rast.pd {phyloraster} | R Documentation |
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 |
branch.length |
numeric. A Named numeric vector of branch length for
each species. See |
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)