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User Manual 2.0 - Big-Leaf Mahogany in Brazil & South America

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1. 64 APPENDIX E MODEL CODE 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 dynamics 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 4 1 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 man
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16. 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 1000 show y0 tree density site area 100 show y0 tree density show y0 comm density site area 100 show y0 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 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 7 largest trees 50 percentile tree s
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18. 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 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
19. If you are using a Windows computer double click the NetLogod4 1 3Installer exe installer file If you are using a Mac OS X computer double click the NetLogo 4 1 3 dmg installer file If you are using a Linux computer double click the netlogo 4 1 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 4 1 3 here http ccl northvvestern edu netlogo 4 1 3 DO NOT USE ANY OTHER VERSION OF NETLOGO THE MODEL ONLY WORKS IN NETLOGO 4 1 3 Refer to the NetLogo User Manual 4 1 3 if you require additional assistance Step 5 Open Model NetLogo File If you have successfully installed the NetLogo 4 1 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 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 t 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 b
20. Experiments Population Growth No Logging 100 runs Population Growth amp Productivity Standard Logging 100 runs Population Growth amp Productivity Diameter Experiment 600 runs Population Growth amp Productivity Retention Experiment 600 runs Population Growth amp Productivity Density Experiment 1500 runs Population Growth amp Productivity Cutting Cycle Experiment 400 runs Population Growth amp Productivity Custom Logging 100 runs New Edit Duplicate Delete Run 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 runs the selected BehaviorSpace experiment 28 Free Landis amp Grogan Mahogany Growth amp Yield Before running an experiment you should select the Edit option and familiarize yourself with the experiment s settings The modification of these settings and the creation of new experiments are discussed more below section 12 2 Step 3 Choose a BehaviorSpace Experiment Choose a baseline BehaviorSpace experiment to match
21. Grogan J Ashton MS z Galvao J 2003 Big leaf mahogany Swietenia macrophylla seedling survival and growth across a topographic gradient in southeast Par Brazil Forest Ecology and Management 186 311 326 Grogan J Galv o J Sim es L amp Ver ssimo A 2003 Regeneration of big leaf mahogany in closed and logged forests of southeastern Par Brazil In Lugo A Figueroa Col n JC amp Alay n M eds Big Leaf Mahogany Genetics Ecology and Management pp 193 208 Springer Verlag New York NY USA Grogan J 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 Par 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 Galv o J 2005 Growth response by big leaf mahogany Swietenia macrophylla advance seedling regeneration to overhead canopy release in southeast Par 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 z Galvao J 2006 Factors limiting post logging seedling regeneration by big leaf mahogany Swietenia macrophylla in southeastern Amazonia Brazil and implic
22. TS sn suoTaeTndod Tdurex fi poz eeze eats jes eupoz ered 49 suorqaeIndod oAOqe suorsueurp oeu3 eeav uoaed zTs u qed q s A mou A M u X4MoU x M u PTAOM ezTsez Aso uot ZeTndog z sn suoTaeTndod jT pue eode yojed a3Tnez p y 5ursn 41 zTs u qed q s A mou A M u X M U x M u PTAOM ezTsez dys uoTraerndodq z sn suoTaeTndod jT suorQae ndod zesn sur ff zTs u qed q s A mou A M u X4MoU x M u pAx uoraerndoq z sn suorae ndod jT eAoqe Tepesy eua ur u ous e zv uoaed ezrs uo3qed 3es 011 OTI 9 Z 9vZ PTIOM ZTS I uozeuy a3s M x v jr ST STY ATTenuew zTs u qed a s GLI GLI 291 Z91 pTaoM zTs zxl eugceor Ied HS suorqaeTndod jr suoTra3erndod e duexe ey suorsueurp un ff eeav uo3ed zTs u qed 4 s 88 88 9 9 pTazoM zTs zxl eupoz ered AS suorqaeTndod JT 4 s sn oboT4eN eours z Aq pue 0 1 lt Z T OT auPreH earsS punoz A M u 3 T ua aunoooe oa T Aq s u qed o4 sz q u WOTF ATeAUOD OI Aq p pTATp ore z T OT 9 punoa A mou 3e A ua os sz q u p pTAoxzd suoTsu uTp qts SUL 3TS p
23. eun oA 4no 4sod eT eunpgoA 3no 3sod ead 2 x 2 weqt z 4 uqaBu T s nTeA u unToA an sd xequnu 3no 3sod eaud T Z x ue31 z 4 uaBu T x qunu an asod 3e z qunu an asod sd 2 x 2 weqt z 4 yjbueT sen ea4 u x qunu an sd 4 T tT 61 z 4 qunu an asod sd T A as Azeu AWATOA 3 94 1904 4 3urad e 13 T lt sxor3 pue JT
24. 3STp u 3e6q umnu soueqinistp edeospue uoraagodoad Tenuue un ff astp puet doid uoTanqTa3sTp Teuzou ymoI6 eua Fo uoTaeTA p pzepueqjs oy zrs Teroz uuroo ueua seer JO gu unToA burpueas TeTaTUT un umToA uuoo 04 ezrs IOJeuuoo ueuqa seer jo eu00I s zqa AaTsu p erarur urL Karsu p uuoo 04 uerp TTeus eua ueuq seer Jo euoor seeag3 AaTsu p erarur eug AaTsu p z3 04 SuoT3eTnuTs pexoega seer 3s TTeus y jo uo x q ueTp wetp TTeus un fi 2 dna s buraeorpur ue Toog v ff SIOII SLNVLSNOO TAAON 75 sTeqoT5 squebe T pou y se sergroeds STUL 00001 OOT xw T Z X SLI T Z X 291 unu eAoqv Z 1 seyojzed GLI x s uoqed 291 suorsueurq ob5oT39N s u qed ge x seyoqjed cee suorsueurq yo ued 0156 x u OSEE ey S8 G TT ee2dv pT4OM euscor 9294 AS SNOISNSWIG HaVOSONVI ey S8 SLTT c T pou erir udoagoeu eTu q rAS Aueboueu T pou p er pue uoraerndod p seq TenpTATpuT ATTetjzeds v ogur s op 1 OBoTa u np uz qs muqxou 1T daaq 1 oB ma N oboT3eN seroeds x quru Te ordoz jo sburasrT SALIDO butjuewetdwurl
25. 9 Aueboyew s TaTL ones ones ogur os rs ASO ANY dHS dAX SdVOT saz 0 i10V4ud Buraano eua eye 4s Azeu uoe usemqeq sieo z qumu eu 001 Seeada q LInwaga 19472 seer TeT z um o jo AaTsu p 08 uorqu 3 dz 0Z 1107444 1947 seer TeT z umo U uo 09 L1nVigd erodgeuuoo 107 an seer go uo s002 onmivg ANY S und TITA suorqaeTnuts T pou aA eura zo ua3bue unurxeu oua s STVEOT 4 44179 GNV HOLIMS IqEMOTTE W oT3u q z ur z qa uerp u GUVGINVILS nurruTrur nurrurur nurrurur IQ V AG eui eui eui eui TTIW uruz q p STUL SuoT3eTnuTrs T pou ede seer YOITMS STUL SuoT3eTnuTs T pou pesn sr uoTraeTndod eed4 YOTYM STYL 4490 uoqed qodsa Ms e ST yo zed e uee oog V uoqaed eouequnasrp e ST yojed e z uq um buraeorpur uee ood V SHUIHVIMVA HOLVa oBe sae A u q obe sieo ouru saqeo Qubre obe sae A u A s obe saze A xTS szeek aaTy obe sae A anoz obe sieo oo4du3 oBe sae A oMaq obe
26. 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 is 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 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 Com
27. seqep peoT ST5 01 dus eq3ep ueed4s gc0or edeu e4eq 3 seqep peoT ST5 eqep ue s3s Gg601 e eu dus eqep za G 01 ezeu eqed 3 seqep peoT sT5 eqep s3 G 01 e eur ST5 stb stb stb 39T 39T 39T 39T SooJ33 gcor ezdzeu dn43es oq s nTeA x3 dn3 s x q ueTp yes uorqaeooT T u qr 200K as uorqeooT 0 WET yes uV6Wd pu 1 20 S43STT X 4342 A ST158 4ASATF JO uorqeooT ST5 eqep z3 0Z eseu jo 3sr eun4399j sT15 uoeo10j z eqep ue x3s 0Zz eseu MeIp ado oo burMedp 3es z ea3ep Aaepunoq p0oz edgeu dus eaep pridow poz ezeu e43eg 3 seqep peoT sT58 2 dus eqep Azepunoq 0z ezeu eqed 3 seqep peoT ST5 02 dys eqep ure xas 0z eseu eqed Josejep peoT sTh eqep ure z3s 0z ezeu dys eqep za 0z ezeu eqed 3 seqep peoT ST5 ejep eed3 poz eae u ST5 ST5 ST5 ST5 ST5 3eT 39T 39T 3eT Sooead3 p0c e aeu dn3es 0 12 sITe3 q s ark dna s pu 5195 STUL s za Aso dna s Aso uotjzetTndog zesn suoTaeTndod S3es s
28. xe A qu s sd eua ur oo14 e Aq xa e Aq peonpoud Tenptsez uaxoz5 uaxoz5 zequnu zequnu pue TejoweTp wory e 5uraTn gO AaTTTqeqousd U34ox5 pue z q ueTp uo4j 9073 e 107 e jo iA uo Tenuue A q ueTp Teseq e eunqoA umes x q ueTp Teseq uozz e go Ew burpueis x q ueTp Teseq uo4gj xa e Fo zu Teseq Teseq weqs y uo OT 991 e z a uerp eua zo W 1 eez3 e ST e z uq uu deb Tey s qe zo zq z uaq uu xe A asaTa ST 9074 e I YJ YM esqeg enag3 ST 9914 e z ua uqM as Aazeu uoee ATTe TeT z unio
29. y eprsur rduex y ATF p uruz q p usd yo Jed e s3 s STYL SVHWV HOLVd IInVaAsua 5145 se ze u oqed suoraerndod ena 9 q s nzqa SIOII q s nzqa SI0II q s qos Ttj ASO e oq asnu ueN TT4 ebessou 4goesn sTej SsS I011 or or ek ueN TT 4 sarTnejg p dna s sarnejg q dna s p sTuL XOT 91 s oqruou dn3 s stun fi saord dna s stun fi sasrr p s dna s 91 3asrr 3asrp dna s stu 3sTp dn3 s stun fi s za dna s stun fi soyoyed dnyes stu stun fi sTeqoT5 dn3 s 91 fi co Sras 4 SNOILIGNOO IVILINI an eur ano dn3 s 1equnu odez uou AT3aTSO e eq snu 3 1equnu z z uou AT3TSO e eq snu U3PTM TS enzq szodzz pergroeds eq asnu eueN e43nqrJ3433V WVIG V ebesseu 4gesn eueN ea4nqr4g33V WVIG c adue jr onda 28 q s nzqa s3aod3dz q s eTTF 3X3 0 q asnu oeueN 9 I14J Bbess u z sn esT ej 91T3 d s e eq asnu weN TFA eueN eIlri Bess u x sn l 3X3 Xequeu jr sTe dus uoraerndog z sn uoraerndog z sn ureN TTA dus u dequeu Ff suorqaeTndod JT suorqeTndod JT e uo eor pue 0 1 eeav uoaed yes Aso uoTaeTndoq z sn suoTaeTndod jr 0 1 eeav uo
30. 083 4 177 GR 3 705 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 85 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 is determined by comparing its probability of mortality to a random number between 0 and 1 If the randomly selected number is smaller than the probability of mortality the tree is marked as dead Before its removal from the population a dead tree is given a 5096 chance of dying standing and a 5096 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
31. 3 T SOILSILWLS 9444 4 IHNGONW ones e rj 4eu d4gesn 9ueu OTTF eua ur uorsu ax 3X43 eu3 se Ta ebessoeu iesn 2 oq SLINSAY 1 4 os ones pue 0 Sbur pees jes 0 3arnag umu jes 0 qoaud a4rn3j Yes oni4 yes edeB TTez yes s ez cbur pees q s s za xse s za a s z 0 uoua q s z ATTenuue oq Aeyo 5 2 OS szeak ur sen eA y Fo quepuedeput st szeeX deu30 ur sen eA eseua jo uoTaeTn Te o z v seuoo4no uorae ndod qeTzuT AT3 Onpoxzd x uou e ueua os ze A Az A jou s nTeA s ur d as 3ax u eua ut deas eura yore jo pue eua qe s TqeTxeA s un 1 9 9478 444 ex en on on on ex on on on on pue u z5 zoTood q s 6aodsa Mss 3es c30ds3ee4s YATM soyo zed yse zoTood q s es eg oueqanastp 3es ceoueqanasrp yATM seyo zed yse sdeb saowez oq ze K e ueua xou seq yodsqeems AOU s oueqanastrp Z aT N ATIenuue edeospue y soouequnisriq SHONVGH OWHLSIG rw 1 uar s zq 459 s x3 Aou z oq uoT3eTndod y
