Biodiversity Assessment Tools


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Documentation for package ‘BAT’ version 2.6.0

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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.
fill Filling missing data.
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)
gower Gower distance.
guadiana Sample data of spiders in Guadiana (Portugal)
hill Hill numbers.
hull.alpha Alpha diversity using convex hull hypervolumes.
hull.beta Beta diversity partitioning using convex hull hypervolumes.
hull.build Build convex hull hypervolumes.
hull.contribution Contribution of each observation to a convex hull hypervolume.
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 kernel density hypervolumes.
kernel.build Build kernel hypervolumes.
kernel.contribution Contribution of each observation to the kernel density hypervolume.
kernel.dispersion Functional dispersion of kernel density hypervolumes.
kernel.evenness Functional evenness of kernel density hypervolumes.
kernel.evenness.contribution Contribution of each observation to the evenness of a kernel density hypervolume.
kernel.originality Functional originality of observations in kernel density hypervolumes.
kernel.similarity Pairwise similarity among kernel density 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 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.
standard Standardize variables.
tree.build Build functional tree.
uniqueness Phylogenetic/functional uniqueness of species.