rast.pd: Calculate phylogenetic diversity for raster data

In phyloraster: Evolutionary Diversity Metrics for Raster Data

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,
  full_tree_metr = TRUE,
  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. 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
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). The default is TRUE.
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$x, data$tree)
plot(pd)

phyloraster documentation built on April 3, 2025, 8:45 p.m.