32. 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 Management 58 259 272 Negreros Castillo P amp Ha
33. 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 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
34. 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 1 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 v A B 71 3 79 4 66 1 80 4 45 5 64 7 72 5 79 Trees DONO ub Ww M A1 Diameters must be measured in centimeters cm Tree diameter measurements should be taken at 1 3 m above the forest floor or at least 30 cm above the reach of the tallest buttress Step 2 Save As CSV File The 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 th
35. 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 37 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 before 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 1 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 1 pre post cut volume commercial density before after harvests show map site area 100 pre post cut number the volume of every tr
36. NetLogo will provide a richer reference section in the Info tab support for international characters throughout the model application and improved performance and processing time The online version of the model will be updated as the computer version of the model becomes more compatible with the web server and applet export services 44 Free Landis amp Grogan Mahogany Growth amp Yield 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 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 Par generous logistical support has been provided by the Marajoara field site owners Sr Cla
37. ST 31 z q urerp eode Teseq s qeTn Te uorqounj STYL eor pue 60 298270 Z96600171 0 3STT xeu qzod rx uerp uerp ieseq o eo TIT3S ST anq ATUO 9407 44 1 40145 UT pesn sr qI x q ueTp Teseq uozj x q ueTp s qeTn Te uoraoung I dT Y STYL pu Z966001 1 60 2 8270 wetp Teseq 0 3STT xeu wetp Teseq uerp o eo SIGduHS HSWHdSIG pue 4 1 ut p sn ST 3I z q uerp WOTF Teseq STYL pu eu5TS u340135 0 Teuzou uopuex OIX x 98 1211610 6X x TS 868170 8X x T8T A4S9Z 0 LX x 1298882070 9X x 9 0 SX x LZEZEOET O PX x A4Z91197070 EX x 8SS 18070 ZX x L91802 0 IX x 06691666 0 qzod z OIX 6X 8X LX 9X GX PX X ZX IX Qe orieo a2odez o43 94449 49444910 pue 974041944 41 44 940 7 4 4 1 40149 UT pesn sr qar 9 eua yAMoIb aze A au s sd g eua s qeTn Te o OF OIWO uL ens rS 6 qsed Ado qsure5e e Ado pezr egqqueo T5B5uTs v T pou y seoe id Auew ur p qeTn Te ey
38. T l aT 200K jas uorqeooT 0 WET I1OOX aS 1 929 61 ASATF 6 3 T 1 eaep xa z e 9 T 6 6 dus eqep pmzou zoe eqed 3 seqep peoT sT5 dus eqep Azepunoq z oe eqed 3 seqep peoT S15 eqep Azepunoq z e WaT dus eqep xa z e eqed 3 seqep peoT sT5 eqep sa x e T s z3 z e dn3 s oa pu s nTeA x3 dn3 s Hga 6 jas uorqeooT T u qr 200K as uorqeooT 0 u qr 1Toox aS 1 20 S3STT X 342 A ST5 4ASATF JO uorqeooT ST5 1 e3 p eeda3 gcoI deu JO 4ST eAnzeez sTH 01 z qeT 3 s ST qar esneoeq 0 3Tn42 FO ASqunn 193e9T 2195 ST AT sne q 0 BuraTn uq z qaeT 39S ST art sne o q 0 ATTET3TUT z qaerT 39S ST qat sneo q 0 ATTET3TUT uaMoz ATT TIT38 sdeb 9ej qe dzO s
39. area is calculated using the equation for the area of a circle a nr The zone of recruitment that is the area of the disturbance available for seedling 61 Free Landis amp Grogan Mahogany Growth amp Yield recruitment is estimated to be 10 m shorter in 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 batch disturbances to add to the landscape 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 batch disturbances 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
40. 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 Procedures tab of the NetLogo interface The structure of the model code is summarized in Model Procedure Code section 12 3 and reviewed briefly below The head of the model code provides basic information about the model 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 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
41. eTT3 3urad eTT3 rS enz3 SOILSILVLS eun oA erodeuuo AqTsueq Teroaz ulloO oouepunqy TeT z unuo AaTsu q TeqoL oouepunqv TeqoL SOILSILVLS sxora3 cgu T eunpoA uuo2 0QA uorsroead eu 001 Seeza3 I Aarsuep uuoo Q0A uorsrioeud s xa 0 001 eeze eqts x AaTsu p un oo 02 10077 eu 001 S9913 1 Aarsuep eedg3 04A uorsrioeud 0 001 eae ears x 10077 eun oA erodeuuo AqTsu q TeT z unuo oouepunqy TeT z unuo AaTsu q TeqoL soouepunqy TeIOL 4SOILSILVLS O SOILSILWLS NOILWINdod FT DLSZAHVH os NOILVIQNIS SIHL du5501 AAAM SHAUL ON NO 444 LON SVM NOILONNA AHL sxeoA r A B5ura3an eU 001 s za rerodeuuoo AaTsu p umnururTur rerozgeuuoo qez uorqu q i uo z q urerp umurruru bur33n5 AqTsu q umnururw
42. 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 ifemp e n item post h1 item pre h2 item post n2 where 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 1 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 1 pre post cut number number of commercial trees after 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 is 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 inclu
43. 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 Hern ndez 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 Par 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 Amaz nia Brasileira Ecologia e Perspectivas de Manejo Mahogany in the Brazilian Amazon Ecology and Perspectives on Management IMAZON Bel m PA Brazil 58 pp
44. n 87 shape 0 6127 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 is estimated as a function of current year stem diameter and diameter increment in a generalized linear model with a gamma error term The gamma distribution function is parameterized with the scale and shape factors alpha a and lambda A The c value is a constant 1 142 while the 2 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 gi
45. 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 1 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 is more elegant than the old harvest ticker method Stratified Random Logging The logging function novv stratifies the logging of trees by diameter size class This change reflects actual logging practices more accurately Minimum Density The logging function novv 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 derived from the incorporation of new data 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 t
46. on your computer Table of Contents Model Schematic The model interface as it appears when installed on your computer 3 I MODEL INTRODUCTION L A L 5 2 MANUAL GUIDE anl a a obese Rs 6 7 3 Webinstallatiohia 7 2 2 nlme Modela pa as na aun mas ana qa h san aa a u hamusa 8 A HELP BUTTONS ZS aS 10 5 A BRIEE GUIDE a Awa ia bre eit V bo UE 11 6 MODEL SETTINGS 13 61 Setup amp Resize Initial Population cei ied hath rident 13 6 2set p Run Simulations 14 7 M o que poa M Y eate tea MO Mie enin 15 SIMULATION RESULTS R A tee 16 Population Memory ati ma l 16 8 2 Population Plots a nanasqa n ht a n de cq rne dee aeu deg 17 8 3 Harvest Productivity Monitors ean 17 9 USER DATA UPLOAD 18 9 1 Spatial Diameter Data User Spreadsheet deter qase Oei Weber ela 18 9 2 Spatial Diameter Data User Shapefile Pria d 21 9 3 Non Spatial Diameter Data User Spreadsheet 23 9 4 Error Messages amp Trouble Shooting a 25 9 5 User Data Uplo
47. pTAosd z sn y go 1 lt Z T OT 9 punoa x M u suorsueurp y uo p seq PTIOM oBom3 N eua jo SUOTSUSUTP Y qeTn Te suoTa ounz eseuj z 1 OT U3PTM 3TS x Aa u SNOISNSWIG dn sags p zoM dn3 s p s uTT e AT sne o q M rv q dn3 s ST TQ TZ A STYL 1 FO s uTT Le seuirnbed qar esneoeq dn3 s ST e qerzeA STYL eqep ueTp p s go s uTT e s zrnb z qt esneoeq dn3 s ST e qerzeA STYL eqep oueq n3sTp s uTT e qt esneoeq dn3 s ST e qerzeA STYL e zxe aqTs as Aazeu uoe 193j9 930gjeq eAr TeT z ummo g gu unTOA eua FO ASTT V ff 3STT eunqoA 3no 4sod eud q s 215 yore 193j9 930g9eq SATTe Seezg4 TeT z un o jo iequnu y go 2911 V 3STT aequnu 4no 4sod eud q s qyseazey uoee seer jo x qumu uns uq jo 2911 V STT Zequnu jseazey Tenuue jas 4S Azeu uoee Buranp seer Fo cu seun oA Burpueas uns y 2911 V ff STT ounToA jseazey Tenuue jos as Azeu qu o rz sow y seer go Ew s umToA HhutTpueqs y zo 4911 V 4 4STT yes sas Azeu 6 ie
48. 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 yahoo com group netlogo users The NetLogo software comes with a Models Library available in Files gt Models Library in the NetLogo menu These models can be used as examples or templates for learning the NetLogo language modifying the growth amp yield model or creating new NetLogo models NetLogo 4 1 3 the version used to run the Big Leaf Mahogany Growth amp Yield Model can be downloaded here http ccl northvvestern edu netlogo 4 1 3 The most recent v
49. 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 shapefile and has the shapefile extension shp A DIAM Attribute Name must be specified You selected the User Population shp option which requires a DIAM Attribute Name but the DIAM Attribute Name field is empty Please provide the name of the shapefile diameter attribute 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
50. 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 Par 204ha 204 ha field site with 158 trees SE Par 1035ha 1035 ha field site with 745 trees Acre West Amazon 685 ha field site with 81 trees SE Par 204ha and SE Par 1035ha present spatial and diameter data for mahogany populations in southeast Par Brazil The forest management and long term research site called Marajoara is located 34 km northwest of Reden o Marajoara was selectively logged for mahogany during 1992 1994 The population in 204 ha is from a 100 inventory for mahogany trees gt 20 cm diameter The population in 1035 ha contains the 204 ha population but at lower sampling resolution representing gt 80 of trees gt 20 cm diameter in this larger forest area Most of the trees presented here are logged stumps For more details see Grogan ez al references section 16 Acre West Amazon presents spatial and diameter data for a mahogany population located 40 km south of Sena Madureira in the wester
