spat.alpha {divraster}

Alpha calculation for raster

Description

Calculates alpha diversity for taxonomic (TD), functional (FD), and phylogenetic (PD) dimensions. Adapted from alpha

Usage

spat.alpha(bin, tree, cores = 1, filename = "", ...)

Arguments

bin

A SpatRaster with presence-absence data (0 or 1) for a set of species.

tree

It can be a 'data.frame' with species traits or a 'phylo' with a rooted phylogenetic tree. Species names in 'tree' and 'bin' must match!

cores

A positive integer. If cores > 1, a 'parallel' package cluster with that many cores is created and used.

filename

Character. Save results if a name is provided.

...

Additional arguments to be passed passed down from a calling function.

Details

Alpha calculations use a tree-based approach for TD, FD, and PD (Cardoso et al. 2014). In the FD calculation, a species traits matrix is transformed into a distance matrix and clustered to create a regional dendrogram (i.e. a dendrogram with all species in the raster stack), from which the total branch length is calculated. When computing FD for each community (i.e. raster cell), the regional dendrogram is subsetted to create a local dendrogram that includes only the species present in the local community. The branch lengths connecting these species are then summed to represent the functional relationships of the locally present species (Petchey and Gaston, 2002, 2006). Similarly, in PD, the cumulative branch lengths connecting species within a community indicate their shared phylogenetic relationships (Faith, 1992). Alpha TD can also be visualized using a tree diagram, where each species is directly connected to the root by an edge of unit length, reflecting the number of different taxa in the community (i.e. species richness) since all taxa are at the same level (Cardoso et al. 2014).

Value

A SpatRaster with alpha result.

References

Cardoso, P. et al. 2014. Partitioning taxon, phylogenetic and functional beta diversity into replacement and richness difference components. - Journal of Biogeography 41: 749–761.

Faith, D. P. 1992. Conservation evaluation and phylogenetic diversity. - Biological Conservation 61: 1–10.

Petchey, O. L. and Gaston, K. J. 2002. Functional diversity (FD), species richness and community composition. - Ecology Letters 5: 402–411.

Rodrigues, A. S. L. and Gaston, K. J. 2002. Maximising phylogenetic diversity in the selection of networks of conservation areas. - Biological Conservation 105: 103–111.

Examples

library(terra)
bin1 <- terra::rast(system.file("extdata", "ref.tif",
package = "divraster"))
traits <- read.csv(system.file("extdata", "traits.csv",
package = "divraster"), row.names = 1)
tree <- ape::read.tree(system.file("extdata", "tree.tre",
package = "divraster"))
spat.alpha(bin1)
spat.alpha(bin1, traits)
spat.alpha(bin1, tree)