BiodiversityR: Package for Community Ecology and Suitability Analysis
Version 2.8-2

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.

Browse man pages Browse package API and functions Browse package files

AuthorRoeland Kindt
Date of publication2017-05-09 06:59:10 UTC
MaintainerRoeland Kindt <R.KINDT@CGIAR.ORG>
LicenseGPL-2
Version2.8-2
URL http://www.worldagroforestry.org/output/tree-diversity-analysis
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("BiodiversityR")

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

BCI.env Man page
BiodiversityR Man page
BiodiversityR-package Man page
BiodiversityRGUI Man page
CAPdiscrim Man page
NMSrandom Man page
PCAsignificance Man page
accumcomp Man page
accumplot Man page
accumresult Man page
add.spec.scores Man page
balanced.specaccum Man page
caprescale Man page
check.datasets Man page
check.ordiscores Man page
crosstabanalysis Man page
deviancepercentage Man page
dist.eval Man page
dist.zeroes Man page
distdisplayed Man page
disttransform Man page
diversitycomp Man page
diversityresult Man page
diversityvariables Man page
ensemble.VIF 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.weights Man page
ensemble.zones Man page
evaluation.strip.data Man page
evaluation.strip.plot Man page
faramea Man page
ifri Man page
import.from.Access Man page
import.from.Access2007 Man page
import.from.Excel Man page
import.from.Excel2007 Man page
importancevalue Man page
importancevalue.comp Man page
loaded.citations Man page
makecommunitydataset Man page
multiconstrained Man page
nested.anova.dbrda Man page
nested.npmanova Man page
nnetrandom Man page
onAttach Source code
ordibubble Man page
ordicluster2 Man page
ordicoeno Man page
ordiequilibriumcircle Man page
ordinearest Man page
ordisymbol Man page
ordivector 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

