Calculates the standardized effect size for phylogenetic endemism. See Details for more information.
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.
- branch.length
numeric. A Named numeric vector of branch length for each species. See
phylo.pres- inv.R
SpatRaster. Inverse of range size. See
inv.range- spat_alg
A function with the algorithm implementing the desired randomization method. It must work with SpatRaster objects. See examples. Example of functions that work are:
bootspat_naive,bootspat_str,bootspat_ff.- spat_alg_args
List of arguments passed to the randomization method chosen in 'spat_alg'. See
bootspat_naive,bootspat_str,bootspat_ff- random
character. A character indicating the type of randomization. The currently available randomization methods are "tip", "site", "species" or "both" (site and species).
- aleats
positive integer. A positive integer indicating how many times the calculation should be repeated.
- cores
positive integer. If
cores > 1, a 'parallel' package cluster with that many cores is created and used. You can also supply a cluster object. Ignored for functions that are implemented by terra in C++ (see under fun)- filename
character. Output filename
- ...
additional arguments passed for terra::app
Details
The spatial randomization (spat) keeps the richness exact and samples species presences proportionally to their observed frequency (i.e. number of occupied pixels). The randomization will not assign values to cells with nodata. The phylogenetic randomization shuffles taxa names across all taxa included in phylogeny.
References
Rosauer, D. A. N., Laffan, S. W., Crisp, M. D., Donnellan, S. C., & Cook, L. G. (2009). Phylogenetic endemism: a new approach for identifying geographical concentrations of evolutionary history. Molecular ecology, 18(19), 4061-4072.
See also
phylo.pres,
inv.range,
geo.phylo.ses,
rast.ed.ses,
rast.pd.ses,
rast.we.ses,
rast.pe.ses,
bootspat_str,
bootspat_naive,
bootspat_ff,
SESraster
Examples
# \donttest{
library(terra)
library(phyloraster)
library(SESraster)
x <- terra::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
range.BL <- inv.range(data$x)
t <- rast.pe.ses(x = data$x, tree, aleats = 3,
random = "spat")
#> 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(t)
# }