51. 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 parameter values Step 3 Set Logging Parameters To simulate the population with a harvest regime select logging On otherwise select logging Off If logging 1 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 L Step 4 Setup Initial Population S Establish the initial population on the landscape The population will appear on the Setup model interface in the landscape middle field The landscape population can be resized using the Patch Area input and the Resize button section 6 1 B 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 a
52. 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 Q3eep sar U3p p MOpeus pees s xza e go eu eurn e ze Mopeus p s y ur 5urarn zoz q za e AaTTTqeqousd eui sar Jo ze K eua ur burpueas 5urAp e zo 4 eui 6 s oueqanasrp go eu oui e eui 4 4 SuoT3eTnurs p qu u Tdur eze s oueqanasrp uee ood V suoraeTndod zesn pue e duexe uqoq SATS 5 eua zo eu 2 24 z 2 ezeolezeW eua FO uoranqrdasrp zu ezrs deb un ff eqep oueqanasrtrp rqrssodur sr u TuM ur deb e u oueasrp un 3asrp 3arnao 1a ou uoqeq ur eouo qe edeospue eua uo eoe d o s oueqanastrp z qumu sayy
53. 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 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 nam
54. 10 4 0 q s IUnvaua s 34rsuep umururiu q s sn nvasq 02 3ex uoT3au q x 3es 2 09 z q ureTp umnurruTu q s snunvauq 7 001 ewTL 3es sLn nvasq 2 enda yes sLnunvauq GL Z e rzv uoqed Wes Lunvaud 21 9 2 9194 AS suoTaeTndoq yes 4 44 44 4 THCOW GNV 9444 4 154 1707440 dN SLAS 48 T 4e x SI1OQIUuOU oeg3za qur eua uo pe Ae dsip se qerdeA uoTaeTndod 3aord eouepunqe pue uoranqT 3sTp 1 4 WeTpP SOTTZ ur BuTpe x Aq suoranqidasrp yAMorb ezts bur pees e Tj e ur BuTrpe z Aq uoranqraasrp eouequnaisrp 4 eouequn4srp uoaeq eua sz q uexed uoTaeTndod p aq T s y uo peseq 30ds3ee s eouequnasrp ou queuuodrAue 3s940j aTnez p uoTaeTndod p aq T s eua uo peseq suorsueurp PTIOM seTqetzea TeqOT5 queasuoo eua jo sen eA 0 aze A uo ur3 Y soeoueApe oua dn ses oua dn sa s oua dn ses oua dn ses oua dn sa s oua dn sa s y dn sa s oua dn sa s oua dn sa3 s s razna s uoqed s48STT oB oma N eua sae T Kzess o u eq ATqeqorzd TTA butztsey oegz qur OY UTYATM sat edeospue eua 2y eunsue o suoTaeTndod zesn uoqed TTeus e s3es STUL Kzess o u oq eu pue Axorurgj ede ey f oeyz quT T pou
55. 3 uuoo umu eqezsqas umu 3911 2911 29 29 3 T it SI zTs uTq 39T 330s see413 uuoo ze Jo z qa uerp gt 16 Aq axos 320s sooe343 umoo q s Soo414 uuoo 4430s 3410S soo44 uuoo S 4STT ad20s seed43 uuoo 3 T AaTsu p unururu JT rerauedgeggip aunoo an unu xeu ano umu xeu 3S5TT uru an TeB T xeu 001 Karsu p ano xeu 4asod Aarsu p unururu 001 eeae ea3rs 2 Aa3rsuep 4no xeu 4jsod 001 x eeqie e4rs seeda uuoo umnu seed4 uuoo unu y qea BoT 3no umu xeu seex4 uuoo auno s zqa uuroo umu a3e3euerp unururu lt z qa uerp ua r s q3 unuo 39T 39T 39T 39T 39T 39T 39T 39T Hmunquooua SONVSH LSIG TVNId pue 476 4 Aq ua sp x uoru peqanistp sem edeospue eua zo 3STp doad SX T3 399a UL qurad I 001 T rteo5 uoaed asrp nza uo3ed asrp q T p s u aqed quno enaa34 uo3ed 4srp uorsroeud a3srp doud 4 6 nsa u qed 3s
56. 30 d aueagdno 3es S3oI d e43epdn oq unurxeu y o 0 uozz spu qx pue d qs ura xze A uoee ST zTs TeToz un o Hutyrew eur uL SUTQ XZ q ueTp wo QI oqur HVIQ TTVNS eua ueua seer 62 14 pez ur uMous UOTAnqIJ4SIp ezrs qQuedagno un werbo sty UOT4nqIJ4SIp ZTS oa s qepdn sToxauo epoo STYL deqs ura reek Az A sord eua s qepdn uor32es STUL SLO Id 9841744 x en on on on sx on S x en on on on on on sx pu xeu A joTd 4 4 0 16 4 dn u d aord Kerb xaoTo u d ao1Td 3 s 0 pou u d 3oTd a3 s s e A 3s Axzeu uoeo10j T etoAo bBuraano x 12 1 T urn saze A 3s Azeu J4exX1ew ILJA 3S AZ H 001 x e ze qTS lt z q uerp u3r 4 qunoo 14 pex 0 pou u d 3oTd a3 s S xL IO42euuo uoed 3o d 4ueagd3no 3es 001 x e ze qTS umeTp TTeus lt Zz q ueTpl u3r qunoo ord xXoerq azoioo ued 4o d 4es 0 epou ued 4or d 3es S IL Te3oL ued 3o d 4ueudno 43es 01 001 x eeae ears qunoo punoa 0 Bbuea A aoTd 3 s eurn 0 ebueza x 3o d 3es AaTsu q xL 2014 unurxeu eua o3 0 uo
57. 3IA 94TUA ut Azepunoq e4TS eua sMeIp STYL oBom3 N SYR jo qu ax eua s3 s STYL 3STT ObOTION UT SIS sez0 4s STUL 29 OBoT3 N UT AZepUNOd 910 s xo3S STYL 3STT OBoT3 N UT 9 SID S I04S STYL 29 ObOTION UT dzq SI s xo3S Srur LOId VHTOZ VHVODVHVW 9444 40 SLAS eqep YATM e uo peseq uoTraeTndod e dn eqep z q ueTp pue Ax yATM erirgj dus e uo peseq uoTraeTndod e dn e43ep z q ueTp pue Ax uaTM 9T IJ 3X4 Aesn e uo p seq uoTaeTndod e dn 8002 Te ueboz5 uoTaeTndod Aueboyeu uozeuy 3s M z v eua dn 1002 ueborz5 uotzetTndod Aueboyeu ezeq eugcor eua dn 100Z ueboz5 uoTraeTndod Aueboueu ered eupoz eua dn saes SNOILWINdOd 44 LNSHHJ4IG AHL an x on on sx on s ex en on on ex os on on x on on on on s TET ex on en on on s OTT ex es oen on en en on on s d qs eura zeo A Az A 4 oueqanasrtrp eua Aq de spueT eua oa peppe eniq zoro Buruesp 3 s T 01 o doT AU ST5 dus eqep priagow gcor eaeu e43eqg 3 seqep peoT sT58 1 dus eqep Azepunoq d 01 e4eu eqaed 3
58. 70 SPPO TITY 3 T Bur55oT 1943 S007 zTs TeT z um o JO WNTOA pue z qunu y spaooed po STYL xl pue STT O43 p qs Azeu seer jo eoun oA uns Sppv pue 4511 p aqs Areu s a JO adequnu uns Sppv enz3 s z3 TIT3 eun oA 34no 4sod edqd 1 ATTe s xa unuo umT1oA pueas uns uorsro zd ndg eun qoA 4no 4sod edd yeas eAr e seezg43 uuoo qunoo ndg x qunu an asod sd jas enia G ATT YATM seed43 uuoo eArI So944 unoo q s un1oA 3s Azeu Tenuue T uns uotstoezd ndg unToA 4as Aa zaeu Tenuue yes 1z qunu qas Azaeu Tenuue andr xz qunu 3s Azeq Tenuue 5 ATTE U31IA S rzqa JSV OF ones s za Aq 4 ATuo ST ednpeoodd stuL nza SNILIQNJ JO ALI IIgSVHONHd SaALWINOTWO ones ceonpoade4g uaTA yse sbur pees eseu4 seszedstp pue e Aq peonpoad jo y stuL sarnag z ua uA s uruz q p pue Burarnaz sium udqndquooua NOILOfGONdsW eupoz B5urunsse qodsa ms ur eu Z AO 9 YATM eo
59. ATTET3TUT Spees burArAunS I93 T 39S ST qat esneooq 0 ATTeET3TUT x qumN X 3 T 3 s ST AT esneoeq 0 ATTetatut A34TTTqeqoxd BuTaTn uq z qeT 3es ST qart sneo q 0 ATTET3TUT AATTeIIOW 2961 BuTTp s eua sr qez u3A4o45 ON TIT3s 6496 ea3eedo seer eT TUT ON s5uTTp s TTV TIW szeek 0 s5uTTp s TTV pedo oo seer S xa se pedeus soeur uo p seq pezrs ode s zxLn x q ureTp WoTF sr cu eunqoA umes z q uerp WOTF sr gu unToA 9 z qa uerp uozz sr zu eseg z qa uerp Teseq eua ur st uo x q umeTda 3STT Zeqowetp BuTTp s y uMeAp St uo x q ueTp Teseg D e lt s lt on on on on on on on sx on su su sx on su s on s su s sx s su x s s s s ATA nS 30ds3eeAs ur burpue 6 ATuo fqodsa Ms 3au uarnao z ngjsseoong e uruarA qurod wopuez e B rx Td pouq u paepue4s y 5ursn eouejsrp wopuezr e pue 092 O 0 uz UOTIANGTAASTp eua uo4j wopuez e Aq sp s s sa ds
60. ATwopuez oq pesn st STYL pe z p u do fi wo UT sa qa uerp eseq sz q ueTda d3o3ouerp e Sbur pees mou ubrsse oq pesn st STYL pe x peuedo 9191 HLMOND 8 WVIG 4 9 NI SAWAN ur sdeb eqep sty uo peseq sr uorqoung uoranqrgasrp euueb oueqanasrtrp eup d3esn eua OF Tq TT AB peu sr anq T pou y ur pesn ena3oe qou ST STYL pe x peuedo VLVG HONVSH LSIG NI SAWAAN 200 D eonpedq 4srp uo3eq x eeae 34srp ueeu eonpea asrp doad y en eA eua JO 566 ATuo Aq z qumu oueqanasrp oy onp x eu0001c s qTs as BbzeT uL S aqTS ASeTTews ueua ss T Zequnu oueqanasrp yoreq eua sezrs I IVLT ezrs aqars uo spuedep eua jo qu ax ua zoz z ua oueqanastTp UT SINS I ued s qars 9 US UT s oueqanastp Auew oo Aq yes zog urebe eq snu s uoqaed oueqanasrp jo zequnu eui ears pierg eua ueua AebzeT edeospue eagra3ue qq go eu y ST STYL euueb soUeqINISTp eua WOTF UMeIP seouequnasrp jo zu ueou y ST STUL uoaeq ur euop eq oa eoueqdunisrp edeospue jo uorqdodoad y STUL z qa uer
61. E 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 Running Experiment Population Growth amp Productivit o normal speed 10 count trees B 1 count trees with E El 2 count trees with 2 3 sum annual har B C 4 sum annual har amp El s annual harvest 8 6 annual harvest Run 4 of 600 step 53 Total elapsed time 0 04 06 Logging true minimum diameter 40 vi Update view vi Update plots and monitors Abort The graph will only be shown when measuring every time step therefore you will only see this graph if you change the default experiment settings The graph displays the measure of each population metric over 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 pleas
62. 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 amyjbot org e207 e209 Lopes JCA Jennings SB amp Matni NM 2008 Planting mahogany in canopy gaps created by commercial harvesting Forest Ecology and Management 255 300
63. L eua TTE JT buruund sdojs T pou eun ST eura doas y JT buruuna sdoas epou un uuqndasoda 7440 D ex on on on on on on on on on on on on on SUTTINO MOZ p XOT S3o d e43epdn sdeb oAouei1 s s3 Aou dz s xa npoxd z s za qanasrp S9943 ITlT3 M s z3 Mox5 S9913 3eso1 3arur s z3a B5orT doas s xa qunoo jr doas uTL SX T3 JT T pou unz S93n3e93 Y o3 1e3euerp umnururu lt z q ueTpl 001 x eae ears z q ueTp umnurTuTu lt 001 x B ze aTSs weTp TTeus lt THQOW NNN p SuoTa s TTE FO 4u Ta3d4 3nd3no i suorarurj q TTY SsSeadd xoq uorarurgjep STY ur a3urdd and4no 8 UO0T1329S ou4 go suoTadTa s p META UuOI329S uoe oq ax u uoaanq ey ss zd 3uTad andano s za zo L umToA pueas1 uns eun oA uuoo2 0 A es 1e3euerp qunoo AaTsu p unmoo 04 yes 1e3euerp seer qunoo AaTsu p za 02A Jes unToA pue Aarsu p erodgeuuo2 9 303 se qerdeA TeTaTuT y dn sies po STYL T x 16 1 ones uo u s oqTuou dn3a s oq epou y uo saoaruou y ur uMous A s 14 dna s if pu xeu A j
64. 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 Encyclopedia of Forest Sciences pp 1720 1726 Elsevier Science P
65. SALIO OLLI s a s e 9943 peeuq os uorsu ax po SI y uo SUING STYL st6 suorsue3xe e SXISVINVA 44 saad SNOISNSILXX 00001 OOT Z X OTT x T Z X 9v2 VHMV ANUL Aoqe Z 1 s u qed 011 X s u qed 9ypz suorsueurg oboT3eN s uoaqaed 122 X seyoqed g6y suorsu urq yo red u 0122 x W 0667 ey S6 601 9euv PTIOM eusg9 uozeuy z ov SNOISNHWIG XdVOSQNV I ey S6 60T ex on on on on 200 00001 OOT x T Z X gg x T Z X 9 VHuMV ANUL Aoqe Z 1 seyojed gg x sayojed suorsueurg OboT EN soyoqed LLI X s uoqaed 21 suorsueurg yo ued w OLLI X u OLZT ey 6L vcc 9 eupoz ered AS SNOISNSWIG HaVOSONVU eu 61 22 ID ID rw aya Aq You sobpe deospueT y sp s ixoq e uTu4TA p urequoo ST un zenbs ui x WOT e ST uoa3ed uoes OJNI HdVOSGNV I xl ol 15391 18 euggo uozeu 3s M zov eu 001 s z3 2 88073 STA 9 9601 9294 HS ey 001 Seedga G LL see2a3 BGT 9 2 pred HS ALISNHG HZIS WANY SNOIZLV IndOd eu 001 Seeza g TT os e en aLII sasn Azas zoq TeotdozL jo qnaT3SuU1 ueboz5 seuep sTpuen M ua4aey u AeydoystTazyD sadouanv 0 Z uorsaoA T pon