inst
inst/CITATION
inst/ChangeLog
inst/doc
inst/doc/Getting-started-ensemble-GUI.txt
inst/etc
inst/etc/Rcmdr-RMarkdown-Template.Rmd
inst/etc/reset.gif
inst/etc/dune.xlsx
inst/etc/redo.gif
inst/etc/edit.gif
inst/etc/dune.xls
inst/etc/view.gif
inst/etc/data.gif
inst/etc/blank.gif
inst/etc/Rcmdr-Markdown-Template.Rmd
inst/etc/ok.gif
inst/etc/Rcmdr-knitr-Template.Rnw
inst/etc/cancel.gif
inst/etc/R-logo.gif
inst/etc/undo.gif
inst/etc/Rcmdr-menus.txt
inst/etc/help-old.gif
inst/etc/model.gif
inst/etc/BiodiversityGUI.R
inst/etc/paste.gif
inst/etc/delete.gif
inst/etc/Rcmdr.xbm
inst/etc/Nations.txt
inst/etc/submit.gif
inst/etc/help.gif
inst/etc/dunestacked.csv
inst/etc/remove.gif
inst/etc/cut.gif
inst/etc/apply.gif
inst/etc/dune.mdb
inst/etc/copy.gif
inst/etc/find.gif
inst/etc/R-logo-old.ico
inst/etc/BiodiversityR-menus.txt
inst/etc/R-logo-old.gif
inst/etc/linux
inst/etc/linux/Rcmdr.svg
inst/etc/linux/Rcmdr.desktop
inst/etc/model-classes.txt
inst/etc/log-exceptions.txt
inst/etc/submit.xbm
inst/etc/R-logo.ico
NAMESPACE
data
data/transfspecies.txt.gz
data/ifri.txt.gz
data/faramea.txt.gz
data/BCI.env.txt.gz
data/warenv.txt.gz
data/warcom.txt.gz
data/transfgradient.txt.gz
R
R/residualssurface.R
R/ensemble.bioclim.graph.R
R/accumcomp.R
R/import.from.Access.R
R/ensemble.simplified.categories.R
R/ensemble.formulae.R
R/ensemble.strategy.R
R/ensemble.calibrate.models.nnet.R
R/ordinearest.R
R/diversityvariables.R
R/spatialsample.R
R/ensemble.VIF.R
R/check.ordiscores.R
R/ensemble.plot.R
R/ensemble.habitat.change.R
R/add.spec.scores.R
R/ensemble.batch.presence.R
R/replaceNAcomm.R
R/diversitycomp.R
R/PCAsignificance.R
R/ensemble.accepted.categories.R
R/NMSrandom.R
R/ensemble.ecocrop.R
R/renyicomp.R
R/ensemble.analogue.R
R/ensemble.zones.R
R/ensemble.calibrate.models.R
R/makecommunitydataset.R
R/ordicoeno.R
R/ensemble.novel.R
R/removezerospecies.R
R/caprescale.R
R/ensemble.centroids.R
R/ordicluster2.R
R/subsetcomm.R
R/same.sites.R
R/rankabuncomp.R
R/ordibubble.R
R/renyiresult.R
R/importancevalue.R
R/renyiaccumresult.R
R/dist.eval.R
R/crosstabanalysis.R
R/disttransform.R
R/ensemble.calibrate.weights.R
R/ensemble.area.R
R/removeNAenv.R
R/nested.npmanova.R
R/stackcommunitydataset.R
R/ordivector.R
R/accumresult.R
R/deviancepercentage.R
R/ensemble.raster.R
R/check.datasets.R
R/BiodiversityRGUI.R
R/ensemble.weights.R
R/nested.anova.dbrda.R
R/distdisplayed.R
R/loaded.citations.R
R/dist.zeroes.R
R/renyiplot.R
R/diversityresult.R
R/evaluation.strip.data.R
R/ensemble.dummy.variables.R
R/accumplot.R
R/ensemble.threshold.R
R/ensemble.bioclim.R
R/ensemble.drop1.R
R/balanced.specaccum.R
R/nnetrandom.R
R/radfitresult.R
R/prepare.bioenv.R
R/rankabundance.R
R/ensemble.calibrate.models.gbm.R
R/ordisymbol.R
R/CAPdiscrim.R
R/evaluation.strip.plot.R
R/removeNAcomm.R
R/rankabunplot.R
R/import.from.Excel.R
R/ordiequilibriumcircle.R
R/zzz.R
R/ensemble.mean.R
R/ensemble.batch.R
R/multiconstrained.R
MD5
DESCRIPTION
man
man/dist.zeroes.Rd
man/nnetrandom.Rd
man/ensemble.bioclim.graph.Rd
man/removeNAcomm.Rd
man/distdisplayed.Rd
man/deviancepercentage.Rd
man/ensemble.bioclim.Rd
man/ordisymbol.Rd
man/accumresult.Rd
man/BiodiversityR-package.Rd
man/caprescale.Rd
man/evaluation.strip.Rd
man/rankabundance.Rd
man/PCAsignificance.Rd
man/loaded.citations.Rd
man/renyiresult.Rd
man/importancevalue.Rd
man/ifri.Rd
man/transfspecies.Rd
man/BCI.env.Rd
man/transfgradient.Rd
man/add.spec.scores.Rd
man/CAPdiscrim.Rd
man/warenv.Rd
man/ensemble.novel.Rd
man/BiodiversityRGUI.Rd
man/ensemble.dummy.variables.Rd
man/ensemble.Rd
man/crosstabanalysis.Rd
man/multiconstrained.Rd
man/ensemble.raster.Rd
man/ordicoeno.Rd
man/makecommunitydataset.Rd
man/spatialsample.Rd
man/disttransform.Rd
man/balanced.specaccum.Rd
man/nested.anova.dbrda.Rd
man/ensemble.zones.Rd
man/radfitresult.Rd
man/ensemble.batch.Rd
man/warcom.Rd
man/residualssurface.Rd
man/dist.eval.Rd
man/ensemble.ecocrop.Rd
man/faramea.Rd
man/diversityresult.Rd
man/ensemble.analogue.Rd
man/NMSrandom.Rd
BiodiversityR documentation built on May 19, 2017, 1:41 p.m.