rast.pd {phyloraster}

Calculate phylogenetic diversity for raster data

Description

Calculate the sum of the branch length for species present in each cell of the raster.

Usage

rast.pd(x, tree, edge.path, branch.length, 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.

edge.path

matrix representing the paths through the tree from root to each tip. See phylo.pres

branch.length

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

filename

character. Output filename

...

additional arguments passed for terra::app

Value

SpatRaster

Author(s)

Neander Marcel Heming and Gabriela Alves-Ferreira

References

Faith, D. P. (1992). Conservation evaluation and phylogenetic diversity. Biological conservation, 61(1), 1-10.

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"))
data <- phylo.pres(x[[1:3]], tree)
pd <- rast.pd(data$x, edge.path = data$edge.path,
branch.length = data$branch.length)
plot(pd)