume Equation The old standing volume equation was replaced with a new equation derived from field studies in Guatemala Kometter 201 1 Site Area The site area is now s
16. 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 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 unlogged population The low landscape scale density is typical of western Amazonian mahogany populations USER POPULATIONS User Population xyd upload spatial diameter data from a spreadsheet User Population shp upload spatial diameter data from a shapefile User Population csv upload non spatial diameter data from a spreadsheet The site is drawn in the landscape middle field of the model interface If the site 1s 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 is drawn too large for the available space decrease the value shown in Patch Area 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
17. 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 specified in File Name does not have a txt extension Please ensure the file is 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 is a
18. establishing the initial population on the landscape The RUN MODEL section successively grows logs kills disturbs and reproduces trees on the landscape This section also resets the trees and landscape in preaparation for the next year of simulation The EXPORT RESULTS section contains the code for exporting the results of a single model simulation to a text file The 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 is BLACK 68
19. fully annotated version of the model code is available in APPENDIX E MODEL CODE page 68 and in the Code tab of the NetLogo interface A close review of the code will help you better understand how the model works Procedure Summary At the top of the model code you will find basic information about the model title authors funders landscape dimensions etc Throughout the code gray text on the right side preceded by repeated semi colons represents comments provided to help interested users understand how the code operates This text 1s not read by the computer The first section of functional model 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 Breeds identify trees as the agents or individuals simulated by the model 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 establishing 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
20. logged in all previous harvests m Total Logged Trees number of trees logged in all previous harvests DATA UPLOAD File Name name of user data file with diameter and or XY data Diameter Attribute Name name of the diameter attribute in the user shapefile Site Width width X of the user field site meters Site Height height Y of the user field site meters Patch Area size of the patches on the landscape pixels Resize resizes the landscape based on the Patch Area listed DEFINITIONS All Definitions displays the definition function of all features on the interface Export Results exports simulation results to a user named and located file COMMAND CENTER Command Center W Clear observer show count trees observer 158 observer show count trees with diameter 60 observer 81 observer show sum stand volume of trees with diameter gt 60 Y A 58 Free Landis amp Grogan Mahogany Growth amp Yield 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 observer gt 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 This button switches the Command Center window between
21. 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 development 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
22. results of each harvest by displaying the year and productivity of successive harvest events The PRE POST HARVEST ABUNDANCE amp VOLUME section summarizes the number and volume of commercial trees before after each harvest if logging is turned on during simulations 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 is 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 2 Free Landis amp Grogan Mahogany Growth amp Yield The following section explains how to run modify and analyze the seven built in BehaviorSpace experiments Step 1 Define Model Parameters BehaviorSpace experiments will systematically vary the harv
23. shapefile and has the shapefile extension shp A Diameter Attribute Name must be specified You selected the User Population shp option which requires a Diameter Attribute Name but the Diameter Attribute Name field is empty Please provide the name of the shapefile diameter attribute in 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 is 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 guidelines 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
24. 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 small diam abundance of trees 7 20 cm diameter count trees with diameter gt minimum diameter abundance of commercial sized trees sum annual harvest number summed number of logged trees sum annual harvest volume summed volume of logged trees annual harvest number number of trees logged in each harvest annual harvest volume volume of trees logged in each harvest pre
25. the browser normally makes available This 1s 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 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 9 Free Landis amp Grogan Mahogany Growth amp Yield http download oracle com javase 1 5 0 docs guide deployment deployment guide jcp 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 available 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 page 56 of this Manual You can also look for help by selecting He
26. the comments The third section of code RUN MODEL successively grows kills disturbs and reproduces trees on the landscape This section also resets the trees and landscape in preaparation for the next year of simulation These steps are also contained within procedures and each procedure is extensively commented in the model code The fourth and final section EXPORT RESULTS contains the code for exporting the results of a single model simulation to a text file In the Code tab of the NetLogo interface use the Procedures menu to view Procedures v 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 42 Free Landis amp Grogan Mahogany Growth amp Yield 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 land dist 0 026 proportion of the landscape disturbed each year seed shadow area 0 91 area ha of a mahogany tree s seed sha
27. 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 55 Free Landis amp Grogan Mahogany Growth amp Yield APPENDIX B MODEL DETAILS amp DEFINITIONS MODEL FEATURES he Button Button A button executes instructions when pressed Setup Defaults Run i 1 Year Run X Years Resize All Definitions Export Results etc are all buttons Slider A slider allows selection from a range of values The model has Maniar sliders for Time and LOGGING PARAMETERS w Plot E Output Met tote Switch A switch allows a variable to be turned on off The Logging switch ghi jki te 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 us
28. the diameter data in the Diameter 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 21 Free Landis amp Grogan Mahogany Growth amp Yield DATA UPLOAD mara 204 tree data shp DIAM2004 1216 1712 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 see examples p 20 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 3 Resize Site Drawing After File Name Diameter Attribute 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 is drawn too small for the available space increase the Patch
29. 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 in the menu options 59 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 E MODEL CODE page 68 provides a similar review alongside the actual model code The fully annotated model code is also available in the Code tab of the NetLogo interface Initial Population The model begins with an initial population selected by the user and represented on the NetLogo 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 on 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
30. with 30 at 5 increments 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 trees with diameter lt 20 only paste median diameter of trees with diameter lt 20 These reporters will provide additional information when running experiments Harvest List Reporters The annual harvest number and annual harvest volume reporters print a list of harvest values in two columns as item item n2 item 55 item n4 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 40 Free Landis amp Grogan Mahogany Growth amp Yield annual harvest volume reporter with the following reporters item
31. 4 number of fruit produced The model simulates logging growth mortality disturbance and reproduction each year with these parameters until the time limit 1s 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 ten years The trees begin the simulation with no growth history so the residuals e 1 year previous e2 2 years previous e3 3 years previous etc are assigned a random value drawn from the distribution N 0 0 45 The present year residual e0 is then calculated as follows e0 0 399 e1 0 321 e2 0 081 e3 0 046 e4 0 130 eS 1 0 143 e6 0 029 e7 0 266 e8 0 190 e9 0 311 e10 o where o N 0 0 45 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 e 0 e9 e9 e8 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 equa
