rast.ed: Calculate Evolutionary distinctiveness for raster data

In phyloraster: Evolutionary Diversity Metrics for Raster Data

Calculate Evolutionary distinctiveness for raster data

Description

This function calculates evolutionary distinctiveness according to the fair-proportion index. The values represents the mean ED for species presents in each raster cell.

Usage

rast.ed(
  x,
  tree,
  edge.path,
  branch.length,
  n.descen,
  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
n.descen	numeric. A Named numeric vector of number of descendants for each branch. 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

Isaac, N. J., Turvey, S. T., Collen, B., Waterman, C. and Baillie, J. E. (2007). Mammals on the EDGE: conservation priorities based on threat and phylogeny. PLoS ONE 2, e296.

Examples

library(terra)
library(phyloraster)
x <- rast(system.file("extdata", "rast.presab.tif",
package="phyloraster"))
# phylogenetic tree
tree <- ape::read.tree(system.file("extdata", "tree.nex",
package="phyloraster"))
data <- phylo.pres(x[[1:3]], tree)
ed <- rast.ed(data$x, edge.path = data$edge.path,
              branch.length = data$branch.length,
              n.descen = data$n.descen)
plot(ed)

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