Biodiversity Assessment Tools

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Documentation for package ‘BAT’ version 2.5.1

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accuracy Scaled mean squared error of accumulation curves.
alpha Alpha diversity (Taxon, Phylogenetic or Functional Diversity - TD, PD, FD).
alpha.accum Alpha diversity accumulation curves (observed and estimated).
alpha.estimate Alpha diversity estimates.
arrabida Sample data of spiders in Arrabida (Portugal)
beta Beta diversity (Taxon, Phylogenetic or Functional Diversity - TD, PD, FD).
beta.accum Beta diversity accumulation curves.
beta.evenness Beta diversity evenness (Taxon, Phylogenetic or Functional Diversity - TD, PD, FD).
beta.multi Beta diversity among multiple communities.
contribution Contribution of species or individuals to total phylogenetic/functional diversity.
coverage Coverage of datasets.
cwd Community Weighted Dispersion.
cwe Community Weighted Evenness.
cwm Community Weighted Mean.
dispersion Phylogenetic/functional dispersion of species or individuals.
dummy Dummify variables.
evenness Taxonomic/phylogenetic/functional evenness of species or individuals.
evenness.contribution Contribution of each species or individual to the total taxonomic/phylogenetic/functional evenness.
functree Functional tree for 338 species of spiders
gdm General dynamic model of oceanic island biogeography (GDM).
geres Sample data of spiders in Geres (Portugal)
guadiana Sample data of spiders in Guadiana (Portugal)
hill.alpha Hill numbers.
hull.alpha Alpha diversity using convex hulls.
hull.beta Beta diversity partitioning using convex hulls.
hull.contribution Contribution of each observation (individuals or species) to the convex hull representing a given species or community.
iaor Interspecific abundance-occupancy relationship (IAOR).
kernel.alpha Alpha diversity using kernel density hypervolumes.
kernel.beta Beta diversity partitioning using kernel density hypervolumes.
kernel.beta.evenness Functional beta diversity evenness using n-dimensional hypervolumes.
kernel.contribution Contribution of each observation (species or individuals) to the n-dimensional hypervolume representing a given species or community.
kernel.dispersion Functional dispersion of a n-dimensional hypervolume representing a given community.
kernel.evenness Functional evenness of a n-dimensional hypervolume representing a given community.
kernel.evenness.contribution Contribution of each observation to the evenness of a n-dimensional hypervolume representing a given species or community.
kernel.originality Functional originality of observations (species or individuals) in a n-dimensional hypervolume representing a given species or community.
kernel.similarity Pairwise similarity among n-dimensional hypervolumes.
linnean Create Linnean tree.
optim.alpha Optimization of alpha diversity sampling protocols.
optim.alpha.stats Efficiency statistics for alpha-sampling.
optim.beta Optimization of beta diversity sampling protocols.
optim.beta.stats Efficiency statistics for beta-sampling.
optim.spatial Optimization of spatial sampling.
originality Phylogenetic/functional originality of species or individuals.
phylotree Taxonomic tree for 338 species of spiders (surrogate for phylogeny)
rao.alpha Rao quadratic entropy.
raster.alpha Maps of alpha diversity (Taxon, Phylogenetic or Functional Diversity - TD, PD, FD).
raster.beta Maps of beta diversity (Taxon, Phylogenetic or Functional Diversity - TD, PD, FD).
raster.dispersion Maps of phylogenetic/functional dispersion of species or individuals.
raster.evenness Maps of phylogenetic/functional evenness of species or individuals.
sad Species-abundance distribution (SAD).
sar Species-area relationship (SAR).
sim.plot Plots of simulated species spatial distributions.
sim.sad Simulation of species abundance distributions (SAD).
sim.sample Simulation of sampling from artificial communities.
sim.spatial Simulation of species spatial distributions.
sim.tree Simulation of phylogenetic or functional tree.
slope Slope of accumulation curves.
uniqueness Phylogenetic/functional uniqueness of species.