32. 5 0500 min pxcor max pxcor min pycor max pycor 61 61 86 86 ou a wN m 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 row 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 coordinates The length of the Y axis of the site is the sum of minimum min pycor and maximum max pycor Y coordinates 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 minimum density Minimum Density 100 ha cutting cycle Cutting Cycle yr step
33. 7 scale 0 0056 All disturbances are circular and the radius of the zone of recruitment is 10 m less than the radius of the whole disturbance therefore a disturbance with a radius gt 10 m is necessary 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 and diameter increment of trees marked as reproductive all non seedling trees and 50 of dead mahogany trees using the following equation log odds fruiting 9 624 0 210 basal diameter 0 182 7 max 0 basal diameter 40 3 201 growth rate 1 165 growth rate 2 which is 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 1s 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 1 142 while the A value is calculated as a function of the value and the mean number of fruit The mean number of fruit for a tree of any given diameter is cal
34. 705 max 0 GR 0 4 3 2 57 max 0 GR 1 5 0 575 BD 0 554 max 0 BD 5 0 027 max 0 BD 25 0 00077 max 0 BD amp 5 where GR is the current year diameter increment and BD is the basal diameter The og odds is subsequently used to calculate the probability of mortality using the logit transformation mortality probability exp log odds 1 exp log odds 4 where the fate of each tree 1s 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 is given a 50 chance of dying standing and a 50 chance of dying before reproducing A tree dying after reproducing will fruit and disperse seeds before being removed from the population whereas a tree dying before reproducing 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 in a treefall gap will create a disturbance area according to the following equation disturbance area m 25 171 1 398 diameter 0 02 diameter 2 5 where diameter is calculated from basal diameter using the following equation diameter cm basal diameter 0 2842709 1 1003362 6 The radius of the disturbance area 1s calculated usin
35. 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 l 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 one reporter per line you may not split a reporter across multiple lines _ Measure runs at every step if unchecked 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 of 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
36. FICATIONS We are interested in using the recently published R Extension for NetLogo Thiele amp Grimm in press http r ext sourceforge net to increase the robustness of the model regressions the potential for in model data analysis and the functionality of the Export Results command Both the computer and online models will be updated as new versions of NetLogo are released 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 44 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 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 WWF Brazil In southeast Para generous logistical support has been
37. Germination and development of sown mahogany Swietenia macrophylla King in secondary tropical dry forest habitats in Costa Rica Journal of Tropical Ecology 12 275 289 Gerhardt K 1998 Leaf defoliation of tropical dry forest tree seedlings implications for survival and growth Trees Structure and Function 13 88 95 Gillies ACM Navarro C Lowe AJ Newton AC Hernandez M Wilson J amp Cornelius JP 1999 Genetic diversity in Mesoamerican populations of mahogany Swietenia macrophylla assessed using RAPDs Heredity 83 722 732 Gouv a CF Dornelas MC amp Martinelli AP 2008 Characterization of unisexual flower development in the endangered mahogany tree Swietenia macrophylla King Meliaceae Botanical Journal of the Linnean Society 156 529 535 Grogan JE 2001 Bigleaf mahogany Swietenia macrophylla King in southeast Para Brazil a life history study with management guidelines for sustained production from natural forests PhD dissertation Yale University School of Forestry amp Environmental Studies New Haven CT 47 Free Landis amp Grogan Mahogany Growth amp Yield 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 Amazonia Brasileira Ecologia e Perspectivas de Manejo Mahogany in the Brazilian Amazon Ecology and Perspective
38. HEADERS The head of your file should look like the example file shown below X Coordinates Y Coordinates Diameters o E B E D 1 579775 8 9136498 4 1 3 2 579744 8 9136501 6 79 4 3 580177 6 9135822 6 66 1 lt 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 74 9 8 5B0406 1 9135441 5 79 0 18 Free Landis amp Grogan Mahogany Growth amp Yield 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 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 saved 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 txt extension in the file name The head of the new text file should
39. LOAD 5desdiciesiti e e ice a bete ee dou itae etv Eae ee tene aee 18 9 1 Spatial Diameter Data User Spreadsheet eec etti tese ees Resa een 18 9 2 Spatial Diameter Data User hapeltile sco coit reete Et E Exe oy ERU PEE eost o ERU PUES 21 9 3 Non Spatial Diameter Data User Spreadsheet 0 cc eeeccccccccecccsaeseeeeecceeeeeeaaeeeees 23 94 Error Messaces amp Trouble Shooting sse ea eure oed E eens 25 9 5 User Data Upload Examples serer ere ette a emite Ce eh ett ipti efe 26 10 EXPORT SIMULATION RESUBELS iieisdtexsseekue ee d eekeneivtab ete dps deve esa eere beoe ce deett us eau ie 26 11 SIMULATION EXPERIMENTS BehaviorSpace ee eee eee eee e eee eene eese eee eSe 27 12 ADVANCED USERS amp NETLOGO RESOURCES esssssssssssscscccccccccccscssseees 36 ZE omman T6 OO conii sete tisk bett o dit eimi atit umet E totus tede dotis 36 12 2 Modifying Behaviorspace Experiments eot n a beh re rea reticere ti 40 12 5 Model Proccdutes6 Od iade iieeiate taedia e eniti eti oluniedi d ecsutettelienisu d usu iedheets 42 124 Netbopo RESOUTCES so usata bb er b b bici o bp bes a ie bob 43 13 LIMITATIONS amp CONSIDERATIONS e eee ee eee eee eee eoo ette eee ett ette eee eesossssssos 44 14 FUTURE MODIFICATIONS isis ctae nete oett e epo ee cet eet eere eed tates 44 IS ACKNOWDLEDGEMEN DS tee eea th Ue eee dedete sete beveeuele a 45 16 REFERENCES amp SUGGESTED READING
40. 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 amp 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 is 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 shown on the next page 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 Type the name of the shapefile from Step 1 containing spatial diameter data located in the User folder in the File Name input box Include the shp file extension when typing the name Type the name of the attribute data column header in the shapefile containing
41. USER MANUAL for the BIG LEAF MAHOGANY GROWTH amp YIELD MODEL CHRISTOPHER FREE R MATTHEW LANDIS JAMES GROGAN Copyright 2013 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 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 tcSv 02 gui auunjoA pa660o7 e01 gw auinjoA pa6607 ALIALLINGOUd LSIAYVH S 001 9 w auin oA e 24200140 EYOOT Ausuag er24auu10 PEYOOT Ausuag e301 NOILLW1NdOd 1N338302 S tev NENNT UNNUREEN E NOILV1NdOd 0 8 v3A peee a sSyJLIWvY Yd DNID201 E saxum marua mr 948607 10 SONILLIS T330N Suo13128S 3uj 119 40 Saunjp2 au NLAJ OF Suoi3luljaQ lV SS9Jd xoq uoii1uljap S14 ul Samjpa S uo13295 3uj JO suolidl 2saop MATA O UO11285 YS 0 XBU UOj1hQ Z BYR SSaJd dys exep n poz esew PPv apa upa gems remos 80 CsBumas sayepdn main Aj _ __ uenng gt Po opui MENNIENNN
42. ala and Mexico pp 61 80 Island Press Washington DC USA Snook LK 2003 Regeneration growth and sustainability of mahogany in M xico s Yucat n forests In Lugo A Figueroa Col n JC amp Alay n M Eds Big Leaf Mahogany Genetics Ecology and Management pp 169 192 Springer Verlag New York NY USA Snook LK Santos Jimenez VA Carre n Mundo M Rivas CC May Ek FJ Mas Kant n P Hern ndez Hern ndez C Nolasco Morales A amp Escobar Ru z C 2003 Managing natural forests for sustainable harvests of mahogany Swietenia macrophylla experiences in Mexico s community forests Unasylva 54 68 73 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 Snook LK 2005 Aprovechamiento sostenido de caoba en la Selva Maya de M xico de la conservaci n fortuita al manejo sostenible Recursos Naturales y Ambiente A4 9 18 Snook LK 2005 Sustaining mahogany research and silviculture in Mexico s community forests Bois et For ts des Tropiques 285 55 65 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 Iskandar H Chow J Cohen J amp O Con
43. ameters 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 cm 5 cm increments Retention Rate 0 100 retention 5 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 Retention Rate 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 Free Landis amp Grogan Mahogany Growth amp Yield 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 volume during year O 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 0 POPULATION Total Density 100ha Commercial
