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BAT (version 2.11.3)

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

1,101

Version

2.11.3

License

GPL-3

Maintainer

Pedro Cardoso

Last Published

August 26th, 2026

Functions in BAT (2.11.3)

hill

Hill numbers.
functree

Functional tree for 338 species of spiders
hyper.arrangement

Functional arrangement within a functional space (generic function).
hull.sad

Species-abundance distribution (SAD) using convex hulls.
hyper.quality

Quality of hyperspace.
gower

Gower distance.
hyper.build

Build hyperspace.
guadiana

Sample data of spiders in Guadiana (Portugal)
cwe

Community Weighted Evenness.
hull.gamma

Gamma diversity using convex hull hypervolumes.
iaor

Interspecific abundance-occupancy relationship (IAOR).
gdm

General dynamic model of oceanic island biogeography (GDM).
hull.contribution

Contribution of each observation to a convex hull hypervolume.
geres

Sample data of spiders in Geres (Portugal)
hull.build

Build convex hull hypervolumes.
kernel.alpha

Alpha diversity using kernel density hypervolumes.
hull.beta

Beta diversity partitioning using convex hull hypervolumes.
kernel.contribution

Contribution of each observation to the kernel density hypervolume.
kernel.build

Build kernel hypervolumes.
kernel.dispersion

Functional dispersion of kernel density hypervolumes.
kernel.similarity

Pairwise similarity among kernel density hypervolumes.
mixture

Mixture model.
kernel.beta.evenness

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

Beta diversity partitioning using kernel density hypervolumes.
kernel.gamma

Gamma diversity using kernel density hypervolumes.
kernel.sad

Species-abundance distribution (SAD) using kernel density hypervolumes.
kernel.evenness.contribution

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

Create Linnean tree.
kernel.arrangement

Functional arrangement of kernel density hypervolumes.
gamma

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

Kernel bandwidth estimation by median heuristic method with bootstrap CI
optim.spatial

Optimization of spatial sampling.
hull.alpha

Alpha diversity using convex hull hypervolumes.
optim.beta.stats

Efficiency statistics for beta-sampling.
kernel.originality

Functional originality of observations in kernel density hypervolumes.
optim.beta

Optimization of beta diversity sampling protocols.
kernel.hotspots

Hotspots in hypervolumes.
sar

Species-area relationship (SAR).
rao

Rao quadratic entropy.
phylotree

Taxonomic tree for 338 species of spiders (surrogate for phylogeny)
ses

Standard Effect Size.
raster.alpha

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

Simulation of sampling from artificial communities.
sim.spatial

Simulation of species spatial distributions.
tree.quality

Quality of tree.
raster.dispersion

Maps of phylogenetic/functional dispersion of species or individuals.
tree.build

Build functional tree.
tree.zero

Convert negative branches of tree.
originality

Phylogenetic/functional originality of species or individuals.
raster.beta

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

Simulation of phylogenetic or functional tree.
slope

Slope of accumulation curves.
sim.sad

Simulation of species abundance distributions (SAD).
uniqueness

Phylogenetic/functional uniqueness of species.
sim.plot

Plots of simulated species spatial distributions.
kernel.evenness

Functional evenness of kernel density hypervolumes.
r2

Model R2.
standard

Standardize variables.
optim.alpha

Optimization of alpha diversity sampling protocols.
optim.alpha.stats

Efficiency statistics for alpha-sampling.
tree.addTip

Add tips to a tree.
sad

Species-abundance distribution (SAD).
raster.evenness

Maps of phylogenetic/functional evenness of species or individuals.
beta.multi

Beta diversity among multiple communities.
beta.evenness

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

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

Alpha diversity accumulation curves (observed and estimated).
evenness.contribution

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

Filling missing data.
accuracy

Scaled mean squared error of accumulation curves.
alpha.estimate

Alpha diversity estimates.
arrabida

Sample data of spiders in Arrabida (Portugal)
dummy

Dummify variables.
aic

Akaike Information Criterion.
contribution

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

Coverage of datasets.
evenness

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

Community Weighted Dispersion.
beta.accum

Beta diversity accumulation curves.
beta

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

Phylogenetic/functional dispersion of species or individuals.
cwm

Community Weighted Mean.