Calculate the sum of the branch length for species present in each cell of the raster.
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
References
Faith, D. P. (1992). Conservation evaluation and phylogenetic diversity. Biological conservation, 61(1), 1-10.
Examples
# \donttest{
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)
#> Warning: Some species in the phylogeny 'tree' are missing from the
#> SpatRaster 'x' and were dropped: Litoria_dorsalis, Litoria_rubella, Litoria_nigrofrenata, Litoria_nasuta, Litoria_tornieri, Litoria_inermis, Litoria_pallida, Litoria_latopalmata, Litoria_bicolor, Litoria_fallax, Litoria_genimaculata, Litoria_andiirrmalin, Litoria_wilcoxii, Litoria_jungguy, Litoria_caerulea, Litoria_gracilenta, Litoria_chloris, Litoria_xanthomera, Cyclorana_brevipes, Cyclorana_novaehollandiae, Cyclorana_manya, Cyclorana_cultripes, Litoria_alboguttata, Cyclorana_longipes, Nyctimystes_dayi, Litoria_nannotis, Litoria_lorica, Litoria_rheocola, Litoria_nyakalensis, Litoria_infrafrenata
pd <- rast.pd(data$x, edge.path = data$edge.path,
branch.length = data$branch.length)
plot(pd)
# }