44. ber 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 is help button returns definitions for a given model section LOGGING PARAMETERS Minimum Diameter minimum diameter of commercial trees cm Retention Rate retention rate of commercial sized trees 9o Minimum Density minimum post harvest density of commercial trees trees 100 ha Cutting Cycle number of years between harvests 57 Free Landis amp Grogan Mahogany Growth amp Yield YEAR 0 CURRENT POPULATION Total Density density of trees gt 20 cm diameter in the field site trees 100 ha Commercial Density density of commercial sized trees in the field site trees 100 ha Commercial Volume volume of timber in the commercial population m Diameter Distribution bar columns 10 cm diam increments gray line commercial diam black initial size distribution red current size distribution Tree Density vertical gray lines harvest years black line total tree density red line commercial tree density 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 Density plots no trees 20 cm diameter are shown HARVEST PRODUCTIVITY Logged Volume volume of trees logged in the most recent harvest m Total Logged Volume volume of trees
45. ble 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 Simultaneous runs in parallel option 2 maximizes run efficiency 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 32 Free Landis amp Grogan Mahogany Growth amp Yield 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 MC Running Experiment Population Growth amp Productivit O normal speed 664 E 0 count trees 8 1 count trees with 7 E 2 count trees with 2 E 3 sum annual har E 4 sum annual har a E 5 annual harvest MM O 6 annual harvest Run 4 of 600 step 53 Total elapsed time 0 04 06 Logging true minimum diameter 40 vi Update view v Update plots and monitors Abort 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 g
46. 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 directions in Harvest List Reporters of Modifying BehaviorSpace Experiments section 12 2 to report the harvest list values in individual columns as opposed to a 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 is 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 35 Free Landis amp Grogan Mahogany Growth amp Yield 12 ADVANCED USERS amp NETLOGO RESOURCES 12 1 Command Line Code The following section provides an introduction to using the
47. cape disturbance Vo show count patches with disturbance true count patches landscape sweetspot 9o 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 seedlings of trees 38 Free Landis amp Grogan Mahogany Growth amp Yield DISTURBANCE SEEDLING DATASETS median disturbance area m show median disturbance data disturbance dataset sample size show length disturbance data view disturbance dataset show disturbance data mean first year seedling diameter show mean seed diam data max first year seedling growth rate show max seed growth data list of disturbance area sizes m observed in the field disturbance data list of first year seedling diameters cm observed in the field seed diam data list of first year seedling growth rates cm yr observed in the field seed growt
48. conspecific adult basal area of Amazonian Swietenia macrophylla Meliaceae Journal of Tropical Ecology 22 451 460 Norghauer JM Malcolm JR Zimmerman B amp Felfili JM 2006 An experimental test of density and distant dependent recruitment of mahogany Swietenia macrophylla in southeastern Amazonia Oecologia 148 437 446 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 Malcolm JR amp Zimmerman B 2008 Experimental establishment of big leaf mahogany Swietenia macrophylla King seedlings on two soil types in native forest of Para Brazil Forest Ecology and Management 255 282 291 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 Norghauer JM Martin AR Mycroft EE James A amp Thomas SC 2011 Island invasion by a threatened tree species evidence for natural enemy release of mahogany Swietenia macrophylla on Dominica Lesser Antilles PLoS ONE 6 e18790 Norghauer JM Nock C amp Grogan J 2011 The importance of tree size and fecundity for wind dispersal of big leaf mahogany PLoS ONE 6 e17488 Norghauer JM amp Grogan J in press The intriguing case of Steniscadia poliophaea Noctuidae potent moth enemy of young mahogany tre
49. culated using the following equation mean fruit exp 0 29583 0 02453 diameter 9 0 00033 basal diameter 2 1 744 10 6 basal diameter 3 62 Free Landis amp Grogan Mahogany Growth amp Yield These values are subsequently used in the calculation of A which in conjunction with a 1s used to parameterize the gamma distribution describing the distribution of fruit production values for a single tree These two equations are as follows lambda a mean fruit 10 fruit production gamma a A 11 where fruit production by a given tree 1s capped at 750 to avoid unrealistically high values After fruit production is determined for reproductive trees these trees disperse their seedlings within the surrounding seed shadow The number of seedlings after one year is calculated as follows 1 year old seedlings fruit S pui f 12 where fruit is the number of fruit produced by tree i Spuit 1s the mean number of seeds per fruit and fsury is the fraction of seeds that germinate and survive to become 1 year old seedlings Spuit and f are constant values of 42 4 and 0 085 respectively based on observations at the Marajoara field site One year old seedlings are dispersed evenly within the 0 91 ha circular seed shadow 53 8 m radius of the parent tree Because seedling recruitment 1s only possible within the interior portions of disturbance areas only seedlings landing in the zone of recruitment sweetspo
50. dow max num fruit 750 maximum number of fruit per tree seeds per fruit 42 4 average number of viable seeds per fruit establishment rate 0 085 proportion of seeds surviving to become first year seedlings 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 land 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 offers resources for learning NetLogo including a User Manual online dictionary example models and publications The NetLogo Users Group an online community of NetLogo users is also available for help and advice http groups yaho
51. e provided commands Likewise any tree variable age alive diameter mort prob seedlings etc can replace a tree variable in the provided commands 39 Free Landis amp Grogan Mahogany Growth amp Yield 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 10 and ending
52. eaf mahogany Swietenia macrophylla in open clearing vs forested conditions in Brazil New Forests 40 335 347 48 Free Landis amp Grogan Mahogany Growth amp Yield 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 Tropical Forestry 8 pp 227 235 Springer Verlag Berlin Heidelberg Germany Grogan J amp Schulze M in press The Impact of annual and seasonal rainfall patterns on growth and phenology of emergent tree species in southeastern Amazonia Brazil Biotropica Gullison RE amp Hubbell SP 1992 Regeneracion natural de la mara Swietenia macrophylla en el bosque Chimanes Bolivia Ecologia en Bolivia 19 43 56 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 G nter S 2001 Impacto de los factores ecol gicos en la regeneraci n de la mara Swietenia macrophylla King en bosques naturales de Bolivia In Mostacedo B amp Fredericksen TS Eds Regeneraci n y Silvicultura de Bosques Tropicales en Bolivia pp 99 118 Proyecto de Manejo Forestal Sostenible BOLFOR Santa Cruz Bolivia Helgason T Russell SJ Monro AK amp Vogel JC 1996 What 1s mahogany The importance of a taxonomic framework for conservation Botanical Journa
53. ecce eee ee eene eene eee e neos eese e esee eese e esee sesso 46 IT CONTACI LS Bidriclieiciidnte dicio iode dO electio aS 54 APPENDIX A DATA SOURCES kirren eei eee eto aee I ee PEE IR eR ee EE eee ao Eco RE DU ERE oe os essa cob eude 55 APPENDIX B MODEL DETAILS amp DEFINITIONS eee e eee eee eee eee eese sette eooe 56 APPENDIX C MODEL FUNCTIONS ieeiicicceic iie oe tiae quo edoea ooo s o ceo uice e iere cuoco 60 APPENDIX D VERSION DIFFERENCES 22 1 eorr eren ese oo Eo Eoo o aea eran eese ana 64 APPENDIX E MODEL CODE ico cce etes too oa ee eren EE Reo toe aee uei Foo Rec e eren EE Ro eo odo aee eae Coena 68 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 management 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 Although the model was developed based on mahogany population dynam
54. ectangle examples shown below Again the width and height of your site must be in meters m Width Height 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 20 Free Landis amp Grogan Mahogany Growth amp Yield 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 is formatted correctly columns X coordinate Y coordinate diameter If you receive an error message refer to Error Messages amp 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 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 projected onto the model interface Step 5
