BiodiversityR: Package for Community Ecology and Suitability Analysis

Graphical User Interface (via the R-Commander) and utility functions (often based on the vegan package) for statistical analysis of biodiversity and ecological communities, including species accumulation curves, diversity indices, Renyi profiles, GLMs for analysis of species abundance and presence-absence, distance matrices, Mantel tests, and cluster, constrained and unconstrained ordination analysis. A book on biodiversity and community ecology analysis is available for free download from the website. In 2012, methods for (ensemble) suitability modelling and mapping were expanded in the package.

AuthorRoeland Kindt
Date of publication2017-01-08 15:42:16
MaintainerRoeland Kindt <R.KINDT@CGIAR.ORG>
LicenseGPL-2
Version2.8-0
http://www.worldagroforestry.org/output/tree-diversity-analysis

View on CRAN

Man pages

accumresult: Alternative Species Accumulation Curve Results

add.spec.scores: Add Species Scores to Unconstrained Ordination Results

balanced.specaccum: Balanced Species Accumulation Curves

BCI.env: Barro Colorado Island Quadrat Descriptions

BiodiversityRGUI: GUI for Biodiversity, Community Ecology and Ensemble...

BiodiversityR-package: GUI for biodiversity, suitability and community ecology...

CAPdiscrim: Canonical Analysis of Principal Coordinates based on...

caprescale: Rescaling of Capscale Results to Reflect Total Sums of...

crosstabanalysis: Presence-absence Analysis by Cross Tabulation

deviancepercentage: Calculate Percentage and Significance of Deviance Explained...

distdisplayed: Compare Distance Displayed in Ordination Diagram with...

dist.eval: Distance Matrix Evaluation

disttransform: Community Matrix Transformation

dist.zeroes: Distance Matrix Transformation

diversityresult: Alternative Diversity Results

ensemble: Suitability mapping based on ensembles of modelling...

ensemble.analogue: Climate analogues from climatic distance raster layers.

ensemble.batch: Suitability mapping based on ensembles of modelling...

ensemble.bioclim: Suitability mapping based on the BIOCLIM algorithm

ensemble.bioclim.graph: Graphs of bioclimatic ranges of species and climates

ensemble.dummy.variables: Suitability mapping based on ensembles of modelling...

ensemble.ecocrop: Mapping of novel environmental conditions (areas where some...

ensemble.novel: Mapping of novel environmental conditions (areas where some...

ensemble.raster: Suitability mapping based on ensembles of modelling...

ensemble.zones: Mapping of environmental zones based on the Mahalanobis...

evaluation.strip: Evaluation strips for ensemble suitability mapping

faramea: Faramea occidentalis abundance in Panama

ifri: Example data from the International Forestry Resources and...

importancevalue: Importance Value

loaded.citations: Give Citation Information for all Loaded Packages

makecommunitydataset: Make a Community Dataset from a Stacked Dataset

multiconstrained: Pairwise Comparisons for All Levels of a Categorical Variable...

nested.anova.dbrda: Nested Analysis of Variance via Distance-based Redundancy...

NMSrandom: Calculate the NMS Result with the Smallest Stress from...

nnetrandom: Calculate the NNET Result with the Smallest Value from...

ordicoeno: Coenoclines for an Ordination Axis

ordisymbol: Add Other Graphical Items to Ordination Diagrams

PCAsignificance: PCA Significance

radfitresult: Alternative Rank Abundance Fitting Results

rankabundance: Rank Abundance Curves

removeNAcomm: Synchronize Community and Environmental Datasets

renyiresult: Alternative Renyi Diversity Results

residualssurface: Show and Interpolate Two Dimensional Distribution of...

spatialsample: Spatial Sampling within a Polygon

transfgradient: Gradient for Hypothetical Example of Turover of Species...

