# Biodiversity analysis (R. Kindt, World Agroforestry Centre) # MAR 2016 menu biodivMenu topMenu "" "" "" "" menu communMenu biodivMenu "" "" "" "" item communMenu command "Select community data set..." selectCommunityDataSet "dataSetsP()" "" item communMenu command "Import datasets from Excel..." importfromExcelGUI "" "" item communMenu command "Import datasets from Excel2007..." importfromExcel2007GUI "" "" item communMenu command "Import datasets from Access..." importfromAccessGUI "" "" item communMenu command "Import datasets from Access2007..." importfromAccess2007GUI "" "" item communMenu command "Make community data set..." makecommunityGUI "activeDataSetP()" "" item communMenu command "View community data set" viewcommunity "communityDataSetP()" "" item communMenu command "Edit community data set" editcommunity "communityDataSetP()" "" item communMenu command "Check data sets" checkdatasets "activeDataSetP() && communityDataSetP()" "" item communMenu command "Same sites for community/environmental..." samesitesGUI "activeDataSetP() && communityDataSetP()" "" item communMenu command "Replace NA with 0" replaceNAs "communityDataSetP()" "" item communMenu command "Remove species with zero total abundance..." removezeroes "communityDataSetP()" "" item communMenu command "Remove NA from environmental data set..." removeNAGUI "activeDataSetP() && communityDataSetP()" "" item communMenu command "Transform community matrix..." disttransGUI "communityDataSetP()" "" item communMenu command "Vegemite community table" vegemite.table "communityDataSetP()" "" item communMenu command "Tabasco community table plot" tabasco.table "communityDataSetP()" "" item communMenu command "Beals smoothing" beals.smoothing "communityDataSetP()" "" item communMenu command "Indicator power" ind.power "communityDataSetP()" "" item communMenu command "Nestedness checks" nested.checks "communityDataSetP()" "" menu enviroMenu biodivMenu "" "" "" "" item enviroMenu command "Select environmental data set..." selectActiveDataSet "dataSetsP()" "" item enviroMenu command "View environmental data set" viewenvironmental "activeDataSetP()" "" item enviroMenu command "Edit environmental data set" editenvironmental "activeDataSetP()" "" item enviroMenu command "Summary..." envirosummaryGUI "activeDataSetP()" "" item enviroMenu command "Box Cox transformation..." boxcoxGUI "activeDataSetP()" "" menu diversityMenu biodivMenu "" "" "" "" item diversityMenu command "Species accumulation curves..." accumGUI "activeDataSetP() && communityDataSetP()" "" item diversityMenu command "Diversity indices..." diversityGUI "activeDataSetP() && communityDataSetP()" "" item diversityMenu command "Add diversity variables to data set" diversityvars "activeDataSetP() && communityDataSetP()" "" item diversityMenu command "Rank abundance..." rankabunGUI "activeDataSetP() && communityDataSetP()" "" item diversityMenu command "Renyi profile..." renyiGUI "activeDataSetP() && communityDataSetP()" "" menu countsMenu biodivMenu "" "" "" "" item countsMenu command "Species abundance as response..." countGUI "activeDataSetP() && communityDataSetP()" "" item countsMenu command "Species presence-absence as response..." presabsGUI "activeDataSetP() && communityDataSetP()" "" item countsMenu command "Set up diversity as response" diversityresponse "activeDataSetP() && communityDataSetP()" "" menu ordinMenu biodivMenu "" "" "" "" item ordinMenu command "Calculate distance matrix..." distmatrixGUI "communityDataSetP()" "" item ordinMenu command "Unconstrained ordination..." unconordiGUI "activeDataSetP() && communityDataSetP()" "" item ordinMenu command "Constrained ordination..." conordiGUI "activeDataSetP() && communityDataSetP()" "" item ordinMenu command "Clustering..." clusterGUI "activeDataSetP() && communityDataSetP()" "" item ordinMenu