55. ed from the incorporation of new data 66 Free Landis amp Grogan Mahogany Growth amp Yield DISTURBANCE FUNCTION Disturbance The disturbance procedure no longer includes mahogany treefall gaps in the landscape disturbance rate of 2 6 A fall gap tree variable was created to accommodate these changes Batch Disturbance The disturbance function now places an initial batch of disturbances on the landscape before adding the disturbances necessary to achieve the specified landscape disturbance rate This function greatly increases the speed of the model REPRODUCTION FUNCTION Fruiting Probability The reproduction function uses a new equation for determining the probability of fruiting The equation was derived from the incorporation of new data Fruit Production The reproduction function uses a new equation for determining fruit production The equation was derived from the incorporation of new data Seed Dispersal The reproduction function uses a new method for dispersing seeds the new method uses the standard approach to uniform seedling dispersal Although the new function might be slightly slower it produces a truly random and uniform distribution Seedling Growth Rate The seedling growth rates are now drawn from the seedling growth rate distribution seedling growth rates were previously set to zero Seedling Growth Residuals The e 0 growth residual is now calculated from seedling growth rate data The e9 e growth r
56. er 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 Diameter Attribute Name input boxes accept text inputs Monitor A monitor displays the value of a built in expression The Site 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 Density plot tracks tree density 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 provided to organize and structure the interface INTERFACE DEFINITIONS see schematic page 3 MODEL CONTROL BAR Interface info Code fe y v view updates P abc Button w T Settings Add normal speed continuous X 56 Free Landis amp Grogan Mahogany Growth amp Yield The Interface tab displays model controls and simulations The Info tab displays basic information about the model The Code tab displays t
57. es in Amazonian forests In Moths Types Ecological Significance and Control Methods Nova Science Publishers Inc Novick RR Dick CW Lemes MR Navarro C Caccone A amp Bermingham E 2003 Genetic structure of Mesoamerican populations of big leaf mahogany Swietenia macrophylla inferred from microsatellite analysis Molecular Ecology 12 2885 2893 P rez Salicrup DR amp Esquivel R 2008 Tree infection by Hypsipyla grandella in Swietenia macrophylla and Cedrela odorata Meliaceae in the southern Yucatan Peninsula region Forest Ecology and Management 324 327 Ramos J amp Grace J 1990 The effects of shade on the gas exchange of seedlings of four tropical trees from Mexico Functional Ecology 4 667 678 Ramos JM amp del Amo S 1992 Enrichment planting in a tropical secondary forest in Veracruz Mexico Forest Ecology and Management 54 289 304 Rice RE Gullison RE amp Reid JW 1997 Can sustainable management save tropical forests Scientific American 276 44 49 Robbins CS 2000 Mahogany Matters the U S Market for Big Leafed Mahogany and its Implications for the Conservation of the Species Report TRAFFIC North America Washington DC USA Rodan B Newton A amp Ver ssimo A 1992 Mahogany conservation status and policy initiatives Environmental Conservation 19 331 342 Rodan BD amp Campbell FT 1996 CITES and the sustainable management of Swietenia macrophylla King Botanical Journal of the Linnean Soci
58. escribes 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 is 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 population density default 5 trees 100 ha Set a cutting cycle length default 30 years D Default harvest parameters can be restored using the Defaults button in the upper Defaults 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 Establish the initial population on the landscape The population will appear on the model interface in the landscape middle field The landscape pop
59. esiduals are set to zero and the e0 growth residual is calculated using a new equation derived from the incorporation of new data EXPORT RESULTS Export Results Function The name of the export results function was changed from export data to export results for increased clarity and accuracy Pre Post Harvest Statistics The export function now displays the abundance and volume of commercial sized trees alive before and after each harvest in the exported text file BEHAVIORSPACE View Plot amp World Export If exporting a view plot or world from a BehaviorSpace experiment use the BehaviorSpace run number code in place of the date and time code when naming the output file The old code does not work on Windows computers 67 Free Landis amp Grogan Mahogany Growth amp Yield APPENDIX E MODEL CODE This section provides a fully annotated copy of the model code This code is identical to the code in the Code 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 title authors funders 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
60. est 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 aM 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 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 experiment Edit opens the selected BehaviorSpace experiment for editing Duplicate duplicates the selected BehaviorSpace experiment Delete deletes the selected BehaviorSpace experiment Run run
61. ety 122 83 87 51 Free Landis amp Grogan Mahogany Growth amp Yield Schulze M Vidal E Grogan J Zweede J amp Zarin D 2005 Madeiras nobres em perigo praticas e leis atuais de manejo florestal nao garantem a explora o sustent vel Ci ncia Hoje 214 66 69 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 Landis 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 Snook LK 1993 Stand dynamics of mahogany Swietenia macrophylla King and associated species after fire and hurricane in the tropical forests of the Yucatan Peninsula Mexico PhD dissertation Yale University School of Forestry amp Environmental Studies New Haven CT USA Snook LK 1996 Catastrophic disturbance logging and the ecology of mahogany Swietenia macrophylla King grounds for listing a major tropical timber species in CITES Botanical Journal of the Linnean Society 122 35 46 Snook LK 1998 Sustaining harvests of mahogany Swietenia macrophylla King from Mexico s Yucatan forests past present and future In Primack B Bray DB amp Galletti H Eds Timber Tourists and Temples Conservation and Development in the Maya Forests of Belize Guatem
62. g the equation for the area of a circle a nr The zone of recruitment that 1s the area of the disturbance available for seedling 61 Free Landis amp Grogan Mahogany Growth amp Yield 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 each circular area Disturbance Function The model disturbs the landscape as follows 1 an initial batch of disturbances is added to the landscape 2 additional disturbances are then added one at a time until a certain proportion of the landscape is disturbed and 3 disturbances representing treefall gaps are added last The model calculates the number of disturbances to add to the landscape in batch based on the area of the field site and the size of the landscape disturbance proportion larger field sites and larger landscape disturbance proportions receive more disturbances in batch After placement of this initial group the model adds disturbances one at a time until the proportion of landscape disturbance matches the specified proportion default 0 026 Treefall gaps are placed after the proportion is achieved in order to prevent them from counting towards the background disturbance rate Disturbance sizes are drawn from a gamma distribution fit to an observed size distribution of gap forming canopy disturbances n 87 shape 0 612
63. gal C Snook LK amp Almeida E 2005 Constraints and opportunities for better silvicultural practice in tropical forestry an interdisciplinary approach Forest Ecology and Management 209 3 18 Weaver PL amp Sabido OA 1997 Mahogany in Belize a Historical Perspective USDA Forest Service International Institute of Tropical Forestry General Technical Report IITF 2 Ashville NC USA Weaver PL amp Bauer GP 2003 Big leaf mahogany in Panama Historical Perspective USDA Forest Service International Institute of Tropical Forestry General Technical Report IITF 24 Ashville NC USA Whigham DF Lynch JF amp Dickinson MB 1998 Dynamics and ecology of natural and managed forests in Quintana Roo Mexico In Primack B Bray DB amp Galletti H Eds Timber Tourists and Temples Conservation and Development in the Maya Forests of Belize Guatemala and Mexico pp 267 281 Island Press Washington DC USA White GM Boshier DH amp Powell W 1999 Genetic variation within a fragmented population of Swietenia humilis Zucc Molecular Ecology 8 1899 1909 White GM amp Boshier DH 2000 Fragmentation in Central American dry forests genetic impacts on Swietenia humilis In Young AG amp Clarke G Eds Genetics Demography and the Viability of Fragmented Populations pp 293 311 Cambridge University Press Cambridge UK White GM Boshier DH amp Powell W 2002 Increased pollen flow counteracts fragmentation in a tropical dry fores
