rast.pe.ses {phyloraster}

Phylogenetic endemism standardized for specie richness

Description

Calculates the standardized effect size for phylogenetic endemism. See Details for more information.

Usage

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 = "",
  ...
)

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.

Value

SpatRaster

Author(s)

Gabriela Alves-Ferreira and Neander Heming

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

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)