Package: BiodiversityR 2.16-1

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.

Authors:Roeland Kindt [cre, aut]

BiodiversityR_2.16-1.tar.gz
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BiodiversityR.pdf |BiodiversityR.html✨
BiodiversityR/json (API)

# Install 'BiodiversityR' in R:
install.packages('BiodiversityR', repos = c('https://roelandkindt.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Datasets:
  • BCI.env - Barro Colorado Island Quadrat Descriptions
  • CucurbitaClim - Baseline and Future WorldClim 2.1 Climatic Data for Cucurbita Species
  • faramea - Faramea occidentalis abundance in Panama
  • ifri - Example data from the International Forestry Resources and Institutions (IFRI) research network
  • transfgradient - Gradient for Hypothetical Example of Turover of Species Composition
  • transfspecies - Hypothetical Example of Turover of Species Composition
  • warcom - Warburgia ugandensis AFLP Scores
  • warenv - Warburgia ugandensis Population Structure

On CRAN:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

132 exports 16 stars 6.30 score 127 dependencies 1 dependents 115 mentions 358 scripts 3.1k downloads

Last updated 6 months agofrom:56b3103e6c. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKSep 10 2024
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R-4.4-winOKSep 10 2024
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R-4.3-macOKSep 10 2024

Exports:accumcompaccumcomp.longaccumplotaccumresultadd.spec.scoresaxis.longbalanced.specaccumBiodiversityR.changeLogBiodiversityRGUICAPdiscrimcaprescalecentroids.longcheck.datasetscheck.ordiscorescrosstabanalysisdeviancepercentagedist.evaldist.zeroesdistdisplayeddisttransformdiversitycompdiversityresultdiversityvariablesensemble.accepted.categoriesensemble.analogueensemble.analogue.objectensemble.areaensemble.batchensemble.bioclimensemble.bioclim.graphensemble.bioclim.graph.dataensemble.bioclim.objectensemble.calibrate.modelsensemble.calibrate.models.gbmensemble.calibrate.models.nnetensemble.calibrate.weightsensemble.centroidsensemble.chull.applyensemble.chull.buffer.distancesensemble.chull.createensemble.chull.MSDMensemble.concave.hullensemble.concave.unionensemble.concave.vennensemble.drop1ensemble.dummy.variablesensemble.ecocropensemble.ecocrop.objectensemble.envBlockensemble.envirem.masterstackensemble.envirem.runensemble.envirem.solradstackensemble.environmentalThinensemble.environmentalThin.claraensemble.evaluateensemble.formulaeensemble.habitat.changeensemble.meanensemble.novelensemble.novel.objectensemble.outliersensemble.outlierThinensemble.pairsensemble.PET.seasonensemble.PET.seasonsensemble.plotensemble.prec.seasonensemble.rasterensemble.redensemble.season.suitabilityensemble.SEDIensemble.simplified.categoriesensemble.spatialBlockensemble.spatialThinensemble.spatialThin.quantensemble.strategyensemble.terraensemble.thresholdensemble.Tjurensemble.tmean.seasonensemble.VIFensemble.VIF.dataframeensemble.weightsensemble.zonesevaluation.strip.dataevaluation.strip.plotimport.with.readxlimportancevalueimportancevalue.comploaded.citationsmakecommunitydatasetmulticonstrainednested.anova.dbrdanested.npmanovaNMSrandomnnetrandomordibubbleordicluster2ordicoenoordiellipse.longordiequilibriumcircleordinearestordisurfgrid.longordisymbolordivectorPCAsignificanceprepare.bioenvpvclust.longradfitresultrankabuncomprankabundancerankabunplotremoveNAcommremoveNAenvremovezerospeciesrenyi.longrenyiaccumresultrenyicomprenyicomp.longrenyiplotrenyiresultreplaceNAcommsame.sitessites.longspatialsamplespecies.longstackcommunitydatasetsubsetcommtreegoer.filtertreegoer.scoretreegoer.widenvectorfit.long