64. gh 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 MODEL SETTINGS section 6 describes example populations available for simulations and how to setup and run the model LOGGING PARAMETERS section 7 explains how to adjust the four logging parameters that determine how the model harvests and grows a population over multiple cutting cycles SIMULATION RESULTS section 8 describes the monitors and charts on the model interface that track harvests and populations during simulations USER DATA UPLOAD section 9 provides instructions for uploading user data into the model framework EXPORT SIMULATION RESULTS section 10 explains how simulation results can be exported to text files for analysis and synthesis SIMULATION EXPERIMENTS BehaviorSpace section 11 provides directions for running repeat simulations of a single harvest regime or multiple simulations of varied harvest regimes ADVANCED USERS amp 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 ca
65. h 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 summary to more powerfully query the model results POPULATION STATISTICS total tree abundance show count trees commercial tree abundance show count trees with diameter gt 60 first year seedling abundance show count trees with seedling true 36 total tree volume m maximum tree basal area cm median small tree diameter cm median tree age yr initial population abundance initial population density initial commercial abundance initial commercial density commercial density trees 100ha Free Landis amp Grogan Mahogany Growth amp Yield show sum stand volume of trees show max basal area of trees show median diameter of trees with diameter lt 20 show median age of trees with age lt 1000 show y0 tree density site area 100 show y0 tree density show y comm density site area 100 show y comm density show count trees with diameter gt 60 site area 100 Note that if you are asking questions about tree ages be sure to omit trees older than 1000 years as shown above see median tree age yr These are the initial trees whose ages are unknown 1000 years is simply a marker FIELD SITE STATISTICS field site area m field site area
66. h data Note that distributions for disturbance seedling diameter and seedling growth rate can be viewed in the Model gt Data folder The disturbance size distribution is called gap data csv The seedling diameter and growth distributions are called seed diam data csv and seed growth data csv respectively EXPORT DATA export landscape image jpg export view user new file export interface 1mage pg export interface user new file export output text txt export output user new file export single plot values csv export plot tree density user new file export all plot values csv export all plots user new file export all variables csv export world user new file Note that you can name and place exported files anywhere on your computer Include file extensions as listed in parenthesis above following each export method AVAILABLE STATEMENTS math statements lt gt lt 5 gt logic statements true false statistical statements max min mean median modes with min with max patch variables disturbance sweetspot tree variables who age alive seedling fall gap reproduce diameter basal diameter basal area stand volume sawn volume growth rate mort prob fruit prob num fruit seedlings These statements can be substituted for similar statement types in the italicized commands provided above For example any statistical statement max min mean etc can replace a statistical statement in th
67. ha field site area km field site width m field site width km field site height m Show site area 10000 show site area show site area 100 Show world width 10 Show world width 10 1000 show world height 10 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 smallest basal area tree tree largest trees 50 percentile tree s HARVEST STATISTICS og trees last harvest number of logged trees last harvest total logged volume m show 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 diameter gt median diameter of trees show length cur logged volume show sum cur logged volume last harvest largest logged tree volume m show max cur logged volume all harvests number of logged trees all harvests total logged volume m show length tot logged volume show sum tot logged volume all harvests largest logged tree volume m show max tot logged volume 97 Free Landis amp Grogan Mahogany Growth amp Yield 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 number of commercial trees befo
68. he workspace where the model code is stored and modified Edit This button is only active when a feature is 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 view 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 1s on off during the simulation s Time num
69. hylla in southeastern Amazonia Brazil and implications for sustainable management Biotropica 38 219 228 Grogan J amp Galvao 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 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 Schulze M 2008 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 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 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 Galvao J 2010 Survival growth and reproduction by big l
70. ia of Forest Sciences pp 1720 1726 Elsevier Science Publishers BV Amsterdam The Netherlands Cornelius JP Navarro CM Wightman KE amp Ward SE 2005 Is mahogany dysgenically selected Environmental Conservation 32 129 139 Cornelius JP 2009 The utility of the predictive decapitation test as a tool for early genetic selection for Hypsipyla tolerance in big leaf mahogany Swietenia macrophylla King Forest Ecology and Management 257 1815 1821 Dickinson MB amp Whigham DF 1999 Regeneration of mahogany Swietenia macrophylla in the Yucatan International Forestry Journal 1 35 39 46 Free Landis amp Grogan Mahogany Growth amp Yield d Oliveira MVN 2000 Artificial regeneration in gaps and skidding trails after mechanised forest exploitation in Acre Brazil Forest Ecology and Management 127 67 76 D nisch O Azevedo CP Gasparotto L Montoia GR Silva GJ amp Schwarz T 2002 Light water and nutrient demand for the growth of three high quality timber species Meliaceae of the Amazon Journal of Applied Botany 76 29 40 D nisch O Bauch J amp Gasparotto L 2002 Cambial growth dynamics and formation of increment zones in the xylem of Swietenia macrophylla King Carapa guianensis Aubl Cedrela odorata L Meliaceae AWA Journal 23 101 119 D nisch O amp Morais RR 2002 Regulation of xylem sap flow in an evergreen a semi deciduous and a deciduous Meliaceae species from the Amazon Trees Berlin 16 404
71. ics in Brazil it can offer useful insights into post harvest recovery by natural populations throughout South and Central America The growth amp yield model uses the NetLogo 5 0 3 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 2010 for nearly 600 mahogany trees and many thousands of seedlings saplings and pole sized trees at multiple field sites in southeast Para 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 Harvest 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
72. ill 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 is 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 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 of each tree DO NOT GIVE THE COLUMNS
73. imeters 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 model software cannot read data from Excel xls or similar files 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 mara 204 tree data csv CSV Leave the Diameter 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 s
74. ite into the Site Height input box If your site is not rectangular estimate the width and height of the smallest bounding rectangle see examples p 20 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 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 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 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 amp Trouble Shooting section 9 4 below for a
75. l of the Linnean Society 122 47 59 Hietz P Wanek W amp D nisch O 2005 Long term trends in cellulose S13 C and water use efficiency of tropical Cedrela and Swietenia in Brazil Tree Physiology 25 745 752 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 nternational 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 30 637 657 Kometter RF Martinez M Blundell AG Gullison RE Steininger MK amp Rice RE 2004 Impacts of unsustainable mahogany logging in Bolivia and Peru Ecology and Society 9 http www ecologyandsociety org vol9 iss art12 Kometter RF 2011 Tablas nacionales de conversi n volum trica de madera en pie a madera aserrada por calidades seg n las reglas internacionales de clasificaci n de madera NHLA de la especie de caoba Swietenia macrophylla Par Guatemala Intercooperation Bras lia DF Brazil Lamb FB 1966 Mahogany of Tropical America Its Ecology and Management University of Michigan Press Ann Arbor MI USA Lee H Y 1967 Studies in Swietenia Meliaceae observations on the sexuality of the flowers Journal of the Arnold Arboretu
