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 |
| imports | graphics , hypervolume , nls2 , raster , spatstat , stats , utils , vegan |
| depends | R (>= 3.0.0) |
| Contributors | Francois Rigal, Pedro Cardoso, Jose Carvalho, Stefano Mammola |
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