BiodiversityR: Package for Community Ecology and Suitability Analysis

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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.

Author
Roeland Kindt
Date of publication
2016-08-29 14:16:03
Maintainer
Roeland Kindt <R.KINDT@CGIAR.ORG>
License
GPL-2
Version
2.7-2
URLs

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 Analysis and Ordination
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.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

Files in this package

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/ordispider.centroids.R
BiodiversityR/R/residualssurface.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/ordinearest.R
BiodiversityR/R/diversityvariables.R
BiodiversityR/R/spatialsample.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/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/ordihull.centroids.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/ensemble.test.R
BiodiversityR/R/ordibubble.R
BiodiversityR/R/ensemble.test.gbm.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.area.R
BiodiversityR/R/removeNAenv.R
BiodiversityR/R/nested.npmanova.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/ensemble.test.splits.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/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/ensemble.test.nnet.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/removeNAcomm.Rd
BiodiversityR/man/distdisplayed.Rd
BiodiversityR/man/deviancepercentage.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