66. Tp JT geoueqanistp s uoqed quno nza uoaqaed asrtrp 3 T s u qed qunoo x 3sTp pueT doqd Teo58 u o3ed 3sTp 3 T sodeospuet ITeus uo ATTeuoTseooo sueddeu sty edeospue y 5 4 oueqanasrtrp yo eq eua JT d3esn y S TJTJOU epoo STYL z pex zojTood q s n 6aodsa Ms jes estes z30ds3ee 4s aTA OT 6 sayojed xse 0 snrped 3eeA4s IT pea zoTood q s n zeouequnasrp jes zeouequnasrp surpea asrp seyojed yse 3srp arnadoed ou 6 AST prsur 4 TNq ST qodsa Ms eua pue suoTraeooT e ur aTTnq s oueqanasrtq e ze qrs eua jo uor4oung e ST Aoqe p uruz q p s oueqanastp go dequnu un ouo qe Te edeospue eua seouequnjisip eua sprirnq pue uoranqrdga3srp euueb e uoij s oueqanastp yo eq eua sA edp eagnpeoodd STYL d4undadoOoWud AONWAYNLSId en en sx s on x on on on on on uo p uzna ST eouequnasrp y JT edeospue uo eouequnasip e s oeTa peep T r agnaeu 09 pue Tes 4247 peep punoze sdeb spttng P TIST36S ST oueqanastrp tT jun eura e qe euo edeospue uo seoe d eouo qe seouequnasip I9 e
67. USER MANUAL for the BIG LEAF MAHOGANY GROWTH amp YIELD MODEL Pad Years 70 ao CHRISTOPHER FREE R MATTHEW LANDIS JAMES GROGAN Copyright O 2011 by the Authors Support for model development and publication provided by USDA Forest Service International Institute of Tropical Forestry ITTO CITES Program for Implementing CITES Listings of Tropical Timber Species On the cover A big leaf mahogany population 204 hectares in southeast Par 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 ALIALLINGOUd 1S3A8 VH 06 95 66 52241 mol gw tunioA p 55o7 mol gw 001 Fu 001 n o Ayisu q IL 619 es B s sim s AINT SUOT329S 943 110 Jo HWY LIV SS24d xoq uol41ulj p SWJ ul soumjpo M TA UO11235 t 0 JX U VOJINA Y 55944 SNOLLINIJ3G ka NOILW1NdOd 14344 02 268 259 auin oA 212 24001 Aursuag eww 6400178 Asua eo L NOILW1NdOd 0 Qvolan viva SONILL3S T3GON stuns uoneuuoju ETR Z uona P o Model Schematic The model interface as it appears when installed
68. 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 T 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 issl 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 Arboretum 48 101 104 Lemes MR Brondani RPV amp
69. 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 pr 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 and 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 the diameter data in the DIAM Attribute Name input box The diameters listed in the shapefile must be measured in centimeters cm Tree diameter measurements should be taken at 1 3 m above the forest floor or at least 30 cm above the reach of the tallest buttress 21 Free Landis amp Grogan Mahogany Growth amp Yield Type the width X in meters of your site into the Site Width input b
70. a3ep uerp pees 3ndg eqep ueTp p s q sllspu ae TTy you elru ASO 3ep urerp peoes e43eq u do TT2 3STT eqep urerp p s jos S3STT p s dn3 s oq pu eso 2 e1173 eqep soueqinistp ndz eqep oueqanasTp a3es zpue 3e e 1r3j you ASO ejep deb ejzeq 3ST1 3ep eouequnasTp yes 3STT1 3STp dn3 s oq sasrT z qa uerq BuTTp Ss oueqanasrq dna s os pu 3srp pue doad 00001 eeage end3 3sTp u aqeq unu jes 10950 eonpea asrp uoaeq 3es 0G gt e x nx3 jT 10250 S 02 gt JT 10850 3es 008 gt eeae enda JT s8 0 eonped a3srp uo3eq yes 0G gt eeade enda3 JT 06 0 eonpeag isrp uoaeq S 0001 gt JT 6 0 49T ID xu rw 001 s uoqaed qunoo T GSOG8E OIT ezge asrp ueou 3 T 2 8 0 eonped asrp doad 3 T 3sTp dn3 s oq sz a uezeq oueqanasrq uoaeg dna s os rs ones on pu OT 69 g L g G po z T Qe o eo g aes Teudxou uopue3 Tewzrou wopuez z 6 Tewz0u wopuez 6 yas Tewzrou wopuez yes 6
71. ad Examples us aa uu etc lecti daaa 26 10 EXPORT SIMULATION RESULTS 26 11 SIMULATION EXPERIMENTS BehaviorSpace 27 12 ADVANCED USERS amp NETLOGO RESOURCES 36 12 1 Command Line Code cese rete ree Vest ee ring 36 12 2 Modifying BehaviorSpace Experiments 40 12 3 Mode Procedure esate east ese qc apostata deua 42 12 4 NetLogo ade Sa ar tei aot de 43 13 LIMITATIONS amp CONSIDERATIONS 44 I4 FUTURE MODIEFICATIONS 44 15 ACKNOWLEDGEMENTS 45 16 REFERENCES amp SUGGESTED READING 46 17 CONTACT ad 54 APPENDIX A DATA SOURCES 55 APPENDIX B MODEL DETAILS amp DEFINITIONS 56 APPENDIX C MODEL FUNCTION S 60 APPENDIX D VERSION DIFFERENCES
72. aed yes dus uorqeTndodq z sn suoT3aeTndod jr 0 1 eeav uoaed 3 sl pAx uoTaeTmndoq z sn suorqeTndod JT o9 0 eeaxv uo3ed Jos uozeuy 3s M z v suoTaeTndod JT 00 1 eeav uo3ed 3es euccor 0194 45 suoTqeTndoq jT S9 Z eeav uo3ed yes eupoz ered AS suorae ndod jT e ze uoqaed 3 s zrs u 3ea aeg 14 pu Jequnu oz z uou ATTSOd e eq asnu eeiy uo3ed ebessow zesn 0 gt e zv uo3 ed JT bess u z sn 0 gt quBr Hn qtS JT Bbess u z sn 0 gt u3pTM 3TS JT ASO 62 qu u jr Aso uoTaeTndoaq suorqeTndod jr odeospueTj dnies p SI0II x sn ueu oo se ze qts 4T qns o3 oot Seuoaed aunoo eaze aqTs jes Aso uoTaeTndoq suorqeTndod JT zesn oy burMo esneoeq xoq oBborm3 N eu3 oot Seuoaed aunoo e ze aqTs jes dus uoTraeTndoq z sn suorqeTndod JT jo eed y se ST s aTS peurgep desn jO eode un fi ool s qu qed unos e xe aqTs S pAx uoTraerndoq z sn suorae ndogd jr eed4 y np x pue aTS oua eseodour sooeds 11 s89 6 jes uozeuy 3s M z v SsuorqeTndod JT s un s rzepunoq p 4OA pue o4rs y ueo 4eq sooeds s qe zo AeTNbuejoer e 1 SCoT 3es uG66 01 gIed 49 suorae ndod prsur s qTS oy 5uT33T2 sneo q se ze
73. al 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 is always 10 cm diameter 11 SIMULATION EXPERIMENTS BehaviorSpace The NetLogo BehaviorSpace tool allows users to easily run repeat simulations of the Big Leaf Mahogany Growth amp Yield Model using either constant or systematically varied harvest parameter settings The BehaviorSpace tool thus enables users to examine the outcomes of multiple harvest regimes with statistical confidence repeat simulations and methodological ease automated process Results from these simulations are then tabulated into a spreadsheet for analysis 27 Free Landis amp Grogan Mahogany Growth amp Yield The following section explains how to run modify and analyze the seven built in BehaviorSpace experiments Step 1 Define Model Parameters BehaviorSpace experiments will systematically vary the harvest parameters but you must define the other model settings before running an experiment Define Populations Logging and Time on the model interface according to the directions above section 6 2 If you intend to simulate one or more harvest regimes be sure that the Logging switch is turned on Step 2 Open BehaviorSpace Open the BehaviorSpace tool by selecting Tools gt BehaviorSpace in the NetLogo menu The BehaviorSpace window will open in the center of your screen aA BehaviorSpace
74. ame Site Width Site Height Patch Area Resize DEFINITIONS All Definitions Export Results volume of trees logged in the most recent harvest m volume of trees logged in all previous harvests m number of trees logged in all previous harvests name of user data file with diameter and or XY data name of the diameter attribute in the user shapefile width X of the user field site meters height Y of the user field site meters size of the patches on the landscape pixels resizes the landscape based on the Patch Area listed displays the definition function of all features on the interface exports simulation results to a user named and located file 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 601 v 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 This pop up menu specifies the Command Center mode t 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 Com
75. and 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 44 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 Connor J 2005 Supervivencia y c
76. aring 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 is mahogany The importance of a taxonomic framework for conservation Botanical Journal of the Linnean Society 122 47 59 Hietz P
77. ations for sustainable management Biotropica 38 219 228 Grogan J amp Galv o J 2006 Physiographic and floristic gradients across topography in transitional seasonally dry evergreen forests of southeastern Amazonia Brazil Acta Amazonica 36 483 496 Grogan J 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 Galv o J 2010 Survival growth and reproduction by big leaf mahogany Swietenia macrophylla in open cle
78. atitude 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 look like this WITHOUT COLUMN HEADERS X Coordinates Y Coordinates Diameters Y Y Y 579775 8 9136498 4 71 3 579744 8 9136561 6 79 4 588177 6 9135822 6 66 1 580265 1 9135778 8 60 4 Trees 580300 9 9135752 5 45 5 580317 3 9135686 3 64 7 588343 1 9135666 1 72 5 536466 1 9135441 5 79 EAna n 7 1 44 Place the new text file in the Model gt User folder Remember the name of the new text file Step 3 NetLogo File Parameter
79. azonian 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 Par 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 trees in Amazonian forests In Moth
80. 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 Command Center to query the landscape for information not displayed in the population monitors or plots or harvest monitors Commands are entered in the command line window the small window labeled observer shown below The results of the commands are printed in the larger output window labeled Command Center Command Center wv Clear Observer show count trees observer 158 observer show count trees with diameter 60 observer 81 observer sh
81. da 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 forest an example from Swieten
82. de Apn3S gz s30egge eouequnasrp ey p V 30ds4eeM s e Avu OF zu 9I vIE ubnoue 5BxeT deb e aqv z WO 1666 FO ASJOWeTpP e oAeu snu 9074 V lt W0 lt snrpeag 3ee s WOT lt snrped 3sip qodsa Ms e WAIOF OF zu OT PTE vey debae eq asnu oeouequnisip V deb Tey qe zO oa WO G8 T JO Z q ueTp e snu 9074 V os sITe3 q s zxL eonpoudeu pu sp s sz dsTp oq os ones SUTTINO sonporzdey ek pue Z pex zoTood q s n gaodsa Mss S esieg 3odsa ms YATM 6 seyojzed yse pea zoTood q s n zeouequnasrp jes esiej ceouequnastip OT s u qed 489 6 OT s zeqo u 44 1910 ey oa qu TeATnb eode ue uqrtA deospueT td 00001 4166 y uo uorqeoorT WopuerT e UT p oeTd ST qat sanooo 9 JI gONd LSIG HD2NVI y uo peseq sanooo eouequnasrp BzeT e s uruz q p sty uo sr uorado eouequnasrp 9u3 FI
83. del 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 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
