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BAT (version 2.11.1)

Biodiversity Assessment Tools

Description

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) .

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Version

Install

install.packages('BAT')

Monthly Downloads

1,168

Version

2.11.1

License

GPL-3

Maintainer

Pedro Cardoso

Last Published

March 30th, 2026

Functions in BAT (2.11.1)

gower

Gower distance.
gdm

General dynamic model of oceanic island biogeography (GDM).
guadiana

Sample data of spiders in Guadiana (Portugal)
dispersion

Phylogenetic/functional dispersion of species or individuals.
hill

Hill numbers.
hull.contribution

Contribution of each observation to a convex hull hypervolume.
hull.alpha

Alpha diversity using convex hull hypervolumes.
hull.gamma

Gamma diversity using convex hull hypervolumes.
geres

Sample data of spiders in Geres (Portugal)
kernel.alpha

Alpha diversity using kernel density hypervolumes.
iaor

Interspecific abundance-occupancy relationship (IAOR).
kernel.bandwidth

Kernel bandwidth estimation by median heuristic method with bootstrap CI
gamma

Gamma diversity (Taxon, Phylogenetic or Functional Diversity - TD, PD, FD).
functree

Functional tree for 338 species of spiders
kernel.beta

Beta diversity partitioning using kernel density hypervolumes.
kernel.arrangement

Functional arrangement of kernel density hypervolumes.
hull.beta

Beta diversity partitioning using convex hull hypervolumes.
kernel.evenness

Functional evenness of kernel density hypervolumes.
kernel.dispersion

Functional dispersion of kernel density hypervolumes.
optim.alpha

Optimization of alpha diversity sampling protocols.
kernel.contribution

Contribution of each observation to the kernel density hypervolume.
originality

Phylogenetic/functional originality of species or individuals.
hull.sad

Species-abundance distribution (SAD) using convex hulls.
kernel.build

Build kernel hypervolumes.
hyper.arrangement

Functional arrangement within a functional space (generic function).
optim.spatial

Optimization of spatial sampling.
optim.alpha.stats

Efficiency statistics for alpha-sampling.
kernel.beta.evenness

Functional beta diversity evenness using kernel density hypervolumes.
optim.beta

Optimization of beta diversity sampling protocols.
kernel.originality

Functional originality of observations in kernel density hypervolumes.
kernel.hotspots

Hotspots in hypervolumes.
sad

Species-abundance distribution (SAD).
ses

Standard Effect Size.
optim.beta.stats

Efficiency statistics for beta-sampling.
sar

Species-area relationship (SAR).
raster.evenness

Maps of phylogenetic/functional evenness of species or individuals.
standard

Standardize variables.
linnean

Create Linnean tree.
phylotree

Taxonomic tree for 338 species of spiders (surrogate for phylogeny)
sim.plot

Plots of simulated species spatial distributions.
r2

Model R2.
sim.tree

Simulation of phylogenetic or functional tree.
hull.build

Build convex hull hypervolumes.
hyper.build

Build hyperspace.
hyper.quality

Quality of hyperspace.
kernel.gamma

Gamma diversity using kernel density hypervolumes.
kernel.evenness.contribution

Contribution of each observation to the evenness of a kernel density hypervolume.
mixture

Mixture model.
slope

Slope of accumulation curves.
raster.alpha

Maps of alpha diversity (Taxon, Phylogenetic or Functional Diversity - TD, PD, FD).
rao

Rao quadratic entropy.
raster.dispersion

Maps of phylogenetic/functional dispersion of species or individuals.
kernel.sad

Species-abundance distribution (SAD) using kernel density hypervolumes.
raster.beta

Maps of beta diversity (Taxon, Phylogenetic or Functional Diversity - TD, PD, FD).
kernel.similarity

Pairwise similarity among kernel density hypervolumes.
sim.sad

Simulation of species abundance distributions (SAD).
tree.quality

Quality of tree.
tree.build

Build functional tree.
sim.spatial

Simulation of species spatial distributions.
sim.sample

Simulation of sampling from artificial communities.
uniqueness

Phylogenetic/functional uniqueness of species.
tree.addTip

Add tips to a tree.
tree.zero

Convert negative branches of tree.
beta.evenness

Beta diversity evenness (Taxon, Phylogenetic or Functional Diversity - TD, PD, FD).
beta.multi

Beta diversity among multiple communities.
beta.accum

Beta diversity accumulation curves.
alpha

Auxiliary function, used only internally Alpha diversity (Taxon, Phylogenetic or Functional Diversity - TD, PD, FD).
aic

Akaike Information Criterion.
alpha.accum

Alpha diversity accumulation curves (observed and estimated).
beta

Beta diversity (Taxon, Phylogenetic or Functional Diversity - TD, PD, FD).
arrabida

Sample data of spiders in Arrabida (Portugal)
accuracy

Scaled mean squared error of accumulation curves.
coverage

Coverage of datasets.
contribution

Contribution of species or individuals to total phylogenetic/functional diversity.
alpha.estimate

Alpha diversity estimates.
cwe

Community Weighted Evenness.
cwd

Community Weighted Dispersion.
evenness

Taxonomic/phylogenetic/functional evenness of species or individuals.
dummy

Dummify variables.
cwm

Community Weighted Mean.
evenness.contribution

Contribution of each species or individual to the total taxonomic/phylogenetic/functional evenness.
fill

Filling missing data.