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BAT (version 2.11.0)

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

1,743

Version

2.11.0

License

GPL-3

Maintainer

Pedro Cardoso

Last Published

July 29th, 2025

Functions in BAT (2.11.0)

contribution

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

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

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

Coverage of datasets.
dummy

Dummify variables.
fill

Filling missing data.
cwm

Community Weighted Mean.
cwe

Community Weighted Evenness.
cwd

Community Weighted Dispersion.
dispersion

Phylogenetic/functional dispersion of species or individuals.
gower

Gower distance.
hull.beta

Beta diversity partitioning using convex hull hypervolumes.
functree

Functional tree for 338 species of spiders
gdm

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

Hill numbers.
guadiana

Sample data of spiders in Guadiana (Portugal)
hull.alpha

Alpha diversity using convex hull hypervolumes.
gamma

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

Interspecific abundance-occupancy relationship (IAOR).
hull.contribution

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

Gamma diversity using convex hull hypervolumes.
hull.sad

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

Build hyperspace.
kernel.arrangement

Functional arrangement of kernel density hypervolumes.
kernel.bandwidth

Kernel bandwidth estimation by median heuristic method with bootstrap CI
geres

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

Build convex hull hypervolumes.
hyper.arrangement

Functional arrangement within a functional space (generic function).
kernel.alpha

Alpha diversity using kernel density hypervolumes.
kernel.gamma

Gamma diversity using kernel density hypervolumes.
kernel.originality

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

Functional dispersion of kernel density hypervolumes.
kernel.evenness

Functional evenness of kernel density hypervolumes.
kernel.hotspots

Hotspots in hypervolumes.
kernel.beta.evenness

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

Quality of hyperspace.
kernel.beta

Beta diversity partitioning using kernel density hypervolumes.
kernel.evenness.contribution

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

Build kernel hypervolumes.
kernel.contribution

Contribution of each observation to the kernel density hypervolume.
optim.spatial

Optimization of spatial sampling.
optim.beta

Optimization of beta diversity sampling protocols.
optim.alpha

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

Efficiency statistics for alpha-sampling.
linnean

Create Linnean tree.
r2

Model R2.
phylotree

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

Species-abundance distribution (SAD).
raster.evenness

Maps of phylogenetic/functional evenness of species or individuals.
kernel.similarity

Pairwise similarity among kernel density hypervolumes.
kernel.sad

Species-abundance distribution (SAD) using kernel density hypervolumes.
sim.plot

Plots of simulated species spatial distributions.
sim.sad

Simulation of species abundance distributions (SAD).
originality

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

Maps of phylogenetic/functional dispersion of species or individuals.
raster.beta

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

Standardize variables.
tree.addTip

Add tips to a tree.
sim.tree

Simulation of phylogenetic or functional tree.
raster.alpha

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

Rao quadratic entropy.
slope

Slope of accumulation curves.
optim.beta.stats

Efficiency statistics for beta-sampling.
mixture

Mixture model.
sar

Species-area relationship (SAR).
sim.sample

Simulation of sampling from artificial communities.
sim.spatial

Simulation of species spatial distributions.
tree.zero

Convert negative branches of tree.
uniqueness

Phylogenetic/functional uniqueness of species.
tree.quality

Quality of tree.
ses

Standard Effect Size.
tree.build

Build functional tree.
alpha.estimate

Alpha diversity estimates.
alpha.accum

Alpha diversity accumulation curves (observed and estimated).
alpha

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

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

Sample data of spiders in Arrabida (Portugal)
accuracy

Scaled mean squared error of accumulation curves.
aic

Akaike Information Criterion.
beta

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

Beta diversity accumulation curves.
beta.multi

Beta diversity among multiple communities.