76. look like this WITHOUT COLUMN HEADERS X Coordinates Y Coordinates Diameters 579775 8 9136498 4 219 579744 8 91365861 6 79 4 568177 6 9135822 6 66 1 536265 1 9135776 8 oB 4 Trees 550300 9 9135752 5 45 5 580317 3 9135666 3 64 7 5608343 1 9135666 1 7e 5 556466 1 915355441 5 79 Read 7 Q1 FR4A F 2 di Place the new text file in the Model gt User folder Remember the name of the new text 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 19 Free Landis amp Grogan Mahogany Growth amp Yield DATA UPLOAD mara 204 tree data txt 1216 1712 Type the name of the text file from Step 2 containing spatial 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 EA Leave the Diameter 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 is not rectangular estimate the width and height of the smallest bounding r
77. lp 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 DEHNITIONS This is the DEFINITIONS box as it appears on the model Press the button next to each section to v e e_o e Baies te afa deftoitkes bas eese UNT Ge interface Feature definitions can be viewed by using the blue bar to scroll across the text content of all the sections 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 S is 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 3 JL A E All Definitions Export Results white background of the model interface Additional questions can be directed to the authors listed at the end of the Manual section 17 10 Free Landis amp Grogan Mahogany Growth amp Yield 5 A BRIEF GUIDE The following guide d
78. m 48 101 104 Lemes MR Brondani RPV amp Grattapaglia D 2002 Multiplexed systems of microsatellite markers for genetic analysis of mahogany Swietenia macrophylla King Meliaceae a threatened Neotropical timber species Journal of Heredity 93 287 291 Lemes MR Gribel R Procter J amp Grattapaglia D 2003 Population genetic structure of mahogany Swietenia macrophylla King Meliaceae across the Brazilian Amazon based on variation at microsatellite loci implications for conservation Molecular Ecology 12 2875 2883 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 49 Free Landis amp Grogan Mahogany Growth amp Yield 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 M Esashika T amp Gaoue OG 2011 Microsatellites for mahoganies twelve new loci for Swietenia macrophylla and its high transferability to Khaya senegalensis American Journal of Botany http www amjbot org e207 e209 Lopes JCA Jennings SB amp Matni NM 2008 Planting mahogany in canopy gaps created by commercial harve
79. m diameter trees 100 hectares in black and the density of commercial sized trees in red The vertical gray lines indicate the harvest years that is 1 31 61 and 91 years in the example shown Diameter Distribution Tree Density 34 80 gt ri e 3 i a Size Class Time yrs 12 Free Landis amp Grogan Mahogany Growth amp Yield 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 HARVEST PRODUCTIVITY Logged Volume m3 Total Logged Volume m3 Total Logged Trees 20 3 452 3 90 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 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 is run The MODEL SETTINGS buttons set up the initial population re set parameters to default conditions and begin model simulations
80. n 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 section 17 Free Landis amp Grogan Mahogany Growth amp Yield 3 MODEL INSTALLATION 3 1 Web Installation The following section explains how to install the NetLogo software from the Big Leaf Mahogany in Brazil amp South America website and how to run the model using the software Step 1 Download Model Package from Website Please visit our website to download 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 http www swietking org model applet html Download the zip file appropriate for your operating system Windows Mac OS X or Linux The zip file contains the files necessary to install the NetLogo software and run the model on your computer Left click on the link to download the file to your default download location 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 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 zip file and select the unzip or uncompress
81. n 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 Density plot shows the density of trees over time trees 100 ha The black line tracks the density of all trees gt 20 cm diameter The red line tracks the density of commercial sized trees The vertical gray lines indicate the harvest years that is 1 31 61 and 91 years in the example shown 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 20 3 452 3 90 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 17 Free Landis amp Grogan Mahogany Growth amp Yield 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 w
82. nor J 2005 Supervivencia y crecimiento de caoba en aperturas post extraccion en Belice a partir de semillas y plantulas Recursos Naturales y Ambiente 44 76 83 Snook LK Negreros Castillo P amp O Connor J 2005 Supervivencia y crecimiento plantulas de caoba en aperturas creadas en la Selva Maya de Belice y M xico Recursos Naturales y Ambiente 44 91 99 Shono K amp Snook LK 2006 Growth of big leaf mahogany Swietenia macrophylla King in natural forests in Belize Journal of Tropical Forest Science 18 66 73 Souza CAS Tucci CAF Silva JF amp Ribeiro WO 2010 Exig ncias nutricionais e crescimento de plantas de mogno Swietenia macrophylla King Acta Amazonica 40 515 522 22 Free Landis amp Grogan Mahogany Growth amp Yield Thiele JC amp Grimm V in press NetLogo meets R Linking agent based models with a toolbox for their analysis Environmental Modelling and Software Verissimo A Barreto P Tarifa R amp Uhl C 1995 Extraction of a high value natural resource in Amazonia the case of mahogany Forest Ecology and Management 72 39 60 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 Wadsworth FH amp Gonzalez E 2008 Sustained mahogany Swietenia macrophylla plantation heartwood increment Forest Ecology and Management 255 320 323 Walters BB Sabo
83. o 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 5 0 3 the version used to run the Big Leaf Mahogany Growth amp Yield Model can be downloaded here http ccl northwestern edu netlogo 5 0 3 The most recent version of the software can be downloaded here http ccl northwestern edu netlogo download shtml 43 Free Landis amp Grogan Mahogany Growth amp Yield 13 LIMITATIONS amp CONSIDERATIONS The Big Leaf Mahogany Growth amp Yield Model functions are derived from demographic data collected annually from 1995 2010 for nearly 600 mahogany trees and many thousands of seedlings saplings and pole sized trees 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 in large gaps are based on data from experimental outplantings across light gradients in large clearings initiated at Marajoara in 1995 These da
84. ommands 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 as follows export view word Results View BehaviorSpace run number jpg export plot Tree Density word Results Density BehaviorSpace run number csv export all plots word Results All Plots BehaviorSpace run number csv export world word Results World BehaviorSpace run number 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 is numbered according to its place in the BehaviorSpace experiment to prevent file overwriting The view image can be saved with any image extension pg 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 below will open in the center of your screen AOC Run options __ Spreadsheet output vi Table output Simultaneous runs in parallel 2 If more than one some runs happen invisibly in the background Defaults to one per processor core Cancel OK C Check the Ta
85. or timber Ecological Applications 17 323 330 Boot RGA amp Gullison RE 1995 Approaches to developing sustainable extraction systems for tropical forest products Ecological Applications 5 896 903 Browder JO 1987 Brazil s export promotion policy 1980 1984 impacts on the Amazon s industrial wood sector The Journal of Developing Areas 21 285 304 Browder JO Matricardi EAT amp Abdala WS 1996 Is sustainable tropical timber production financially sustainable A comparative analysis of mahogany silviculture among small farmers in the Brazilian Amazon Ecological Economics 16 147 159 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 Camara Cabrales L amp Kelty MJ 2009 Seed dispersal of big leaf mahogany Swietenia macrophylla and its role in natural forest management in the Yucatan Peninsula Mexico Journal of Tropical Forest Science 21 235 245 Chimeli AB amp Boyd RG 2010 Prohibition and the supply of Brazilian mahogany Land Economics 86 191 208 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 J Wightman K Grogan J amp Ward S 2004 Swietenia American mahogany In Burley J Ed Elsevier Encycloped
86. 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 pre installed on your computer free alternatives are available online For Windows users Another Notepad 1s 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 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 site the data file name if 26 Free Landis amp Grogan Mahogany Growth amp Yield 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
