Biodiversity Assessment Tools

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Documentation for package ‘BAT’ version 2.9.6

• DESCRIPTION file.

Help Pages

accuracy	Scaled mean squared error of accumulation curves.
aic	Akaike Information Criterion.
alpha	Alpha diversity (Taxon, Phylogenetic or Functional Diversity - TD, PD, FD).
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 - TD, PD, FD).
beta.accum	Beta diversity accumulation curves.
beta.evenness	Beta diversity evenness (Taxon, Phylogenetic or Functional Diversity - TD, PD, FD).
beta.multi	Beta diversity among multiple communities.
contribution	Contribution of species or individuals to total phylogenetic/functional diversity.
coverage	Coverage of datasets.
cwd	Community Weighted Dispersion.
cwe	Community Weighted Evenness.
cwm	Community Weighted Mean.
dispersion	Phylogenetic/functional dispersion of species or individuals.
dummy	Dummify variables.
evenness	Taxonomic/phylogenetic/functional evenness of species or individuals.
evenness.contribution	Contribution of each species or individual to the total taxonomic/phylogenetic/functional evenness.
fill	Filling missing data.
functree	Functional tree for 338 species of spiders
gamma	Gamma diversity (Taxon, Phylogenetic or Functional Diversity - TD, PD, FD).
gdm	General dynamic model of oceanic island biogeography (GDM).
geres	Sample data of spiders in Geres (Portugal)
gower	Gower distance.
guadiana	Sample data of spiders in Guadiana (Portugal)
hill	Hill numbers.
hull.alpha	Alpha diversity using convex hull hypervolumes.
hull.beta	Beta diversity partitioning using convex hull hypervolumes.
hull.build	Build convex hull hypervolumes.
hull.contribution	Contribution of each observation to a convex hull hypervolume.
hull.gamma	Gamma diversity using convex hull hypervolumes.
hull.sad	Species-abundance distribution (SAD) using convex hulls.
hyper.build	Build hyperspace.
hyper.quality	Quality of hyperspace.
iaor	Interspecific abundance-occupancy relationship (IAOR).
kernel.alpha	Alpha diversity using kernel density hypervolumes.
kernel.beta	Beta diversity partitioning using kernel density hypervolumes.
kernel.beta.evenness	Functional beta diversity evenness using kernel density hypervolumes.
kernel.build	Build kernel hypervolumes.
kernel.contribution	Contribution of each observation to the kernel density hypervolume.
kernel.dispersion	Functional dispersion of kernel density hypervolumes.
kernel.evenness	Functional evenness of kernel density hypervolumes.
kernel.evenness.contribution	Contribution of each observation to the evenness of a kernel density hypervolume.
kernel.gamma	Gamma diversity using kernel density hypervolumes.
kernel.hotspots	Hotspots in hypervolumes.
kernel.originality	Functional originality of observations in kernel density hypervolumes.
kernel.sad	Species-abundance distribution (SAD) using kernel density hypervolumes.
kernel.similarity	Pairwise similarity among kernel density hypervolumes.
linnean	Create Linnean tree.
mixture	Mixture model.
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.
originality	Phylogenetic/functional originality of species or individuals.
phylotree	Taxonomic tree for 338 species of spiders (surrogate for phylogeny)
r2	Model R2.
rao	Rao quadratic entropy.
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).
raster.dispersion	Maps of phylogenetic/functional dispersion of species or individuals.
raster.evenness	Maps of phylogenetic/functional evenness of species or individuals.
sad	Species-abundance distribution (SAD).
sar	Species-area relationship (SAR).
ses	Standard Effect Size.
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.
standard	Standardize variables.
tree.build	Build functional tree.
tree.quality	Quality of tree.
tree.zero	Convert negative branches of tree.
uniqueness	Phylogenetic/functional uniqueness of species.