Calculate the sum of the inverse of the range size multiplied by the branch length for the species present in raster data.
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.
- inv.R
SpatRaster. Inverse of range size. See
inv.range- 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).
- filename
character. Output filename
- ...
additional arguments passed for terra::app
References
Laffan, S. W., Rosauer, D. F., Di Virgilio, G., Miller, J. T., González‐Orozco, C. E., Knerr, N., ... & Mishler, B. D. (2016). Range‐weighted metrics of species and phylogenetic turnover can better resolve biogeographic transition zones. Methods in Ecology and Evolution, 7(5), 580-588.
Rosauer, D. A. N., Laffan, S. W., Crisp, M. D., Donnellan, S. C. and Cook, L. G. (2009). Phylogenetic endemism: a new approach for identifying geographical concentrations of evolutionary history. Molecular ecology, 18(19), 4061-4072.
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"))
pe <- rast.pe(x = 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
plot(pe)
# }