rast.pe.ses {phyloraster} | R Documentation |
Calculates the standardized effect size for phylogenetic endemism. See Details for more information.
rast.pe.ses(
x,
tree,
branch.length,
inv.R,
spat_alg = "bootspat_str",
spat_alg_args = list(rprob = NULL, rich = NULL, fr_prob = NULL),
random = c("tip", "spat")[2],
aleats = 10,
cores = 1,
filename = "",
...
)
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 |
inv.R |
SpatRaster. Inverse of range size. See |
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: |
spat_alg_args |
List of arguments passed to the randomization method
chosen in 'spat_alg'. See |
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 |
filename |
character. Output filename |
... |
additional arguments passed for terra::app |
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.
SpatRaster
Gabriela Alves-Ferreira and Neander Heming
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.
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
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)
range.BL <- inv.range(data$x)
t <- rast.pe.ses(x = data$x, tree, aleats = 3,
random = "spat")
plot(t)