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BAT (version 2.9.6)

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

1,083

Version

2.9.6

License

GPL-3

Maintainer

Pedro Cardoso

Last Published

February 17th, 2024

Functions in BAT (2.9.6)

beta.multi

Beta diversity among multiple communities.
beta

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

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

Beta diversity partitioning using convex hull hypervolumes.
kernel.alpha

Alpha diversity using kernel density hypervolumes.
contribution

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

Beta diversity accumulation curves.
kernel.evenness.contribution

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

Gower distance.
kernel.similarity

Pairwise similarity among kernel density hypervolumes.
hyper.build

Build hyperspace.
dummy

Dummify variables.
optim.alpha.stats

Efficiency statistics for alpha-sampling.
iaor

Interspecific abundance-occupancy relationship (IAOR).
hyper.quality

Quality of hyperspace.
hull.build

Build convex hull hypervolumes.
linnean

Create Linnean tree.
kernel.beta

Beta diversity partitioning using kernel density hypervolumes.
originality

Phylogenetic/functional originality of species or individuals.
accuracy

Scaled mean squared error of accumulation curves.
evenness

Taxonomic/phylogenetic/functional evenness of species or individuals.
kernel.gamma

Gamma diversity using kernel density hypervolumes.
optim.beta

Optimization of beta diversity sampling protocols.
phylotree

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

Community Weighted Evenness.
kernel.originality

Functional originality of observations in kernel density hypervolumes.
cwm

Community Weighted Mean.
sim.sad

Simulation of species abundance distributions (SAD).
sim.sample

Simulation of sampling from artificial communities.
aic

Akaike Information Criterion.
tree.zero

Convert negative branches of tree.
cwd

Community Weighted Dispersion.
geres

Sample data of spiders in Geres (Portugal)
alpha

Alpha diversity (Taxon, Phylogenetic or Functional Diversity - TD, PD, FD).
standard

Standardize variables.
gdm

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

Contribution of each observation to the kernel density hypervolume.
hull.sad

Species-abundance distribution (SAD) using convex hulls.
hill

Hill numbers.
arrabida

Sample data of spiders in Arrabida (Portugal)
alpha.estimate

Alpha diversity estimates.
hull.gamma

Gamma diversity using convex hull hypervolumes.
alpha.accum

Alpha diversity accumulation curves (observed and estimated).
coverage

Coverage of datasets.
uniqueness

Phylogenetic/functional uniqueness of species.
hull.alpha

Alpha diversity using convex hull hypervolumes.
kernel.dispersion

Functional dispersion of kernel density hypervolumes.
sar

Species-area relationship (SAR).
sad

Species-abundance distribution (SAD).
sim.spatial

Simulation of species spatial distributions.
guadiana

Sample data of spiders in Guadiana (Portugal)
kernel.beta.evenness

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

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

Build kernel hypervolumes.
kernel.hotspots

Hotspots in hypervolumes.
slope

Slope of accumulation curves.
kernel.evenness

Functional evenness of kernel density hypervolumes.
mixture

Mixture model.
optim.alpha

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

Efficiency statistics for beta-sampling.
r2

Model R2.
functree

Functional tree for 338 species of spiders
dispersion

Phylogenetic/functional dispersion of species or individuals.
sim.plot

Plots of simulated species spatial distributions.
sim.tree

Simulation of phylogenetic or functional tree.
optim.spatial

Optimization of spatial sampling.
ses

Standard Effect Size.
raster.beta

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

Contribution of each observation to a convex hull hypervolume.
kernel.sad

Species-abundance distribution (SAD) using kernel density hypervolumes.
tree.build

Build functional tree.
rao

Rao quadratic entropy.
raster.dispersion

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

Quality of tree.
raster.evenness

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

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

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

Filling missing data.