BAT: Biodiversity Assessment Tools

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 depicting species relationships.

AuthorPedro Cardoso, Francois Rigal, Jose Carlos Carvalho
Date of publication2016-12-03 19:41:52
MaintainerPedro Cardoso <>

View on CRAN

Man pages

accuracy: Scaled mean squared error of accumulation curves.

alpha: Alpha diversity (Taxon, Phylogenetic or Functional Diversity...

alpha.accum: Alpha diversity accumulation curves (observed and estimated).

alpha.estimate: Alpha diversity estimates.

arrabida: Sample data of spiders in Arrabida (Portugal)

beta: Beta diversity (Taxon, Phylogenetic or Functional Diversity -...

beta.accum: Beta diversity accumulation curves.

beta.multi: Beta diversity among multiple communities.

contribution: Contribution of species or individuals to total PD or FD.

dispersion: Phylogenetic/functional dispersion of species or individuals.

functree: Functional tree for 338 species of spiders

gdm: General dynamic model of oceanic island biogeography (GDM).

geres: Sample data of spiders in Geres (Portugal)

guadiana: Sample data of spiders in Guadiana (Portugal)

iaor: Interspecific abundance-occupancy relationship (IAOR).

optim.alpha: Optimization of alpha diversity sampling protocols.

optim.alpha.stats: Efficiency statistics for alpha-sampling.

optim.beta: Optimization of beta diversity sampling protocols.

optim.beta.stats: Efficiency statistics for beta-sampling.

optim.spatial: Optimization of spatial sampling.

phylotree: Taxonomic tree for 338 species of spiders (surrogate for...

sar: Species-area relationship (SAR).

sim.plot: Plots of simulated species spatial distributions.

sim.sad: Simulation of species abundance distributions (SAD).

sim.sample: Simulation of sampling from artificial communities.

sim.spatial: Simulation of species spatial distributions.

sim.tree: Simulation of phylogenetic or functional tree.

slope: Slope of accumulation curves.

uniqueness: Phylogenetic/functional uniqueness of species or individuals.

Questions? Problems? Suggestions? or email at

All documentation is copyright its authors; we didn't write any of that.