BAT v2.1.1

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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 or functional kernel n-dimensional hypervolumes depicting species relationships.

Functions in BAT

Name Description
alpha.accum Alpha diversity accumulation curves (observed and estimated).
contribution Contribution of species or individuals to total phylogenetic/functional diversity.
alpha Alpha diversity (Taxon, Phylogenetic or Functional Diversity - TD, PD, FD).
beta Beta diversity (Taxon, Phylogenetic or Functional Diversity - TD, PD, FD).
accuracy Scaled mean squared error of accumulation curves.
beta.accum Beta diversity accumulation curves.
arrabida Sample data of spiders in Arrabida (Portugal)
cwm Community Weighted Mean.
beta.multi Beta diversity among multiple communities.
alpha.estimate Alpha diversity estimates.
optim.alpha.stats Efficiency statistics for alpha-sampling.
kernel.alpha Alpha diversity using kernel density hypervolumes.
kernel.evenness Functional evenness of a n-dimensional hypervolume representing a given community.
kernel.dispersion Functional dispersion of a n-dimensional hypervolume representing a given community.
iaor Interspecific abundance-occupancy relationship (IAOR).
dispersion Phylogenetic/functional dispersion of species or individuals.
kernel.originality Functional originality of observations (species or individuals) in a n-dimensional hypervolume representing a given species or community.
sad Species-abundance distribution (SAD).
evenness Phylogenetic/functional evenness of species or individuals.
functree Functional tree for 338 species of spiders
sim.plot Plots of simulated species spatial distributions.
gdm General dynamic model of oceanic island biogeography (GDM).
optim.beta Optimization of beta diversity sampling protocols.
originality Phylogenetic/functional originality of species or individuals.
phylotree Taxonomic tree for 338 species of spiders (surrogate for phylogeny)
kernel.beta Beta diversity partitioning using kernel density hypervolumes.
kernel.contribution Contribution of each observation (species or individuals) to the n-dimensional hypervolume representing a given species or community.
linnean Create Linnean tree.
optim.alpha Optimization of alpha diversity sampling protocols.
raster.dispersion Maps of phylogenetic/functional dispersion of species or individuals.
sar Species-area relationship (SAR).
raster.evenness Maps of phylogenetic/functional evenness of species or individuals.
sim.sample Simulation of sampling from artificial communities.
sim.sad Simulation of species abundance distributions (SAD).
sim.spatial Simulation of species spatial distributions.
uniqueness Phylogenetic/functional uniqueness of species.
guadiana Sample data of spiders in Guadiana (Portugal)
optim.spatial Optimization of spatial sampling.
optim.beta.stats Efficiency statistics for beta-sampling.
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).
geres Sample data of spiders in Geres (Portugal)
slope Slope of accumulation curves.
sim.tree Simulation of phylogenetic or functional tree.
kernel.similarity Pairwise similarity among n-dimensional hypervolumes.
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Details

Date 2020-08-29
Encoding UTF-8
License GPL-3
LazyData true
RoxygenNote 7.1.1
NeedsCompilation no
Packaged 2020-08-29 08:00:02 UTC; ungol
Repository CRAN
Date/Publication 2020-08-29 10:00:02 UTC

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