Package: BAT 2.9.6

Pedro Cardoso

BAT: Biodiversity Assessment Tools

Includes algorithms to assess alpha and beta diversity in all their dimensions (taxonomic, phylogenetic and functional). It allows performing a number of analyses based on species identities/abundances, phylogenetic/functional distances, trees, convex-hulls or kernel density n-dimensional hypervolumes depicting species relationships. Cardoso et al. (2015) <doi:10.1111/2041-210X.12310>.

Authors:Pedro Cardoso [aut, cre], Stefano Mammola [aut], Francois Rigal [aut], Jose Carvalho [aut]

BAT_2.9.6.tar.gz
BAT_2.9.6.tar.gz(r-4.5-noble)BAT_2.9.6.tar.gz(r-4.4-noble)
BAT_2.9.6.tgz(r-4.4-emscripten)BAT_2.9.6.tgz(r-4.3-emscripten)
BAT.pdf |BAT.html✨
BAT/json (API)

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

Peer review:

Datasets:
  • arrabida - Sample data of spiders in Arrabida
  • functree - Functional tree for 338 species of spiders
  • geres - Sample data of spiders in Geres
  • guadiana - Sample data of spiders in Guadiana
  • phylotree - Taxonomic tree for 338 species of spiders

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

73 exports 5.21 score 124 dependencies 3 dependents 60 mentions 66 scripts 1.3k downloads

Last updated 7 months agofrom:d43ab82395. Checks:OK: 2. Indexed: yes.

TargetResultDate
Doc / VignettesOKSep 15 2024
R-4.5-linuxOKSep 15 2024

Exports:accuracyaicalphaalpha.accumalpha.estimatebetabeta.accumbeta.evennessbeta.multicontributioncoveragecwdcwecwmdispersiondummyevennessevenness.contributionfillgammagdmgowerhillhull.alphahull.betahull.buildhull.contributionhull.gammahull.sadhyper.buildhyper.qualityiaorkernel.alphakernel.betakernel.beta.evennesskernel.buildkernel.contributionkernel.dispersionkernel.evennesskernel.evenness.contributionkernel.gammakernel.hotspotskernel.originalitykernel.sadkernel.similaritylinneanmixtureoptim.alphaoptim.alpha.statsoptim.betaoptim.beta.statsoptim.spatialoriginalityr2raoraster.alpharaster.betaraster.dispersionraster.evennesssadsarsessim.plotsim.sadsim.samplesim.spatialsim.treeslopestandardtree.buildtree.qualitytree.zerouniqueness

Dependencies:abindapecaretclasscliclockclusterclusterGenerationcodacodetoolscolorspacecombinatcpp11crayondata.tableDEoptimdiagramdigestdoParalleldplyre1071expmfansifarverfastclusterfastmatchFNNforeachfuturefuture.applygenericsgeometryggplot2globalsgluegowergtablehardhathitandrunhmshypervolumeigraphipredisobanditeratorskernlabKernSmoothkslabelinglatticelavalifecyclelinproglistenvlpSolvelubridatemagicmagrittrmapsMASSMatrixmclustmgcvmnormtModelMetricsmulticoolmunsellmvtnormnlmenls2nnetnumDerivoptimParallelpalmerpenguinsparallellypbapplypdistpermutephangornphytoolspillarpkgconfigplyrpracmaprettyunitspROCprodlimprogressprogressrprotoproxypurrrquadprogR6rasterrcddRColorBrewerRcppRcppArmadilloRcppProgressrecipesreshape2rlangrpartscalesscatterplot3dshapespSQUAREMstringistringrsurvivalterratibbletidyrtidyselecttimechangetimeDatetzdbutf8vctrsveganviridisLitewithr

