BAT: Biodiversity Assessment Tools
Version 1.5.5

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 <pedro.cardoso@helsinki.fi>
LicenseGPL-3
Version1.5.5
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("BAT")

Popular man pages

alpha.accum: Alpha diversity accumulation curves (observed and estimated).
alpha.estimate: Alpha diversity estimates.
beta.accum: Beta diversity accumulation curves.
geres: Sample data of spiders in Geres (Portugal)
optim.beta: Optimization of beta diversity sampling protocols.
sar: Species-area relationship (SAR).
uniqueness: Phylogenetic/functional uniqueness of species or individuals.
See all...

All man pages Function index File listing

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.

Functions

AIC Source code
AICc Source code
accuracy Man page Source code
alpha Man page Source code
alpha.accum Man page Source code
alpha.estimate Man page Source code
arrabida Man page
beta Man page Source code
beta.accum Man page Source code
beta.multi Man page Source code
betaObs Source code
chao Source code
contribution Man page Source code
dispersion Man page Source code
functree Man page
gdm Man page Source code
geres Man page
guadiana Man page
iaor Man page Source code
jack1ab Source code
jack1in Source code
jack2ab Source code
jack2in Source code
logit Source code
minBranch Source code
optim.alpha Man page Source code
optim.alpha.stats Man page Source code
optim.beta Man page Source code
optim.beta.stats Man page Source code
optim.spatial Man page Source code
pcorr Source code
phylotree Man page
prep Source code
qrare Source code
r2 Source code
rarefaction Source code
raster.lat Source code
raster.long Source code
revLogit Source code
rss Source code
sar Man page Source code
sim.plot Man page Source code
sim.sad Man page Source code
sim.sample Man page Source code
sim.spatial Man page Source code
sim.tree Man page Source code
slope Man page Source code
sobs Source code
srare Source code
uniqueness Man page Source code
xTree Source code

Files

NAMESPACE
data
data/phylotree.rda
data/guadiana.rda
data/geres.rda
data/arrabida.rda
data/functree.rda
R
R/BAT.R
MD5
DESCRIPTION
man
man/guadiana.Rd
man/optim.spatial.Rd
man/arrabida.Rd
man/sar.Rd
man/accuracy.Rd
man/uniqueness.Rd
man/iaor.Rd
man/phylotree.Rd
man/sim.sad.Rd
man/contribution.Rd
man/optim.beta.stats.Rd
man/geres.Rd
man/sim.spatial.Rd
man/alpha.estimate.Rd
man/gdm.Rd
man/alpha.accum.Rd
man/beta.accum.Rd
man/alpha.Rd
man/sim.plot.Rd
man/beta.multi.Rd
man/sim.tree.Rd
man/optim.alpha.stats.Rd
man/functree.Rd
man/sim.sample.Rd
man/beta.Rd
man/slope.Rd
man/optim.beta.Rd
man/dispersion.Rd
man/optim.alpha.Rd
BAT documentation built on May 19, 2017, 11:46 p.m.

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