Calculate weighted endemism standardized for species richness

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

Usage

rast.we.ses(
  x,
  inv.R,
  spat_alg = "bootspat_str",
  spat_alg_args = list(rprob = NULL, rich = NULL, fr_prob = NULL),
  aleats = 10,
  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.
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
aleats: positive integer. A positive integer indicating how many times the calculation should be repeated.
filename: character. Output filename
...: additional arguments passed for terra::app

Value

SpatRaster

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

Williams, P.H., Humphries, C.J., Forey, P.L., Humphries, C.J., VaneWright, R.I. (1994). Biodiversity, taxonomic relatedness, and endemism in conservation. In: Systematics and Conservation Evaluation (eds Forey PL, Humphries CJ, Vane-Wright RI), p. 438. Oxford University Press, Oxford.

Crisp, M., Laffan, S., Linder, H., Monro, A. (2001). Endemism in the Australian flora. Journal of Biogeography, 28, 183–198.

Author

Neander Marcel Heming and Gabriela Alves-Ferreira

Examples

# \donttest{
library(terra)
library(SESraster)
x <- terra::rast(system.file("extdata", "rast.presab.tif",
package="phyloraster"))
t <- rast.we.ses(x[[1:10]], aleats = 3)
plot(t)

# }