Learn R Programming
⚠️There's a newer version (2.11.0) of this package.Take me there.

BAT (version 2.5.1)

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) .

Copy Link

Version

Install

install.packages('BAT')

Monthly Downloads

1,250

Version

2.5.1

License

GPL-3

Maintainer

Pedro Cardoso

Last Published

April 27th, 2021

Functions in BAT (2.5.1)

alpha.accum

Alpha diversity accumulation curves (observed and estimated).
arrabida

Sample data of spiders in Arrabida (Portugal)
beta.evenness

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

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

Beta diversity among multiple communities.
accuracy

Scaled mean squared error of accumulation curves.
beta

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

Beta diversity accumulation curves.
alpha.estimate

Alpha diversity estimates.
cwe

Community Weighted Evenness.
functree

Functional tree for 338 species of spiders
dummy

Dummify variables.
kernel.beta

Beta diversity partitioning using kernel density hypervolumes.
dispersion

Phylogenetic/functional dispersion of species or individuals.
sad

Species-abundance distribution (SAD).
optim.beta

Optimization of beta diversity sampling protocols.
hull.contribution

Contribution of each observation (individuals or species) to the convex hull representing a given species or community.
optim.alpha.stats

Efficiency statistics for alpha-sampling.
hull.beta

Beta diversity partitioning using convex hulls.
raster.evenness

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

Functional beta diversity evenness using n-dimensional hypervolumes.
gdm

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

Community Weighted Mean.
iaor

Interspecific abundance-occupancy relationship (IAOR).
sim.sad

Simulation of species abundance distributions (SAD).
kernel.dispersion

Functional dispersion of a n-dimensional hypervolume representing a given community.
phylotree

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

Simulation of species spatial distributions.
originality

Phylogenetic/functional originality of species or individuals.
kernel.contribution

Contribution of each observation (species or individuals) to the n-dimensional hypervolume representing a given species or community.
alpha

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

Alpha diversity using kernel density hypervolumes.
sim.sample

Simulation of sampling from artificial communities.
coverage

Coverage of datasets.
linnean

Create Linnean tree.
sim.tree

Simulation of phylogenetic or functional tree.
geres

Sample data of spiders in Geres (Portugal)
optim.spatial

Optimization of spatial sampling.
cwd

Community Weighted Dispersion.
optim.beta.stats

Efficiency statistics for beta-sampling.
kernel.evenness

Functional evenness of a n-dimensional hypervolume representing a given community.
evenness

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

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

Hill numbers.
evenness.contribution

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

Alpha diversity using convex hulls.
rao.alpha

Rao quadratic entropy.
kernel.originality

Functional originality of observations (species or individuals) in a n-dimensional hypervolume representing a given species or community.
kernel.similarity

Pairwise similarity among n-dimensional hypervolumes.
raster.alpha

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

Slope of accumulation curves.
uniqueness

Phylogenetic/functional uniqueness of species.
optim.alpha

Optimization of alpha diversity sampling protocols.
raster.beta

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

Plots of simulated species spatial distributions.
kernel.evenness.contribution

Contribution of each observation to the evenness of a n-dimensional hypervolume representing a given species or community.
sar

Species-area relationship (SAR).
raster.dispersion

Maps of phylogenetic/functional dispersion of species or individuals.