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.


accuracy Man page
alpha Man page
alpha.accum Man page
alpha.estimate Man page
arrabida Man page
beta Man page
beta.accum Man page
beta.multi Man page
contribution Man page
dispersion Man page
functree Man page
gdm Man page
geres Man page
guadiana Man page
iaor Man page
optim.alpha Man page
optim.alpha.stats Man page
optim.beta Man page
optim.beta.stats Man page
optim.spatial Man page
phylotree Man page
sar Man page
sim.plot Man page
sim.sad Man page
sim.sample Man page
sim.spatial Man page
sim.tree Man page
slope Man page
uniqueness Man page

Questions? Problems? Suggestions? or email at

Please suggest features or report bugs with the GitHub issue tracker.

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