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.

Author
Pedro Cardoso, Francois Rigal, Jose Carlos Carvalho
Date of publication
2016-12-03 19:41:52
Maintainer
Pedro Cardoso <pedro.cardoso@helsinki.fi>
License
GPL-3
Version
1.5.5

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.

Files in this package

BAT
BAT/NAMESPACE
BAT/data
BAT/data/phylotree.rda
BAT/data/guadiana.rda
BAT/data/geres.rda
BAT/data/arrabida.rda
BAT/data/functree.rda
BAT/R
BAT/R/BAT.R
BAT/MD5
BAT/DESCRIPTION
BAT/man
BAT/man/guadiana.Rd
BAT/man/optim.spatial.Rd
BAT/man/arrabida.Rd
BAT/man/sar.Rd
BAT/man/accuracy.Rd
BAT/man/uniqueness.Rd
BAT/man/iaor.Rd
BAT/man/phylotree.Rd
BAT/man/sim.sad.Rd
BAT/man/contribution.Rd
BAT/man/optim.beta.stats.Rd
BAT/man/geres.Rd
BAT/man/sim.spatial.Rd
BAT/man/alpha.estimate.Rd
BAT/man/gdm.Rd
BAT/man/alpha.accum.Rd
BAT/man/beta.accum.Rd
BAT/man/alpha.Rd
BAT/man/sim.plot.Rd
BAT/man/beta.multi.Rd
BAT/man/sim.tree.Rd
BAT/man/optim.alpha.stats.Rd
BAT/man/functree.Rd
BAT/man/sim.sample.Rd
BAT/man/beta.Rd
BAT/man/slope.Rd
BAT/man/optim.beta.Rd
BAT/man/dispersion.Rd
BAT/man/optim.alpha.Rd