87. pecified for example populations and calculated for user populations in the setup world procedure The specification of example population site areas allows calculation of more accurate population densities World Shapefiles The example populations are now constructed using shapefiles that define the extent of the population on the landscape world This prevents trees rivers and boundaries from being placed against the edge of the NetLogo world boundary User Shapefile Upload The code for displaying user shapefiles was modified to fix a bug which halted the model when trees were placed on the world landscape edge The new code expands the world envelope to contain the tree envelope and eliminate the bug 65 Free Landis amp Grogan Mahogany Growth amp Yield PLOTTING The plotting code is now contained within the plots on the interface This is the convention for NetLogo 5 0 3 and reduces processing time The new plotting setup function sets the initial X and Y axis sizes to minimize auto adjusting during model runs The Tree Abundance plot has been replaced by the Tree Density plot The new plot shows the density of trees per 100 hectares over time using the symbology of the original abundance plot all trees shown in black commercial trees shown in red GROWTH FUNCTION Growth Residuals The growth function now incorporates 10 years of growth autocorrelation and therefore has ten years of growth residuals In Year 0 the gro
88. post cut number number of commercial trees before after each harvest pre post cut volume volume of commercial trees before after 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 volume statistics 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 3l Free Landis amp Grogan Mahogany Growth amp Yield 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 image file The export plot and export all plots c
89. pro prob die no seeds specifies the probability of a tree dying before fruiting 1n the year of its death establishment rate surv prob specifies seedling survival rate seed diam data seed diam list contains seedling diameter data Diameter Attribute Name D IAM Attribute Name specifies the name of the diameter attribute in a user provided shapefile Tree Variables diameter dbh specifies stem diameter basal diameter diameter specifies stem basal diameter stand volume volume specifies standing volume mort prob mort rate specifies probability of mortality seedlings surv seeds specifies number of seedlings NEW VARIABLES The following variables have been added to increase functionality of the model Global Variables small diam specifies minimum size of trees to plot monitor erowth sigma specifies standard deviation of growth residuals num batch dist specifies how many disturbances to add in batch no recruit dist specifies non recruitment distance in canopy gaps large dist specifies whether large scale disturbances occur large dist prob specifies probability of large scale disturbance large dist area specifies area of large scale disturbance 64 Free Landis amp Grogan Mahogany Growth amp Yield e seed shadow area specifies the area of a tree s seed shadow eliminates seed radius e seed growth data new list contains seedling growth data e pre post
90. r harvest X The item code numbers items in a list from zero onwards so item 0 is the first value item 1 is the second value item 2 1s the third value etc You must enter two item reporters for each expected harvest You can determine the expected number of harvests using the following formula floor time 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 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 ength 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 4 Free Landis amp Grogan Mahogany Growth amp Yield diameter lt 10 In this example simulations would stop when commercial abundance falls below 10 trees 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 Procedure Code This section provides insight into understanding and modifying the underlying model code A
91. raph displays the measure of each population metric over time 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 33 Free Landis amp Grogan Mahogany Growth amp Yield 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 Step 7 Format Data Output The Running Experiment window will close when the experiment is 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 A B i D BehaviorSpace results NetLogo 5 0 3 Growth amp Yield Model 2 1 nlogo Population Growth amp Productivity Standard Logging 01 18 2013 17 09 33 26
92. re after harvests before show n values length pre post cut number 2 item 2 pre post cut number after show n values length pre post cut number 2 item 2 I pre post cut number commercial volume before harvest x show item x 1 2 pre post cut volume commercial volume after harvest x show item x 1 2 I pre post cut volume commercial density before after harvests show map site area 100 pre post cut number the volume of every tree logged during the simulation tot logged volume the volume of every tree logged during the most recent harvest cur logged volume the total number of trees logged during each harvest annual harvest number the total volume of trees logged during each harvest annual harvest volume the total number of commercial trees before after each harvest pre post cut number the total volume of commercial trees before after each harvest pre post cut volume MORTALITY STATISTICS kill trees specific tree mortality probability show mort prob of tree 17 median tree mortality probability show median mort prob of trees live tree mortality probabilities show mort prob of trees with alive true dead tree abundance show count trees with alive 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 DISTURBANCE STATISTICS disturb trees lands
93. s 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 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 et al 1996 The example populations discussed at greater length in section 6 1 were derived from 1 a 100 area inventory of mahogany trees gt 20 cm diameter in a 204 ha subplot of the Marajoara field site 2 a randomly stratified transect survey of mahogany trees gt 20 cm diameter in 1035 ha at Marajoara 10 of the total area and 3 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
94. s on Management IMAZON Bel m PA Brazil 58 pp Grogan J Ashton MS amp Galvao J 2003 Big leaf mahogany Swietenia macrophylla seedling survival and growth across a topographic gradient in southeast Para 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 Para Brazil In Lugo A Figueroa Colon JC amp Alayon M eds Big Leaf Mahogany Genetics Ecology and Management pp 193 208 Springer Verlag New York NY USA Grogan J 2005 Mogno Swietenia macrophylla Meliaceae In Shanley P amp Medina G eds Frutiferas e Plantas Uteis na Vida Amaz nica pp 115 122 Mulheres da Mata Imazon Bel m Para Brazil Grogan J amp Barreto P 2005 Big leaf mahogany on CITES Appendix II big challenge big opportunity Conservation Biology 19 973 976 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 Para Brazil Forest Ecology and Management 204 399 412 Grogan J Vidal E amp Schulze M 2005 Apoio cient fico Par os padr es de manejo de madeira na floresta amaz nica a questao da sustentabilidade Ci ncia amp Ambiente 32 103 117 Grogan J amp Galvao J 2006 Factors limiting post logging seedling regeneration by big leaf mahogany Swietenia macrop
95. s 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 population recovery after logging 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 productivity 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
96. 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 as described in section 11 The lines following these reminders define Total 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 density commercial density and commercial volume of the population 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 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
97. should be viewed as templates when uploading your own data into the model framework You will place your data files in this folder when uploading your own tree data section 9 The Results folder 1s the recommended destination for all results exports and is the default destination for certain BehaviorSpace simulation results sections 10 amp 11 Step 4 Install NetLogo 5 0 3 Double click on the NetLogo folder to view its contents If you are using a Windows computer double click the NetLogo5 0 3Installer exe installer file If you are using a Mac OS X computer double click the NetLogo 5 0 3 dmg installer file If you are using a Linux computer double click the NetLogo 5 0 3 tar gz installer file The installer file will open when double clicked Follow the installation instructions to install the NetLogo software on your computer If you would prefer to download the NetLogo software from the NetLogo website download NetLogo 5 0 3 here http ccl northwestern edu netlogo 5 0 3 DO NOT USE ANY OTHER VERSION OF NETLOGO THE MODEL ONLY WORKS IN NETLOGO 5 0 3 Refer to the NetLogo User Manual 5 0 3 if you require additional assistance Step 5 Open Model NetLogo File If you have successfully installed the NetLogo 5 0 3 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