Dependencies:abindbackportsbase64encbitbit64bootbroombslibcachemcarcarDatacellrangercheckmateclassclicliprclustercolorspacecowplotcpp11crayondata.tableDBIDerivdigestdoBydplyre1071effectsestimabilityevaluatefansifarverfastmapfontawesomeforcatsforeignFormulafsgenericsggplot2gluegridExtragtablehavenhighrHmischmshtmlTablehtmltoolshtmlwidgetsinsightisobandjquerylibjsonliteknitrlabelinglatticelifecyclelme4magrittrMASSMatrixMatrixModelsmemoisemgcvmicrobenchmarkmimeminqamitoolsmodelrmunsellnlmenloptrnnetnortestnumDerivpbkrtestpermutepillarpkgconfigprettyunitsprogressproxypurrrquantregR6rappdirsRcmdrRcmdrMiscRColorBrewerRcppRcppArmadilloRcppEigenreadrreadstata13readxlrelimprematchrlangrmarkdownrpartrstudioapisandwichsassscalesSparseMstringistringrsurveysurvivaltcltk2tibbletidyrtidyselecttinytextzdbutf8vctrsveganviridisviridisLitevroomwithrxfunyamlzoo

Readme and manuals

Help Manual

Help pageTopics
GUI for biodiversity, suitability and community ecology analysisBiodiversityR-package BiodiversityR
Alternative Species Accumulation Curve Resultsaccumcomp accumplot accumresult
Add Species Scores to Unconstrained Ordination Resultsadd.spec.scores
Balanced Species Accumulation Curvesbalanced.specaccum
Barro Colorado Island Quadrat DescriptionsBCI.env
changeLog file for BiodiversityRBiodiversityR.changeLog
GUI for Biodiversity, Community Ecology and Ensemble Suitability AnalysisBiodiversityRGUI
Canonical Analysis of Principal Coordinates based on Discriminant AnalysisCAPdiscrim
Rescaling of Capscale Results to Reflect Total Sums of Squares Of Distance Matrixcaprescale
Presence-absence Analysis by Cross Tabulationcrosstabanalysis
Baseline and Future WorldClim 2.1 Climatic Data for Cucurbita SpeciesCucurbitaClim
Calculate Percentage and Significance of Deviance Explained by a GLMdeviancepercentage
Distance Matrix Evaluationdist.eval prepare.bioenv
Distance Matrix Transformationdist.zeroes
Compare Distance Displayed in Ordination Diagram with Distances of Distance Matrixdistdisplayed
Community Matrix Transformationdisttransform
Alternative Diversity Resultsdiversitycomp diversityresult diversityvariables
Climate analogues from climatic distance raster layers.ensemble.analogue ensemble.analogue.object
Suitability mapping based on ensembles of modelling algorithms: batch processingensemble.batch ensemble.mean ensemble.plot
Suitability mapping based on the BIOCLIM algorithmensemble.bioclim ensemble.bioclim.object
Graphs of bioclimatic ranges of species and climatesensemble.bioclim.graph ensemble.bioclim.graph.data
Suitability mapping based on ensembles of modelling algorithms: calibration of models and weightsensemble.calibrate.models ensemble.calibrate.models.gbm ensemble.calibrate.models.nnet ensemble.calibrate.weights ensemble.drop1 ensemble.formulae ensemble.pairs ensemble.strategy ensemble.threshold ensemble.VIF ensemble.VIF.dataframe ensemble.weights
Analysis of Niche Overlap in Environmental Space for Changed Climates via Concave Hullsensemble.concave.hull ensemble.concave.union ensemble.concave.venn ensemble.outliers
Suitability mapping based on ensembles of modelling algorithms: handling of categorical dataensemble.accepted.categories ensemble.dummy.variables ensemble.simplified.categories
Suitability mapping via absolute and optimal precipitation and temperature limits as in the ECOCROP model.ensemble.ecocrop ensemble.ecocrop.object
Calculate bioclimatic variables via the 'envirem' package for data.frames.ensemble.envirem.masterstack ensemble.envirem.run ensemble.envirem.solradstack
Model evaluation including True Skill Statistic (TSS), AUCdiff and Symmetric Extremal Dependence Index (SEDI).ensemble.evaluate ensemble.SEDI ensemble.Tjur