transfspecies: Hypothetical Example of Turover of Species Composition

warcom: Warburgia ugandensis AFLP Scores

warenv: Warburgia ugandensis Population Structure

Functions

accumcomp Man page
accumplot Man page
accumresult Man page
add.spec.scores Man page
balanced.specaccum Man page
BCI.env Man page
BiodiversityR Man page
BiodiversityRGUI Man page
BiodiversityR-package Man page
CAPdiscrim Man page
caprescale Man page
check.datasets Man page
check.ordiscores Man page
crosstabanalysis Man page
deviancepercentage Man page
distdisplayed Man page
dist.eval Man page
disttransform Man page
dist.zeroes Man page
diversitycomp Man page
diversityresult Man page
diversityvariables Man page
ensemble.accepted.categories Man page
ensemble.analogue Man page
ensemble.analogue.object Man page
ensemble.area Man page
ensemble.batch Man page
ensemble.bioclim Man page
ensemble.bioclim.graph Man page
ensemble.bioclim.graph.data Man page
ensemble.bioclim.object Man page
ensemble.calibrate.models Man page
ensemble.calibrate.models.gbm Man page
ensemble.calibrate.models.nnet Man page
ensemble.calibrate.weights Man page
ensemble.centroids Man page
ensemble.drop1 Man page
ensemble.dummy.variables Man page
ensemble.ecocrop Man page
ensemble.ecocrop.object Man page
ensemble.formulae Man page
ensemble.habitat.change Man page
ensemble.mean Man page
ensemble.novel Man page
ensemble.novel.object Man page
ensemble.plot Man page
ensemble.raster Man page
ensemble.simplified.categories Man page
ensemble.strategy Man page
ensemble.threshold Man page
ensemble.VIF Man page
ensemble.weights Man page
ensemble.zones Man page
evaluation.strip.data Man page
evaluation.strip.plot Man page
faramea Man page
ifri Man page
importancevalue Man page
importancevalue.comp Man page
import.from.Access Man page
import.from.Access2007 Man page
import.from.Excel Man page
import.from.Excel2007 Man page
loaded.citations Man page
makecommunitydataset Man page
multiconstrained Man page
nested.anova.dbrda Man page
nested.npmanova Man page
NMSrandom Man page
nnetrandom Man page
ordibubble Man page
ordicluster2 Man page
ordicoeno Man page
ordiequilibriumcircle Man page
ordinearest Man page
ordisymbol Man page
ordivector Man page
PCAsignificance Man page
prepare.bioenv Man page
radfitresult Man page
rankabuncomp Man page
rankabundance Man page
rankabunplot Man page
removeNAcomm Man page
removeNAenv Man page
removezerospecies Man page
renyiaccumresult Man page
renyicomp Man page
renyiplot Man page
renyiresult Man page
replaceNAcomm Man page
residualssurface Man page
same.sites Man page
spatialsample Man page
stackcommunitydataset Man page
subsetcomm Man page
transfgradient Man page
transfspecies Man page
warcom Man page
warenv Man page