84. deospue uo s oueqanastp Fo yo req Seoe d z qaeT pe q nposd x o eua U ATB 0G pue sdeb qc z uqe p qoz pesieu s x3 JO 0S Sppo boT sppo TITX eua go ua ua sr AaTTeqxou AaTTTqeqoqd un udqnduooud TIIM D D sz Zz q ueTp Teseq 3STT xeu x 0 2070 S uqndasoda SoNVSWQLSIG ex en on on PR td eeae asrp 3abs 3 T epque eudTe euureb uopuedi e ze 3STp eT TEZ60SSS0070 EpqureT 3 T SIEZTA4Z19 0 eudie 3 T s uoaed qasrp uoaqaeq umu zo u 499 qanasrp uoqaeq oF pue ex en on s PR s za qanasrp yes oadead ou erp qoad gt n1 2466 38s 6 gt 1 qozd 320u 4 I Sppo TITX s xL qIN4STA 6496 qanasrp IeUurjg q n srp uo3eq oF e pu T 390 g uopuez2 JT T 390Tg uopuez2 FT 9AT 4 S gt 1 FT dx qoud 420u q s z q ueTp Teseq 0 4STT xeu 1200070 z a uerp Teseq 0 ASTT xeu x vvGG8 0 z q ueTp Teseq x d493 0 s 1 qez uamozb5 0 3STT xeu x S Z v 0 qex uaMox5 4STT xeu x GOL E eaea uaModb x 44177 80
85. ding 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 41 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 fully annotated version of the model code is available in APPENDIX E MODEL CODE page 68 and in the Procedures 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
86. dis amp Grogan Mahogany Growth amp Yield Schulze M Vidal E Grogan J Zweede J amp Zarin D 2005 Madeiras nobres em perigo pr ticas e leis atuais de manejo florestal n o garantem a explora o sustent vel Ci ncia Hoje 214 66 69 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 Guatemala and Mexico pp 61 80 Isl
87. e specifies age of tree ages of initial trees are unknown fall gap specifies whether a tree creates a treefall gap sawn volume specifies sawn volume 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 e0 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 specified 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 no
88. e Model gt User folder Remember the name of the csv file Step 3 NetLogo File Parameters The final steps towards uploading your data into the model are completed in the DATA UPLOAD portion of the model interface These parameters specify the name of the user data file the dimensions of the user field site and the resolution of the resulting landscape Type the name of the csv file from Step 2 containing diameter data located in the User folder into the File Name input box Be sure to include the csv file extension when typing the name 23 Free Landis amp Grogan Mahogany Growth amp Yield DATA UPLOAD mara 204 tree data csv Resize Leave the DIAM Attribute Name input blank This input is only necessary for data uploaded from a user shapefile section 9 2 Input here will interfere with the present upload Type the width X in meters of your site into the Site Width input box and the height Y in meters of your site into the Site Height input box If your site 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 mo
89. e 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 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 vvvvvv svvietking org Java Versions The Big Leaf Mahogany Growt
90. e 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 E D BehaviorSpace results NetLogo 4 1 3 Growth amp Yield Mode 2 0 nlogo Population Growth No Logging 01 02 2012 10 21 17 259 0500 min pxcor max pxcor min pycor max pycor 63 63 88 B8 Oui UM 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 repo
91. e field at the top of the window Experiment Variables The second field lists the variables to be examined during the BehaviorSpace simulation In this experiment logging is turned permanently on logging true and the minimum diameter 15 varied from 40 cm to 90 cm by increments of 10 cm 1 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 e OO Experiment j Experiment name Population Growth amp Productivity Diameter Experiment Vary variables as follows note brackets and quotation marks Logging true minimum diameter 40 10 9011 Either list values to use for example l my slider 1 2 7 8 or specify start increment and end for example T my slider 0 1 10 note additional brackets to go from 0 1 ata time to 10 You may also vary max pxcor min pxcor max pycor min pycor random seed Re
92. ears 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 2 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 96 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 Commercial Density Commercial Volume Diameter Distribution Tree Density density of trees gt 20 cm diameter in the field site trees 100 ha density of commercial sized trees in the field site trees 100 ha volume of timber in the commercial population m bar columns 10 cm diam increments gray line commercial diam black initial size distribution red current size distribution 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 lt 20 cm diameter are shown HARVEST PRODUCTIVITY Logged Volume Total Logged Volume Total Logged Trees DATA UPLOAD File Name DIAM Attribute N
93. ee 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 posf cut number the total volume of commercial trees before after each harvest pre posf 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 landscape disturbance 7o show count patches with disturbance true count patches landscape sweetspot 70 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
94. eer TET3TUT ON ATTeTau qod eade TeT3TUT TIW sbuTT pees s z3 TeTITUT ON SAT S90 TeTITUT TTY uMOuxun ST S90 TeT3TUT JO oby pezOTOO s zxu 0073 se pedeus soeur uo peseq p zTs seer x q ureTp cu unToA umes x q ueTp uo3j gu umToA burpueas z a uerp zu eseg x q umeTp WOTF uo x q ueTp Teseg SHUHVIMVA SHAUL SLAS 9074 5uTuTeu x y dn s4 S 9401 441 4 0189 eqep reraeds ou o q s qeuTpxoo uopuez seer eui 34STI oua ur z q ueTp uoe YATM s av x po STYL 29 ODBoT3 N oqur sz q ueTp y spe z pue eqep z q ueTp Tetzeds uou Burureaquo ASO e su do po STYL NOILWIndOd LXL HHLHNVIQ TWILWdS NON HHSn SHAUL dn SLAS 9074 5uTuTeu x y dn s3 s 9407 41 4 199 eueu y uaTA e rgjedeus y ur anqT a3e eu3 z q uerp e s Ar o rz YOeRY oboT49eN eua ur STU3 qe 9974 s aqvc z pue STI NOILVOOT y oaur e rgjedeus y ur 98073 uoee jo AX eua speed po STYL doT Au Meu eua s xeu pue s u u
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96. ersion 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 Par 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 data 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
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99. est 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 48 6 590 9 96 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 The area in hectares or ha of the field site is also displayed in this section MODEL zn NGS Site Area ha WS e 212 8 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
100. esults 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 is 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 jpg png bmp tif etc but the plots and world files must be saved with the csv extension Step 5 Run BehaviorSpace Experiment Run the chosen experiment by selecting the experiment in the BehaviorSpace window and pressing the Run button The Run Options window shown below will open in the center of your screen e 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 Check the Table output option and leave the Spreadsheet output option unchecked Enter 2 into the Simultaneous runs in parallel field The Table output option creates a more analysis friendly output and the 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 FIL
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102. gap forming disturbance events necessary for mahogany regeneration and recruitment to adult size Finally the model does not formally incorporate density dependent population regulation which may allow overestimation of population growth amp yield Steniscadia poliophaea a nocturnal specialist moth preys more regularly and intensely upon mahogany seedlings in close proximity to large fruiting trees or groups of clumped adults The population level influence of this density dependent seedling predator could be strong if population growth is sensitive to observed reductions in seedling survival and growth See Norghauer ef 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 MODIFICATIONS We are interested in using the recently published R Extension for NetLogo Thiele amp Grimm in press http netlogo r ext berlios de to increase the robustness of the model regressions the potential for in model data analysis and the functionality of the Export Results command We also plan to make the model compatible with NetLogo 5 0 when it is officially released Wilensky 1999 http ccl northwestern edu netlogo 5 0 docs The new version of
103. gement area in southeast Para Brazil 7 50 S 50716 W The site was selectively logged for mahogany between 1992 1994 Model demographic parameters are derived from a sample mahogany population consisting of 358 surviving trees gt 10 cm diameter in an area of 2050 ha These trees were censused annually for survival stem diameter growth and fruit production from 1997 2010 Other phases of mahogany s life cycle including temporal and spatial patterns of seed dispersal seed germination and seedling establishment rates were quantified in observational and experimental studies at Marajoara Fruit production data are supplemented by observations of 325 mahogany trees at three additional sites in southeast Para and at the Acre West Amazon site Because few large gt 100 cm diameter adult trees survived logging at Marajoara or were available for observation at the other study sites fruit production data are supplemented with data from Gullison ez 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 7 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 the study mortality and gro
104. h 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 Windows users Vista XP or 2000 can download the Java browser plug in from here http www java com en download windows manual jsp Mac OS X users require version 10 4 or higher No plug in is necessary Linux and Unix system users need the Sun Java Runtime Environment Version 5 or higher This is available for download here http 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 is 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 the browser normally makes available This is more likely to happen when simulating large populations On Windows you can increase the available memory heap space in the Java Control Panel s applet runtime settings In the Java tab of the Java Control Panel view the Java Applet Runtime Settings Enter the following in the Java Runtime Parameters field Xmx1024M Include the initial hyphen but not the final per
