rast.pe {phyloraster}

Calculate phylogenetic endemism for raster data

Description

Calculate the sum of the inverse of the range size multiplied by the branch length for the species present in raster data.

Usage

rast.pe(
  x,
  tree,
  inv.R,
  branch.length,
  full_tree_metr = FALSE,
  filename = "",
  ...
)

Arguments

x

SpatRaster. A SpatRaster containing presence-absence data (0 or 1) for a set of species. The layers (species) will be sorted according to the tree order. See the phylo.pres function.

tree

phylo. A dated tree.

inv.R

SpatRaster. Inverse of range size. See inv.range

branch.length

numeric. A Named numeric vector of branch length for each species. See phylo.pres

full_tree_metr

logical. Whether edge.path, branch length and number of descendants should be calculated with the full (TRUE) or the prunned tree (FALSE).

filename

character. Output filename

...

additional arguments passed for terra::app

Value

SpatRaster

Author(s)

Gabriela Alves-Ferreira and Neander Marcel Heming

References

Laffan, S. W., Rosauer, D. F., Di Virgilio, G., Miller, J. T., González‐Orozco, C. E., Knerr, N., ... & Mishler, B. D. (2016). Range‐weighted metrics of species and phylogenetic turnover can better resolve biogeographic transition zones. Methods in Ecology and Evolution, 7(5), 580-588.

Rosauer, D. A. N., Laffan, S. W., Crisp, M. D., Donnellan, S. C. and Cook, L. G. (2009). Phylogenetic endemism: a new approach for identifying geographical concentrations of evolutionary history. Molecular ecology, 18(19), 4061-4072.

Examples

library(terra)
library(phyloraster)
x <- rast(system.file("extdata", "rast.presab.tif",
package = "phyloraster"))
tree <- ape::read.tree(system.file("extdata", "tree.nex",
package = "phyloraster"))
pe <- rast.pe(x = x[[1:3]], tree)
plot(pe)