Files

BiodiversityR
BiodiversityR/inst
BiodiversityR/inst/CITATION
BiodiversityR/inst/ChangeLog
BiodiversityR/inst/doc
BiodiversityR/inst/doc/Getting-started-ensemble-GUI.txt
BiodiversityR/inst/etc
BiodiversityR/inst/etc/Rcmdr-RMarkdown-Template.Rmd
BiodiversityR/inst/etc/reset.gif
BiodiversityR/inst/etc/dune.xlsx
BiodiversityR/inst/etc/redo.gif
BiodiversityR/inst/etc/edit.gif
BiodiversityR/inst/etc/dune.xls
BiodiversityR/inst/etc/view.gif
BiodiversityR/inst/etc/data.gif
BiodiversityR/inst/etc/blank.gif
BiodiversityR/inst/etc/Rcmdr-Markdown-Template.Rmd
BiodiversityR/inst/etc/ok.gif
BiodiversityR/inst/etc/Rcmdr-knitr-Template.Rnw
BiodiversityR/inst/etc/cancel.gif
BiodiversityR/inst/etc/R-logo.gif
BiodiversityR/inst/etc/undo.gif
BiodiversityR/inst/etc/Rcmdr-menus.txt
BiodiversityR/inst/etc/help-old.gif
BiodiversityR/inst/etc/model.gif
BiodiversityR/inst/etc/BiodiversityGUI.R
BiodiversityR/inst/etc/paste.gif
BiodiversityR/inst/etc/delete.gif
BiodiversityR/inst/etc/Rcmdr.xbm
BiodiversityR/inst/etc/Nations.txt
BiodiversityR/inst/etc/submit.gif
BiodiversityR/inst/etc/help.gif
BiodiversityR/inst/etc/dunestacked.csv
BiodiversityR/inst/etc/remove.gif
BiodiversityR/inst/etc/cut.gif
BiodiversityR/inst/etc/apply.gif
BiodiversityR/inst/etc/dune.mdb
BiodiversityR/inst/etc/copy.gif
BiodiversityR/inst/etc/find.gif
BiodiversityR/inst/etc/R-logo-old.ico
BiodiversityR/inst/etc/BiodiversityR-menus.txt
BiodiversityR/inst/etc/R-logo-old.gif
BiodiversityR/inst/etc/linux
BiodiversityR/inst/etc/linux/Rcmdr.svg
BiodiversityR/inst/etc/linux/Rcmdr.desktop
BiodiversityR/inst/etc/model-classes.txt
BiodiversityR/inst/etc/log-exceptions.txt
BiodiversityR/inst/etc/submit.xbm
BiodiversityR/inst/etc/R-logo.ico
BiodiversityR/NAMESPACE
BiodiversityR/data
BiodiversityR/data/transfspecies.txt.gz
BiodiversityR/data/ifri.txt.gz
BiodiversityR/data/faramea.txt.gz
BiodiversityR/data/BCI.env.txt.gz
BiodiversityR/data/warenv.txt.gz
BiodiversityR/data/warcom.txt.gz
BiodiversityR/data/transfgradient.txt.gz
BiodiversityR/R
BiodiversityR/R/residualssurface.R BiodiversityR/R/ensemble.bioclim.graph.R BiodiversityR/R/accumcomp.R BiodiversityR/R/import.from.Access.R BiodiversityR/R/ensemble.simplified.categories.R BiodiversityR/R/ensemble.formulae.R BiodiversityR/R/ensemble.strategy.R BiodiversityR/R/ensemble.calibrate.models.nnet.R BiodiversityR/R/ordinearest.R BiodiversityR/R/diversityvariables.R BiodiversityR/R/spatialsample.R BiodiversityR/R/ensemble.VIF.R BiodiversityR/R/check.ordiscores.R BiodiversityR/R/ensemble.plot.R BiodiversityR/R/ensemble.habitat.change.R BiodiversityR/R/add.spec.scores.R BiodiversityR/R/ensemble.batch.presence.R BiodiversityR/R/replaceNAcomm.R BiodiversityR/R/diversitycomp.R BiodiversityR/R/PCAsignificance.R BiodiversityR/R/ensemble.accepted.categories.R BiodiversityR/R/NMSrandom.R BiodiversityR/R/ensemble.ecocrop.R BiodiversityR/R/renyicomp.R BiodiversityR/R/ensemble.analogue.R BiodiversityR/R/ensemble.zones.R BiodiversityR/R/ensemble.calibrate.models.R BiodiversityR/R/makecommunitydataset.R BiodiversityR/R/ordicoeno.R BiodiversityR/R/ensemble.novel.R BiodiversityR/R/removezerospecies.R BiodiversityR/R/caprescale.R BiodiversityR/R/ensemble.centroids.R BiodiversityR/R/ordicluster2.R BiodiversityR/R/subsetcomm.R BiodiversityR/R/same.sites.R BiodiversityR/R/rankabuncomp.R BiodiversityR/R/ordibubble.R BiodiversityR/R/renyiresult.R