Readme and manuals

Help Manual

Help pageTopics
Scaled mean squared error of accumulation curves.accuracy
Akaike Information Criterion.aic
Alpha diversity (Taxon, Phylogenetic or Functional Diversity - TD, PD, FD).alpha
Alpha diversity accumulation curves (observed and estimated).alpha.accum
Alpha diversity estimates.alpha.estimate
Sample data of spiders in Arrabida (Portugal)arrabida
Beta diversity (Taxon, Phylogenetic or Functional Diversity - TD, PD, FD).beta
Beta diversity accumulation curves.beta.accum
Beta diversity evenness (Taxon, Phylogenetic or Functional Diversity - TD, PD, FD).beta.evenness
Beta diversity among multiple communities.beta.multi
Contribution of species or individuals to total phylogenetic/functional diversity.contribution
Coverage of datasets.coverage
Community Weighted Dispersion.cwd
Community Weighted Evenness.cwe
Community Weighted Mean.cwm
Phylogenetic/functional dispersion of species or individuals.dispersion
Dummify variables.dummy
Taxonomic/phylogenetic/functional evenness of species or individuals.evenness
Contribution of each species or individual to the total taxonomic/phylogenetic/functional evenness.evenness.contribution
Filling missing data.fill
Functional tree for 338 species of spidersfunctree
Gamma diversity (Taxon, Phylogenetic or Functional Diversity - TD, PD, FD).gamma
General dynamic model of oceanic island biogeography (GDM).gdm
Sample data of spiders in Geres (Portugal)geres
Gower distance.gower
Sample data of spiders in Guadiana (Portugal)guadiana
Hill numbers.hill
Alpha diversity using convex hull hypervolumes.hull.alpha
Beta diversity partitioning using convex hull hypervolumes.hull.beta
Build convex hull hypervolumes.hull.build
Contribution of each observation to a convex hull hypervolume.hull.contribution
Gamma diversity using convex hull hypervolumes.hull.gamma
Species-abundance distribution (SAD) using convex hulls.hull.sad
Build hyperspace.hyper.build
Quality of hyperspace.hyper.quality
Interspecific abundance-occupancy relationship (IAOR).iaor
Alpha diversity using kernel density hypervolumes.kernel.alpha
Beta diversity partitioning using kernel density hypervolumes.kernel.beta
Functional beta diversity evenness using kernel density hypervolumes.kernel.beta.evenness
Build kernel hypervolumes.kernel.build
Contribution of each observation to the kernel density hypervolume.kernel.contribution
Functional dispersion of kernel density hypervolumes.kernel.dispersion
Functional evenness of kernel density hypervolumes.kernel.evenness
Contribution of each observation to the evenness of a kernel density hypervolume.kernel.evenness.contribution
Gamma diversity using kernel density hypervolumes.kernel.gamma
Hotspots in hypervolumes.kernel.hotspots
Functional originality of observations in kernel density hypervolumes.kernel.originality
Species-abundance distribution (SAD) using kernel density hypervolumes.kernel.sad
Pairwise similarity among kernel density hypervolumes.kernel.similarity
Create Linnean tree.linnean
Mixture model.mixture
Optimization of alpha diversity sampling protocols.optim.alpha
Efficiency statistics for alpha-sampling.optim.alpha.stats
Optimization of beta diversity sampling protocols.optim.beta
Efficiency statistics for beta-sampling.optim.beta.stats
Optimization of spatial sampling.optim.spatial
Phylogenetic/functional originality of species or individuals.originality
Taxonomic tree for 338 species of spiders (surrogate for phylogeny)phylotree
Model R2.r2
Rao quadratic entropy.rao
Maps of alpha diversity (Taxon, Phylogenetic or Functional Diversity - TD, PD, FD).raster.alpha
Maps of beta diversity (Taxon, Phylogenetic or Functional Diversity - TD, PD, FD).raster.beta
Maps of phylogenetic/functional dispersion of species or individuals.raster.dispersion
Maps of phylogenetic/functional evenness of species or individuals.raster.evenness
Species-abundance distribution (SAD).sad
Species-area relationship (SAR).sar
Standard Effect Size.ses
Plots of simulated species spatial distributions.sim.plot
Simulation of species abundance distributions (SAD).sim.sad
Simulation of sampling from artificial communities.sim.sample
Simulation of species spatial distributions.sim.spatial
Simulation of phylogenetic or functional tree.sim.tree
Slope of accumulation curves.slope
Standardize variables.standard
Build functional tree.tree.build
Quality of tree.tree.quality
Convert negative branches of tree.tree.zero
Phylogenetic/functional uniqueness of species.uniqueness