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BAT (version 2.1.1)

Biodiversity Assessment Tools

Description

Includes algorithms to assess alpha and beta diversity in all their dimensions (taxon, phylogenetic and functional diversity), whether communities are completely sampled or not. It allows performing a number of analyses based on either species identities or phylogenetic/functional trees or functional kernel n-dimensional hypervolumes depicting species relationships.

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Version

Install

install.packages('BAT')

Monthly Downloads

1,674

Version

2.1.1

License

GPL-3

Maintainer

Pedro Cardoso

Last Published

August 29th, 2020

Functions in BAT (2.1.1)

alpha.accum

Alpha diversity accumulation curves (observed and estimated).
contribution

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

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

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

Scaled mean squared error of accumulation curves.
beta.accum

Beta diversity accumulation curves.
arrabida

Sample data of spiders in Arrabida (Portugal)
cwm

Community Weighted Mean.
beta.multi

Beta diversity among multiple communities.
alpha.estimate

Alpha diversity estimates.
optim.alpha.stats

Efficiency statistics for alpha-sampling.
kernel.alpha

Alpha diversity using kernel density hypervolumes.
kernel.evenness

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

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

Interspecific abundance-occupancy relationship (IAOR).
dispersion

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

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

Species-abundance distribution (SAD).
evenness

Phylogenetic/functional evenness of species or individuals.
functree

Functional tree for 338 species of spiders
sim.plot

Plots of simulated species spatial distributions.
gdm

General dynamic model of oceanic island biogeography (GDM).
optim.beta

Optimization of beta diversity sampling protocols.
originality

Phylogenetic/functional originality of species or individuals.
phylotree

Taxonomic tree for 338 species of spiders (surrogate for phylogeny)
kernel.beta

Beta diversity partitioning using kernel density hypervolumes.
kernel.contribution

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

Create Linnean tree.
optim.alpha

Optimization of alpha diversity sampling protocols.
raster.dispersion

Maps of phylogenetic/functional dispersion of species or individuals.
sar

Species-area relationship (SAR).
raster.evenness

Maps of phylogenetic/functional evenness of species or individuals.
sim.sample

Simulation of sampling from artificial communities.
sim.sad

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

Simulation of species spatial distributions.
uniqueness

Phylogenetic/functional uniqueness of species.
guadiana

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

Optimization of spatial sampling.
optim.beta.stats

Efficiency statistics for beta-sampling.
raster.alpha

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

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

Sample data of spiders in Geres (Portugal)
slope

Slope of accumulation curves.
sim.tree

Simulation of phylogenetic or functional tree.
kernel.similarity

Pairwise similarity among n-dimensional hypervolumes.