105. he 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 48 6 590 9 96 Logged Volume reports the volume m of trees logged in the most recent harvest Total Logged Volume reports the volume m of trees logged in all previous harvests Total Logged Trees reports the number of trees logged in 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 will need diameter data for the trees within your site If you have both spatial distribution mapping and tree diameter data you can upload the data from a spreadsheet or if available from a GIS shapefile Refer below to Spatial Diameter Data User Spreadsheet and Spatial Diameter Data User Shapefile sections 9 1 amp 9 2 respectively for instructions If you only have diameter data you can upload the data from a spreadsheet but
106. hese 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 66 Free Landis amp Grogan Mahogany Growth amp Yield 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 e70 growth residual is now calculated from seedling growth rate data The e9 e growth residuals 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
107. ia 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 is a forest industry owned mana
108. ield 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 is 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 is 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 4 1 3 installer necessary for your operating systems This folder also contains the NetLogo 4 1 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 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 is 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 4 1 3 Double click on the NetLogo folder to view its contents
109. ility of fruit production and 4 number of fruit produced The model simulates logging growth mortality disturbance and reproduction each year with these parameters until the time limit is exceeded or all trees are harvested or die Growth Function The growth function incorporates growth autocorrelation the tendency of fast growing trees to remain fast growing in order to account for past growth history Diameter increment is estimated as a function of stem diameter using generalized least squares to incorporate an autoregressive error term accounting for growth autocorrelation over the preceding 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 48 The present year residual e0 is then calculated as follows e0 0 399 e1 0 321 e2 0 081 e3 0 046 e4 0 1130 65 1 0 143 e6 0 029 e7 0 266 0 190 e9 0 311 e10 o where N 0 0 48 The residuals are recalculated each time step because as a year passes the residual of the previous year becomes the residual of two years before The residuals are therefore recalculated as e10 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 is then calcu
110. in a value for a variable There are two types of inputs number and text The Site Width Site Height and Patch Area input boxes accept number inputs The File Name and DIAM Attribute Name input boxes accept text inputs Monitor A monitor displays the value of a built in expression The Area Population and Harvest Productivity monitors report the area of the field site the density volume of trees in the initial and current populations and the number volume of trees logged during harvests Plot A plot provides a real time graph of model results The Diameter Distribution plot tracks the size distribution of the population and the Tree 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 nformation Procedures P wx Button o E view updates Settings Edit Delete Add normal speed continuous 56 Free Landis amp Grogan Mahogany Growth amp Yield The Interface tab displays model controls and simulations The Information tab displays basic information about the model The Procedures tab displays the wo
111. iod 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 Help in the NetLogo menu bar The Search option can direct you to specific menu items or help topics The Look Up In Dictionary F1 option opens a web browser with the dictionary entry for the selected code The NetLogo User Manual and NetLogo Dictionary links will open the manual and dictionary in a web browser The NetLogo Users Group option will link you to the NetLogo Users Group also in a web browser DEFINITIONS This i
112. is a csv file and has the csv file extension csv Site VVidth 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 Pateh 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 this manual to ensure proper formatting 9 5 User Data Upload Examples There are example user files in the Model gt User folder to help illustrate the user data upload process The folder contains the files necessary to set up the SE Par 204ha population using each of the three user data upload methodologies The files and inputs required for each methodology are listed below If you have any questions about formatting look to these files as templates If you have questions about the inputs look
113. lated using the following equation 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 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 0 is 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
114. ll 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 conspecific adult basal area of Am
115. ll trees are Run X Years 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 67 2 40 9 546 4 CURRENT POPULATION Total Density 100ha Commercial Density 100ha Commercial Volume m3 27 3 5 6 87 5 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 cm 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 25 87 gt ml 2 u 0 WL Time yrs Size Class 12 Free Landis amp Grogan Mahogany Growth amp Yield Harv
116. mand Center window between vertical window and horizontal views Other resizing options include Drag the gray bar separating the window from the interface to a new position Or press the small gray arrows above the Clear button to hide the window or make it very large Clear Press this button to clear the contents of the Command Center window To clear the History pop up menu choose Clear History 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 Procedures 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 probab
117. mand 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 itemp item item n3 item where each item represents the harvest value 40 Free Landis amp Grogan Mahogany Growth amp Yield for harvest number x If you prefer that each item receive its own column you must replace the annual harvest volume reporter with the following reporters item 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 is harvest 1 item 1 is 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
118. mulations 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 thorough understanding of how the model works It can also be queried with specific questions using the section guide below MODEL INSTALLATION section 3 details the model installation process HELP BUTTONS section 4 explains where to find help while working in the model interface A BRIEF GUIDE section 5 provides basic instructions for navigating the model interface MODEL SETTINGS section 6 describes example populations available for
119. n Brazilian state of Acre This data is from a 10096 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 and diameter data from a spreadsheet User Population shp upload spatial and 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 is drawn too small for the available space increase the value shown in Patch Area and press the Resize button upper right on interface If the site 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 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 populatio
120. n sTpuer fW 01 1707444 eTqtssodwut ST qu uqrnao r ur deb e u ousasTp un OL 3STp 3Tnxo z ou 3es 49002 oeA e5 9 ueboz5 920 0 170 44404 oueqanasrp edeospue uoraagodoad Tenuue sur 920 0 3S Tp pueT dousd jas SrpueT f0 ueeW T 8482970 LINYAHA Teuzou YyAMoAH eua jo uoTaeTA p pdepueas 1 8 8 0 eubrs ua odg5 yes uo oz 170 4404 suorqeTnurs pexoedga seod4 4s TTeus y jo uo zegeuerp oy ff 02 wetp TTeus jos SLNVLSNOO 1400 S TYEOT an 5185 sTeqoT5 dna s sTeqoT dnaes aa uo os on u ex os on on ex es en os pue enTq ur su qsAs ueod4s y sMeJ3p STYL uo jo sseuxoru3 SUTT 9 U3TM M Azepunoq e4TS eua sMeIp Srur oBom3 N SYR FO qu ax eua s3 s STYL ObOT3eN UT PTIOM SI STUL STT ODBoT3 N UT eAep Azepunoq SI sez04s STUL 3STT OBoT3 N UT 6 SID S I04S STYL 3STT ObOTION UT 99874 SI S9JO3S STYL LOId WHSE OT VGYOTPVUHVN SAJAL dN SLAS Sen eA 9074 burureuea y dn sqes SHNIVA HaaL dNLES z q uerp peisr sar zq eui S ATB pue s qeurpaooo perjroeds y qe 9074 e s qe z o rjedeus SIS y jo MOI uoee speed STYL OM qo SSOUXOTU3 UTT 8 YFM en q ur sweqysks ueod4s y SMLIP STYL OMA JO ss uyoTua UTT U
121. n 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 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 Y
122. n until the time limit is reached or until all trees are harvested or die whichever happens first Population growth and harvests can be simulated up to 150 years Changes to the simulation length can be made in 5 year increments 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 Par 1 204 ha Logging On Patch Area 2 75 pixels Time 100 years 7 LOGGING PARAMETERS The default harvest parameters are set according to 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 ee a Harvest parameters can be changed according to user preference Each parameter can be reset using the computer cursor to move the red bar across the green slider Movements to the right increase the parameter values while movements to the left decrease the parameter values The minimum value maximum value and value increment are listed for each parameter below Minimum Diameter 0 100 em 5 cm i
123. nce 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 is 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 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 is always contained within the second largest size class that is the fin