98. sting Forest Ecology and Management 255 300 307 Loveless MD amp Gullison RE 2003 Genetic variation in natural mahogany populations in Bolivia In Lugo A Figueroa Col n JC amp Alay n M Eds Big Leaf Mahogany Genetics Ecology and Management pp 9 28 Springer Verlag New York NY USA Lugo A 1999 Point counterpoints on the conservation of big leaf mahogany General Technical Report WO 64 USDA Forest Service International Institute of Tropical Forestry San Juan PR Lugo A Figueroa Col n JC amp Alay n M Eds 2003 Big Leaf Mahogany Genetics Ecology and Management Springer Verlag New York NY USA Mansoor M Noor NM amp Krishnapillay B 1997 Collection and handling of mahogany Swietenia macrophylla seeds for optimum viability Journal of Tropical Forest Science 9 398 410 Mayhew JE amp Newton AC 1998 The Silviculture of Mahogany CABI Publishing New York NY USA Morris MH Negreros Castillo P amp Mize C 2000 Sowing date shade and irrigation affect big leaf mahogany Swietenia macrophylla King Forest Ecology and Management 132 173 181 Negreros Castillo P 1991 Ecology and management of mahogany Swietenia macrophylla King regeneration in Quintana Roo Mexico PhD dissertation Iowa State University Ames IO Negreros Castillo P amp Mize C 1993 Effects of partial overstory removal on the natural regeneration of a tropical forest in Quintana Roo Mexico Forest Ecology and Managemen
99. t an example from Swietenia humilis Zuccarini Proceedings of the National Academy of Sciences 99 2038 2042 White S 1978 Cedar and mahogany logging in eastern Peru The Geographical Review 68 394 416 Whitman AA Brokaw NVL amp Hagan JM 1997 Forest damage caused by selection logging of mahogany Swietenia macrophylla in northern Belize Forest Ecology and Management 92 87 96 Wightman KE Ward SE Haggar JP Santiago BR amp Cornelius JP 2008 Performance and genetic variation of big leaf mahogany Swietenia macrophylla King in provenance and progeny trials in the Yucatan Peninsula of Mexico Forest Ecology and Management 255 346 355 Wilensky U 1999 NetLogo http ccl northwestern edu NetLogo Center for Connected Learning and Computer Based Modeling Northwestern University Evanston IL USA 53 Free Landis amp Grogan Mahogany Growth amp Yield 17 CONTACT US If you have questions about the model please email 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 jgrogan swietking org jgrogan crocker com More information on our research can be found on our website http www swietking org or in the publications listed above 54 Free Landis amp Grogan Mahogany Growth amp Yield APPENDIX A DATA SOURCES This research program s principal study site Marajoara i
100. t of a disturbance survive All others die and are no longer tracked in the model 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 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 63 Free Landis amp Grogan Mahogany Growth amp Yield APPENDIX D VERSION DIFFERENCES The following document summarizes the changes made to the Big Leaf Mahogany Growth amp Yield Model Version 1 0 since it was first released in January 2011 The most significant change is the upgrade from NetLogo 4 1 3 to 5 0 3 This upgrade provides improved handling of foreign characters a richer Info tab and increased speed and stability VARIABLE NAMES The following variable names have been updated for increased clarity The new names in bold provide a better summary of function and purpose than the old names italics Global Variables y0 tree density y0 tot density specifies tree density 1n initial year prop land dist prop dist specifies proportion landscape disturbance disturbance data disturbance dataset contains gap size data prob die no re
101. t 58 259 272 Negreros Castillo P amp Hall RB 1996 First year results of partial overstory removal and direct seeding of mahogany Swietenia macrophylla King in Quintana Roo Mexico Journal of Sustainable Forestry 3 65 76 Negreros Castillo P amp Mize CW 2003 Enrichment planting of big leaf mahogany and Spanish cedar in Quintana Roo M xico In Lugo A Figueroa Col n JC amp Alay n M Eds Big Leaf Mahogany Genetics Ecology and Management pp 278 287 Springer Verlag New York NY USA 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 Negreros Castillo P amp Mize CW 2008 Regeneration of mahogany and Spanish cedar in gaps created by railroad tie extraction in Quintana Roo Mexico Forest Ecology and Management 255 308 312 Newton AC Baker P Ramnarine S Mesen JF amp Leakey RRB 1993 The mahogany shoot borer prospects for control Forest Ecology and Management 57 301 328 Newton AC Cornelius JP Baker P Gillies ACM Hernandez M Ramnarine S Mesen JF amp Watt AD 1996 Mahogany as a genetic resource Botanical Journal of the Linnean Society 122 61 73 50 Free Landis amp Grogan Mahogany Growth amp Yield Norghauer JM Malcolm JR amp Zimmerman B 2006 Juvenile mortality and attacks by a specialist herbivore increase with
102. ta present optimistic estimates of juvenile performance due to manual removal of competing vines and secondary vegetation during the experiments initial three years 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 1f population growth is sensitive to observed reductions in seedling survival and growth See Norghauer et al references section 16 for more information on this topic 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 neotropical trees 14 FUTURE MODI
103. 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 ogging 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 Vary variables section has a similar structure in each experiment Population Growth No Logging is the only experiment with logging turned off because it is 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 parameters because it is designed to monitor populations under current legal management practices for mahogany in Brazil a0 Experiment Experiment name Population Growth amp Productivity
104. 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 Para 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 DIAM Site Site Data Upload Type File Name Attribute Name Width Height Patch 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 Non Spatial CSV file mara 204 tree data csv 1216 1 1712 4 1 0 The mara 204 tree data dbf file in the Model gt User folder is associated with this shapefile and is necessary for data upload using this method 10 EXPORT SIMULATION RESULTS Export Results The monitors plots and landscape features provide a means for observing simulation results in real time but these 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
105. tion growth rate cm yr 0 42 basal diameter 0 007 2 0 009 max 0 basal diameter 40 e0 where the max 0 diameter 40 evaluates to zero when a tree is lt 40 cm diameter and evaluates to diameter 40 when a tree is gt 40 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 60 Free Landis amp Grogan Mahogany Growth amp Yield 0 given the impossibility of negative growth 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 number of trees larger than the minimum commercial size without violating either retention rate or post harvest density requirements Trees selected for logging are randomly stratified across the size distribution of eligible trees Half of logged trees are allowed to disperse seeds prior to death and all logged trees create canopy gaps proportional to stem diameter based on equations in the Mortality Function section below equations 5 amp 6 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 0 083 4 177 GR 3
106. ulation can be resized using the Patch Area input and the Resize button section 6 1 11 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 and commercial sized tree volume m during Year 0 and the Current simulation year YEAR 0 POPULATION Total Density 100ha Commercial Density 100ha Commercial Volume m3 65 7 39 7 423 8 CURRENT POPULATION Total Density 100ha Commercial Density 100ha Commercial Volume m3 44 1 7 4 65 1 Current Population plots show changes in tree size class distribution and density trees 100 hectares 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 Density plot shows the density of all trees gt 20 c
107. wth residuals of previous years are randomly drawn from a normal distribution The present year e0 growth residual is calculated using a new equation derived from the incorporation of new data Growth Rate The growth function uses a new equation for determining the annual growth increment The equation was derived from the incorporation of new data LOGGING FUNCTION Year 1 Logging The logging of trees in Year now occurs before the growth function and all others logging still occurs after the growth function in other harvest years Harvest Years The logging function uses a new method for determining whether the present year is a harvest year comparing the present year to the list of harvest years This method 1s more elegant than the old harvest ticker method Stratified Random Logging The logging function now stratifies the logging of trees by diameter size class This change reflects actual logging practices more accurately Minimum Density The logging function now prevents the violation of the minimum density requirement Previously a bug often allowed an extra tree to be logged in violation of the minimum density parameter Pre Post Harvest Statistics The logging function now records the abundance and volume of commercial sized trees alive before and after each harvest MORTALITY FUNCTION Mortality Probability The mortality function uses a new equation for determining the probability of mortality The equation was deriv

User Manual 2.1 - Institute of Marine and Coastal Sciences

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