command "Compare distance matrices..." mantelGUI "activeDataSetP() && communityDataSetP()" "" menu ensMenu biodivMenu "" "" "" "" item ensMenu command "Getting started" ens.start "" "" item ensMenu command "Species Distribution Modelling with R" dismo.pdf "" "" item ensMenu command "Change working directory..." ens.directory "" "" item ensMenu command "Save R workspace as..." saveWorkspaceAs "" "" menu stackMenu ensMenu "" "" "" "" item stackMenu command "Select calibration stack..." stack.select.GUI "stack.listP()" "" item stackMenu command "View calibration stack" viewstack "stack.focalP()" "" item stackMenu command "Create stack of raster layers..." stack.create.GUI "" "" item stackMenu command "Update list of available stacks..." update.stacklist.menu "" "" item stackMenu command "Change files to raster grd format..." ens.grd.menu "" "" item stackMenu command "Delete layers from calibration stack..." stack.delete.GUI "stack.focalP()" "" item stackMenu command "Rename layers for calibration stack..." stack.rename.GUI "stack.focalP()" "" item stackMenu command "Identify factors for calibration stack..." stack.factors.GUI "stack.focalP()" "" item stackMenu command "Identify dummies for calibration stack..." stack.dummies.GUI "stack.focalP()" "" menu presMenu ensMenu "" "" "" "" item presMenu command "Select presence data set..." presence.select.GUI "dataSetsP()" "" item presMenu command "View selected presence data set" viewpresence "presence.focalP()" "" item presMenu command "Select data set to create presence data..." selectActiveDataSet "dataSetsP()" "" item presMenu command "Create species presence data set..." make.presence.GUI "activeDataSetP()" "" menu absMenu ensMenu "" "" "" "" item absMenu command "Select absence data set..." absence.select.GUI "dataSetsP()" "" item absMenu command "View selected absence data set" viewabsence "absence.focalP()" "" item absMenu command "Select focal stack of raster layers..." stack.select.GUI "stack.listP()" "" item absMenu command "Select focal presence data set..." presence.select.GUI "dataSetsP()" "" item absMenu command "Create species absence data set..." make.absence.GUI "stack.focalP() && presence.focalP()" "" menu calibMenu ensMenu "" "" "" "" item calibMenu command "Ensemble suitability modelling..." batch.GUI "" "" item calibMenu command "Plot suitability maps..." ensemble.plot.GUI "stack.focalP() && presence.focalP() && absence.focalP()" "" item calibMenu command "Select ensemble models..." model.select.menu "" "" item calibMenu command "Evaluation strips..." eval.strip.GUI "stack.listP() && ensmodelsP()" "" item calibMenu command "Predict ensembles..." ens.predict.GUI "stack.listP() && ensmodelsP()" "" menu helpbioMenu biodivMenu "" "" "" "" item helpbioMenu command "Help about BiodiversityR" helpBiodiversityR "" "" item helpbioMenu command "Citations for loaded packages" allcitations "" "" item helpbioMenu command "Go to website for BiodiversityR" browseTDAwebsite "" "" item helpbioMenu command "Tree Diversity Analysis PDF (7.7 MB)" browseTDAmanual "" "" item topMenu cascade "BiodiversityR" biodivMenu "" "" item biodivMenu cascade "Community matrix" communMenu "" "" item biodivMenu cascade "Environmental matrix" enviroMenu "" "" item biodivMenu cascade "Analysis of diversity" diversityMenu "" "" item biodivMenu cascade "Analysis of species as response" countsMenu "" "" item biodivMenu cascade "Analysis of ecological distance" ordinMenu "" "" item biodivMenu cascade "Ensemble suitability modelling" ensMenu "" "" item ensMenu cascade "Stacks of environmental layers" stackMenu "" "" item ensMenu cascade "Presence data set" presMenu "" "" item ensMenu cascade "Absence data set" absMenu "" "" item ensMenu cascade "Ensemble suitability modeling" calibMenu "" "" item biodivMenu cascade "Help about BiodiversityR" helpbioMenu "" ""