124. ncrements 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 Minimum Retention 20 trees Minimum Density 5 trees 100 ha Cutting Cycle 30 years If you do not want to simulate logging turn logging off using the Logging switch discussed above 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 0 and the current simulation year respectively YEAR 0 POPULATION monitors are static while CURRENT POPULATION monitors are updated each year according to simulation results YEAR D POPULATION Total Density 100ha Commercial Density 100ha Commercial Volume m3 67 2 40 9 546 4 CURRENT POPULATION Total Density 100ha Commercial Density 100ha Commercial Volume m 27 3 5 6 87 5 Density monitors report tree density as the number of trees per 100 hectares Density can be converted to abundance using the following equation Abundance Density Area 100 where density trees 100 ha is either to
125. ndroecological 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 TAVVA 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 Germination and development of sown mahogany Swietenia
126. o STUL nzqa 2 9 5 cdequeu yATM seeda3 uumoo jo euo 3 4 26 3es ued s za zou ii an TeBb T xeu T ATTE u3r seed43 uuoo Arle s z4a uuroo 3 T 1 gt 3STT za BOT uaBu T JT wopuez 38 3es 3STT za BoT T 1 29 1 2 ua5u T JT 3asrr za BoT 22 16 eoueques 3STT za 5oOT jes 3asrr za BoT NdT 4STT xa 5oT q s eAoueag unu 0 2 38T1qns x 2 punoz Aou dq unu 3 T 1 astT e7er4s 4STT 3STT x3a BoT 4 3ST1T uru 3 T seei4 uuoo unu lerauedeggrp 3unoo aqn o unu xeu 3asrr eqaeaas eqerqs Mou andT 3STT e4qea3S q s e3aea3s M u o jjnUS eqeaas M u q s a33os seedg4 uuoo uaBbu T ezrs urq zTs uTq x 2 4STT uru zrs urq x 2 a3d30s seed4 uuoo STINS eqeaas M u T 21 e3ezas unu s nTeA u uoeo1og HE ezrs urq seeag
127. oTd uMop ued 4o d 0 16 4 dn u d aoTrd Kerb xaoTo u d aoTd 3 s 0 pou u d 3oTd a3 s s ze A 3s Axzeu uoeo10j 1 T A BuTaan eurL sen ea u sae A 3s Azeu 1 MX MV 4e X 3S AZ H 001 x exe ears z q ureTp umumurTu lt z q ueTpl YITM qunoo 14 pez azoro o u d aoTd a3 s 1 e se ALVY DOT ey 2 04 sd qs 4S4T2 eui sunqaoodqa LSSAHNVH pue grauepr c 13STT umTOA y dna s T uorqounz s za 3s Azeu y Bursn ede uO st pue as Azeu e sr ze K qu zzno Y JI SHVHA LSHANVH Sze 4soazey JO 3STT uq sxor3 Zeek y 5urzeduo Aq ze Z qseazey e sr IVL qu zzno eua z ua uM poo STYL SuVHA LSHAHVH NI SAJAL DOT ex sx s PR s x on sx on s sxeo 1947470 TTe ur 3 qge sanooo sznmooo 4T esnedeq poo x uqo eua uo3j p qezed s ST po STYL T NI SHHHL SOT z qa urerp WOTF sr cu eunqoA umeg WOTF sr cu unToA 9 st zu eseg z qa uerp Teseq
128. oductivity 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 gt 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 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 col
129. one of recruitment sweetspot 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 is a summary of the changes made to the Big Leaf Mahogany Growth amp Yield Model Version 1 0 since it was first released in January 2011 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 in initial year prop land dist prop dist specifies proportion landscape disturbance disturbance data disturbance dataset contains gap size data prob die no repro prob die no seeds specifies the probability of a tree dying before fruiting in the year of its death establishment rate surv prob s
130. ow sum stand volume of trees with diameter gt 601 v Copy and paste any of the italicized commands listed below into the command line window Press Return Enter to run the command ALWAYS LEAVE THE COMMAND LINE IN OBSERVER MODE DO NOT SUBMIT COMMANDS IN TURTLES PATCHES OR LINKS MODES You can access previous commands using the history popup menu the small downward pointing triangle to the right of the command line window Press the triangle to see a menu of previously entered commands Alternatively you can access previous commands with the UP and DOWN keys on the computer keyboard as long as the cursor is in the command line window Pressing the Clear button in the upper right corner of the Command Center window will erase the contents of the output window Additionally the Command Center can be resized by grabbing and moving the gray bar at the top of the Command Center window The following is a list of commands that may be useful to your analysis For sections with bold italicized commands i 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
131. ox 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 DIAM Attribute Name Site VVidth 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 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
132. p Teseq ATaTsod e seu z q ueTp u qs AT3aTSod e UaTM 9924 V X q ueTp qs ATJTSOd e eAeu OF WO g8Z 0 lt AejoWeTp Teseq e sey snu 9074 V unTOA umes SATATSOd e OF WO 6 vpy e oAeu asnu 99074 V eun OoA puegs sATATSOd e OF WO 6 T lt e snu 9074 V 01 ut ST aieo queseud p q T s ATwopuez ST rzesk 4satg peqoetes sr zeek puodes p ao T s ATuopuex sr sr xe Z uq nouq p q T s ATwopuez ST sr ze ZXK uaxrs ATuopuex sr xe A uqu A s ST xe ZA uauBbTu ATwopuez ST ageo uQurN ATuopuex sr ze ZK uqu r x qeT 39S ST qat sneo q 0 ATTeTATUT sBuTTp s ex on on on on on on on sx on ex en on on on on on on on sa s saord dn3 s i pue sorTo TTJ and qa sllespu ae TT 30u uedo e rj 4STT eaep ua odb5 pees q s eso 2 e1173 e
133. pecifies seedling survival rate seed diam data seed diam list contains seedling diameter data 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 growth sigma specifies standard deviation of growth residuals num batch dist specifies how many batch disturbances to build 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 seed shadow area specifies the area of a tree s seed shadow eliminates seed radius seed growth data new list contains seedling growth data pre post cut number new list contains live tree abundance pre amp post harvest pre post cut volume new list contains live tree volume pre amp post harvest harvest ticker removed removed because of new harvest method 64 Free Landis amp Grogan Mahogany Growth amp Yield Tree Variables ag
134. petitions 100 run each combination this many times Measure runs using these reporters count trees with diameter gt 201 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 Time limit 0 stop after this many steps 0 no limit I Cancel 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 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 Pr
135. r 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 for timber Ecological Applications 17 323 330 Boot
136. recimiento de caoba en aperturas post extracci n en Belice a partir de semillas y pl ntulas Recursos Naturales y Ambiente 44 76 83 Snook LK Negreros Castillo P amp O Connor J 2005 Supervivencia y crecimiento pl ntulas 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 52 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 Gonz lez E 2008 Sustained mahogany Swietenia macrophylla plantation heartwood increment Forest Ecology and Management 255 320 323 Walters BB Sabogal C Snook LK amp Almei
137. res v In the Procedures tab of the NetLogo interface use the Procedures menu to view a list of model procedures and zoom to a specific procedure Procedures are color coded according to the following scheme keywords are green constants are orange comments are built in NetLogo commands are blue primitive reporters are purple and everything else is 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 shadow 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
138. rkspace 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 is 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 is on off during the simulation s Time number of y
139. rp 21 qu zed y zo Mopeus pees eua ur s5urTp s s sz dsTp uorqounj STUL SONI IQHHS SHSNddSIG ex en on on en on on ex s lt on en en on on sbur pees BuTATAznSs JO 9303 eua uruz q p oa AAT Tqeqozd BuTTp s p s eua Aq sr zequnu STYL sp s jo y oq queasuo o ded spees eua Aq ST qarna jo dequnu urLt sen eA epque pue eudre Aq p zTz q uexed uoranqragasrp euueb e TnI jo zequnu y s aqaeTnoTeo uorqounj STYL LINAJ JO 9417 7 s lt sx sx s 1 0I9 69 g Z g q z T Qe o eo g Woes I9 3es z 3es 3es yo jos Ge jes g 3es L9 3es g jos 69 3es ueou OTe Wes 0 s5uTTp s jes 0 3Tnagg unu yes 0 qoaud a4rn3gj jes 0 qoad 4z2ou q s eaep uauoz5 p s jo euo yes yes edeBb TTez aes nzqa yes 9nJ4 9AI 3 s I ebe yes AOTOO yes 9943 edeus yes 0S I zTS 3es J93euerp eunT oA uMes S eun oA pue4s o eo eun oA pue4s jos z qa uerp e ze Teseq oTe e ze Teseq jes z a uerp Teseq uerp o eo ejep uerp pees jo euo z q ueTp Tes
140. rted 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 96 minimum density Minimum Density 100 ha cutting cycle Cutting Cycle yr step Time yr count trees Trees count trees with diameter gt 20 Trees gt 20 cm diameter count trees with diameter gt minimum diameter Commercial Trees sum annual harvest number Logged Trees sum annual harvest volume Logged Tree Volume m 34 Free Landis amp Grogan Mahogany Growth amp Yield annual harvest number Harvest Number List 7 yr annual harvest volume Harvest Volume List m yr pre post cut number Pre Post Harvest Commercial
141. ruTul SMAL4MNYMVa 001 S 1091T 0 euri 440 NO 5uT55or p asrT suoTaeTndodq 94414 4 THCOW a3odsa ns oueqanasrp os oN s s rw rS umo sayo zed OTe 69 ge L g ge y z 0e sbur pees 31Tn4gg umu qoad 431n2j qoad 4aour o3e4a u43 4o4b unToA umMes eun oA pue4s p ze Teseq z qa uerp Teseq z qa urerp 2866 119 G ATT obe uuo s za eunioA 4no 4sod eud Q1equnu 4no 4sod eud x qunu 3s Azeu Tenuue un1ToA 3s Azeu Tenuue qe4 3u uusTTqe3s 431n4gg 4ed spees 31Tn3g umu xeur enda gsz077e 30S pergjrioeds eq asnu oeueN e r4 V ebessow zresn eueN e r4 e43d jT 1 As zesn suoraeTndoq zo dus uoraermndoq 3 sn 4o pAx uoraemndodq z sn suoTaeTndod jr nzqa 3 s p q T s eq asnu uoraerndoaq z sn v Bbess u z snl SNOILWINdOd 449 suorqaeTIndod jT enia SI0II 3 s p a T s eq asnu uoraemndoq eTdwexg v Bbess u z snl SNOILWINdOd 414 suotjzetndog jT suoraerndoa JT estes SsSIOII yes xXoeuo 41o43e oq enda pea3oe es eq asnu uoTraeTndod v ebesseuriesn
142. s 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 1 1712 4 1 Resize 1216 1 1712 4 ia Type the name of the text file from Step 2 containing spatial and diameter data located in the User folder into the File Name input box Be sure to include the txt file extension when typing the name Leave the DIAM Attribute Name input blank This input 1s 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 rectangle examples shown below Again the width and height of your site must be in meters m Width WO 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 Height