BiodiversityR/R/importancevalue.R BiodiversityR/R/renyiaccumresult.R BiodiversityR/R/dist.eval.R BiodiversityR/R/crosstabanalysis.R BiodiversityR/R/disttransform.R BiodiversityR/R/ensemble.calibrate.weights.R BiodiversityR/R/ensemble.area.R BiodiversityR/R/removeNAenv.R BiodiversityR/R/nested.npmanova.R BiodiversityR/R/stackcommunitydataset.R BiodiversityR/R/ordivector.R BiodiversityR/R/accumresult.R BiodiversityR/R/deviancepercentage.R BiodiversityR/R/ensemble.raster.R BiodiversityR/R/check.datasets.R BiodiversityR/R/BiodiversityRGUI.R BiodiversityR/R/ensemble.weights.R BiodiversityR/R/nested.anova.dbrda.R BiodiversityR/R/distdisplayed.R BiodiversityR/R/loaded.citations.R BiodiversityR/R/dist.zeroes.R BiodiversityR/R/renyiplot.R BiodiversityR/R/diversityresult.R BiodiversityR/R/evaluation.strip.data.R BiodiversityR/R/ensemble.dummy.variables.R BiodiversityR/R/accumplot.R BiodiversityR/R/ensemble.threshold.R BiodiversityR/R/ensemble.bioclim.R BiodiversityR/R/ensemble.drop1.R BiodiversityR/R/balanced.specaccum.R BiodiversityR/R/nnetrandom.R BiodiversityR/R/radfitresult.R BiodiversityR/R/prepare.bioenv.R BiodiversityR/R/rankabundance.R BiodiversityR/R/ensemble.calibrate.models.gbm.R BiodiversityR/R/ordisymbol.R BiodiversityR/R/CAPdiscrim.R BiodiversityR/R/evaluation.strip.plot.R BiodiversityR/R/removeNAcomm.R BiodiversityR/R/rankabunplot.R BiodiversityR/R/import.from.Excel.R BiodiversityR/R/ordiequilibriumcircle.R BiodiversityR/R/zzz.R BiodiversityR/R/ensemble.mean.R BiodiversityR/R/ensemble.batch.R BiodiversityR/R/multiconstrained.R
BiodiversityR/MD5
BiodiversityR/DESCRIPTION
BiodiversityR/man
BiodiversityR/man/dist.zeroes.Rd BiodiversityR/man/nnetrandom.Rd BiodiversityR/man/ensemble.bioclim.graph.Rd BiodiversityR/man/removeNAcomm.Rd BiodiversityR/man/distdisplayed.Rd BiodiversityR/man/deviancepercentage.Rd BiodiversityR/man/ensemble.bioclim.Rd BiodiversityR/man/ordisymbol.Rd BiodiversityR/man/accumresult.Rd BiodiversityR/man/BiodiversityR-package.Rd BiodiversityR/man/caprescale.Rd BiodiversityR/man/evaluation.strip.Rd BiodiversityR/man/rankabundance.Rd BiodiversityR/man/PCAsignificance.Rd BiodiversityR/man/loaded.citations.Rd BiodiversityR/man/renyiresult.Rd BiodiversityR/man/importancevalue.Rd BiodiversityR/man/ifri.Rd BiodiversityR/man/transfspecies.Rd BiodiversityR/man/BCI.env.Rd BiodiversityR/man/transfgradient.Rd BiodiversityR/man/add.spec.scores.Rd BiodiversityR/man/CAPdiscrim.Rd BiodiversityR/man/warenv.Rd BiodiversityR/man/ensemble.novel.Rd BiodiversityR/man/BiodiversityRGUI.Rd BiodiversityR/man/ensemble.dummy.variables.Rd BiodiversityR/man/ensemble.Rd BiodiversityR/man/crosstabanalysis.Rd BiodiversityR/man/multiconstrained.Rd BiodiversityR/man/ensemble.raster.Rd BiodiversityR/man/ordicoeno.Rd BiodiversityR/man/makecommunitydataset.Rd BiodiversityR/man/spatialsample.Rd BiodiversityR/man/disttransform.Rd BiodiversityR/man/balanced.specaccum.Rd BiodiversityR/man/nested.anova.dbrda.Rd BiodiversityR/man/ensemble.zones.Rd BiodiversityR/man/radfitresult.Rd BiodiversityR/man/ensemble.batch.Rd BiodiversityR/man/warcom.Rd BiodiversityR/man/residualssurface.Rd BiodiversityR/man/dist.eval.Rd BiodiversityR/man/ensemble.ecocrop.Rd BiodiversityR/man/faramea.Rd BiodiversityR/man/diversityresult.Rd BiodiversityR/man/ensemble.analogue.Rd BiodiversityR/man/NMSrandom.Rd

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