Mapping of novel environmental conditions (areas where some of the environmental conditions are outside the range of environmental conditions of a reference area).ensemble.novel ensemble.novel.object
Calculate the balance between precipitation and potential evapotranspiration for the dry season with the largest balance (maximum climatological water deficit, accumulated aridity).ensemble.PET.season
Raster calculations of beginnings and lengths of growing seasons from the difference between precipitation (P) and potential evapotranspiration (PET), defining dry months with 2 * P < PET.ensemble.PET.seasons ensemble.prec.season ensemble.season.suitability ensemble.tmean.season
Suitability mapping based on ensembles of modelling algorithms: consensus mappingensemble.area ensemble.habitat.change ensemble.raster
Area of Occupancy (AOO) and Extent of Occurrence (EOO) via the 'red' library.ensemble.chull.apply ensemble.chull.buffer.distances ensemble.chull.create ensemble.chull.MSDM ensemble.red
Spatially or environmentally separated folds for cross-validation via blockCV::spatialBlock or blockCV::envBlockensemble.envBlock ensemble.spatialBlock
Thinning of presence point coordinates in geographical or environmental spaceensemble.environmentalThin ensemble.environmentalThin.clara ensemble.outlierThin ensemble.spatialThin ensemble.spatialThin.quant
Suitability mapping based on ensembles of modelling algorithms: consensus mapping via the terra packageensemble.terra
Mapping of environmental zones based on the Mahalanobis distance from centroids in environmental space.ensemble.centroids ensemble.zones
Evaluation strips for ensemble suitability mappingevaluation.strip.data evaluation.strip.plot
Faramea occidentalis abundance in Panamafaramea
Example data from the International Forestry Resources and Institutions (IFRI) research networkifri
Importance Valueimportancevalue importancevalue.comp
Give Citation Information for all Loaded Packagesloaded.citations
Make a Community Dataset from a Stacked Datasetmakecommunitydataset stackcommunitydataset
Pairwise Comparisons for All Levels of a Categorical Variable by RDA, CCA or Capscalemulticonstrained
Nested Analysis of Variance via Distance-based Redundancy Analysis or Non-parametric Multivariate Analysis of Variancenested.anova.dbrda nested.npmanova
Calculate the NMS Result with the Smallest Stress from Various Random StartsNMSrandom
Calculate the NNET Result with the Smallest Value from Various Random Startsnnetrandom
Coenoclines for an Ordination Axisordicoeno
Add Other Graphical Items to Ordination Diagramsordibubble ordicluster2 ordinearest ordisymbol ordivector
PCA Significanceordiequilibriumcircle PCAsignificance
Alternative Rank Abundance Fitting Resultsradfitresult
Rank Abundance Curvesrankabuncomp rankabundance rankabunplot
Synchronize Community and Environmental Datasetscheck.datasets check.ordiscores import.with.readxl removeNAcomm removeNAenv removezerospecies replaceNAcomm same.sites subsetcomm
Alternative Renyi Diversity Resultsrenyiaccumresult renyicomp renyiplot renyiresult
Helper Functions to Prepare Plotting of Accumulation, Diversity Profile and Ordiplot Results via ggplot2accumcomp.long axis.long centroids.long ordiellipse.long ordisurfgrid.long pvclust.long renyi.long renyicomp.long sites.long species.long vectorfit.long
Spatial Sampling within a Polygonspatialsample
Gradient for Hypothetical Example of Turover of Species Compositiontransfgradient
Hypothetical Example of Turover of Species Compositiontransfspecies
Calculate climate scores with the Tree Globally Observed Environmental Ranges (TreeGOER) database.treegoer.filter treegoer.score treegoer.widen
Warburgia ugandensis AFLP Scoreswarcom
Warburgia ugandensis Population Structurewarenv