143. s 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 Society 122 83 87 51 Free Lan
144. s the DEFINITIONS box as it appears on the model Press the button next to each section to v features in this definition box Press All De interface Feature definitions can be viewed by using the d blue bar to scroll across the text content All definitions can be accessed by pressing A on the keyboard This is the shortcut for the All Definitions button Button shortcuts are displayed in the upper right corners of the buttons E is the shortcut for the Export Results button S 1s the shortcut for the Setup button D is the shortcut for the Defaults button etc S93 2 A button shortcut will appear black when enabled and gray when disabled To enable shortcuts click anywhere in the Export Results 7 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 S A BRIEF GUIDE The following guide describes the most basic method for simulating a pre defined big leaf mahogany population Step 1 Designate Initial Population to Simulate Select either a pre defined example population or upload your own data SEPar 204ha 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
145. show mean diameter of trees with reproduce true max large tree fruit probability show max fruit prob of trees with diameter x 30 median fruit production show median num fruit of trees with reproduce true 38 Free Landis amp Grogan Mahogany Growth amp Yield potential seed production show floor sum num fruit of trees seeds per fruit actual seed production show sum seedlings of trees 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 growth 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 pg export view user new file export interface image pg export interface user new file export output text txt export output
146. 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 can be read in advance or when specific questions arise If you still have questions after reading this User Manual or have any feedback on the model please contact the authors 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 ru
147. tal or commercial density and area ha is 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 25 87 gt ml I L z 0 B eee Se 0 Size Class 145 0 Time yrs The Diameter Distribution plot shows the initial size class distribution in black This distribution is static The current year size class distribution is shown in red This distribution updates each year according to simulation results The diameter size classes are defined by 10 cm intervals and only trees gt 20 cm diameter are plotted The vertical gray line divides commercial and non commercial trees as determined by the minimum diameter cutting limit The Tree 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 T
148. 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 is a simple and free text editor http www pc shareware com anotepad htm For Mac users Plain Text Editor is also a simple and free text editor http www macupdate com app mac 8724 plain text editor 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 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 Abunda
149. 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 2004 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 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 7 indicates
150. to help interested users understand how the code operates This text is 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 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 Procedu
151. tun fi seeaa4 dus dn3es dys uotjzetndog z sn suotjzetndog jT 5195 STUL 11 seeaa4 pA x dn3es pAx zesn jT S3es STUL ff s za zoe dna3a s uozeuy a3s M z v suoTaeTndod jr sqes STYL ff seed3 sgcor eaeu dna3es euS 01 ered HS suoTaeTndodq jr sTuL s xa 0z esceu dna s eupoz ered 45 6 jr 9719 714 s xa dn3 s oa 1 eur a3no seer dnaes 1 pu u M3a q s u aqed eui s ua se se ze qodsa ms xo s oueq n3sTp ou u zB5 st deospueT eui LNSWNOHIANHS HOLVd IVILINI dn SLAS on s on ex es on on on u zB5 z0ToOoOd yes 3aodsa ms 5 oueqanastp yes seuoaed xse s u aqed dna s o4 e 9074 5uTuTeu x y dn s3 s SunTIVA usWL d nss qu A dad uorae ndod eua er ieos suor3eTn Te ppe un ebpe y uo euos 4 s qaeurpaooo zd y xoq e UTYATM p urequoo ST uoTaeTndod y esneoeq x A Mou fs qeurpzoo oBom3 N Oq s qeuTpxoo eoraeuds Ax y s qeTsueaa po eui Sen eA pue A x go yes uoe uaTA e9J43 e qe d3O oa S38STT uerp pue A x y ubnozua sdooT po STUL
152. ublishers 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 Mont ia 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 16 404 416 D nisch O Mont ia VR amp Bauch J 2003 De
153. udiomar 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 Amaz nia IMAZON for providing institutional affiliation and collegial support especially Edson Vidal Paulo Barreto and Adalberto Ver ssimo 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 Par Jurandir Galv o was instrumental in setting up field studies and training field assistants for long term studies Mark Cochrane provided the original geospatial data that mapping studies were built upon In Acre nothing would have been possible without Frank Pantoja s unflagging commitment and determination In the field we thank Miguel Alves de Jesus Valdemi
154. umns 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 31 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 commands export either a specific plot or all plots to an external csv file The export world command exports the values of all variables both built in and user defined including all observer turtle and patch variables and the plot contents The commands for exporting each feature are as follows export view word Results View behaviorspace run number jpg export plot Tree Density word R
155. 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 de lt 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 the 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
156. ven diameter 1s calculated 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 2 which in conjunction with a is 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 gammato 2 11 vvhere fruit production by a given tree is 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 8 pun fan 12 where fruit is the number of fruit produced by tree i Spuit is the mean number of seeds per fruit and is the fraction of seeds that germinate and survive to become 1 year old seedlings Spuit and fiw 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 is only possible within the interior portions of disturbance areas only seedlings landing in the z
157. w 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 PLOTTING Plotting is now done through a setup update procedure This both prepares the current model for eventual upgrade to NetLogo 5 0 and reduces processing time The new plotting setup function also 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 65 Free Landis amp Grogan Mahogany Growth amp Yield 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 growth 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
158. wth 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 Button Button A button executes instructions when pressed Setup Defaults Run Z85 slider 1 Year Run X Years Resize All Definitions Export Results etc are 1182 Switch all buttons zi Chooser Input Slider A slider allows selection from a range of values The model has Monitor sliders for Time and LOGGING PARAMETERS c Plot E Output pape Switch A switch allows a variable to be turned on off The Logging switch e NE turns the logging function on off before simulation Chooser A chooser allows a user to choose among variable values The Populations chooser allows the user to select between three example populations and three user defined population options Input An input box allows the user to type
159. y ur JO xz q ueTp unurxeu y 0 ux spu ax xeqeuerp srxe x Zeek erarur QL TeeA TET3TUT 9u3 ur uesboqsru uoranqraastrp 3 a uerp y dn sqes uorqo s STYL 91074 dN SLAS x on on on on on on on on ex on on on on on on on on sTenptsez pue snorAedd y worF YAMOTH MoU y srur 6 eua s qepdn dznp oodd stu ze ouo seer y ounpeoougd srur udqndasoda HLMOWS ex os on on ex os on on uau4ox5 qeTn Te sTenprs z qepdn T e5e yes xse s z3 Moz5 ze A euo d qs eura euo z y T3a eua seoueApe STUL 62014 eouepunqe pue uor4nqrJ4STp ezrs eua s qepdn styL edeospue y worF seouequni4srp s Aou z stuL edeospue y uodj peep s Aou z stuL edeospue eua uo spees s sz dsrp pue seer styL sz qa uezed oouequnisip y uo peseq edeospue y sqan sTp ezgnpeoodgd srur z q uerp pue ymoIb uo p seq STITY egnpeoodgd sT L sz a uezed peurgep desn oq 5urpxoooe s5oT znp ooadad styuL uoT3eT zzoooane YAMOTH bursn seer eunpeoodgd styL uni uoe sen eA UTLJI D sa s x styL uo sr JT 0 UT sbo stu
160. y thousands of seedlings saplings and pole sized trees at multiple field sites in southeast Par and Acre Model simulations can be run with or without harvesting Under logging scenarios the model harvests kills trees at specified intervals During intervals between harvests surviving individuals grow reproduce and die at rates observed in field studies Harvest simulations are based on current legal management practices 60 cm minimum diameter cutting limit 20 commercial sized tree retention rate minimum 5 commercial sized trees 100 ha retention density 30 year cutting cycle Forest managers can input mahogany population data from field inventories in order to project recovery and production outcomes following multiple harvests 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 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 si
161. 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 1 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 HEADERS The head of your file should look like the example file shown below X Coordinates Y Coordinates Diameters gt A B C D 1 579775 8 9136498 4 71 3 2 579744 8 9136501 6 79 4 B 580177 6 9135822 6 66 1 z 580265 1 9135770 8 B0 4 Trees 5 580300 9 9135752 5 45 5 6 580317 3 9135686 3 64 7 7 580343 1 9135666 1 72 5 8 580406 1 9135441 5 79 0 18 Free Landis amp Grogan Mahogany Growth amp Yield The XY coordinates longitude l
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