R: Biodiversity Assessment Tools

# Biodiversity Assessment Tools

## Documentation for package ‘BAT’ version 2.11.1

- DESCRIPTION file

## Help Pages

accuracy | Scaled mean squared error of accumulation curves.
aic | Akaike Information Criterion.
alpha | Auxiliary function, used only internally 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.arrangement | Functional arrangement within a functional space (generic function).
hyper.build | Build hyperspace.
hyper.quality | Quality of hyperspace.
iaor | Interspecific abundance-occupancy relationship (IAOR).
kernel.alpha | Alpha diversity using kernel density hypervolumes.
kernel.arrangement | Functional arrangement of kernel density hypervolumes.
kernel.bandwidth | Kernel bandwidth estimation by median heuristic method with bootstrap CI
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.addTip | Add tips to a tree.
tree.build | Build functional tree.
tree.quality | Quality of tree.
tree.zero | Convert negative branches of tree.
uniqueness | Phylogenetic/functional uniqueness of species.