geo.phylo.ses {phyloraster}

Calculate phylogenetic community metrics and their standardized effect sizes for raster data

Description

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

Usage

geo.phylo.ses(
  x,
  tree,
  inv.R,
  edge.path,
  branch.length,
  n.descen,
  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.

inv.R

SpatRaster. Inverse of range size. See inv.range

edge.path

matrix representing the paths through the tree from root to each tip. See phylo.pres

branch.length

numeric. A Named numeric vector of branch length for each species. See phylo.pres

n.descen

numeric. A Named numeric vector of number of descendants for each branch. See phylo.pres

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.

Value

SpatRaster

Author(s)

Neander Marcel Heming

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 C.J., 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.

See Also

phylo.pres, inv.range, geo.phylo, rast.ed.ses, rast.pd.ses, rast.we.ses, rast.pe.ses, bootspat_str, bootspat_naive, bootspat_ff, SESraster

Examples

library(terra)
library(phyloraster)
require("SESraster")
x <- terra::rast(system.file("extdata", "rast.presab.tif",
package="phyloraster"))
tree <- ape::read.tree(system.file("extdata", "tree.nex",
package="phyloraster"))
tses <- geo.phylo.ses(x = x,
                     tree = tree,
                      # FUN_args = list(range.BL=area.branch$range.BL,
                      # inv.R=area.branch$inv.R,
                      # branch.length=data$branch.length,
                      # n.descen = data$n.descendants),
                      spat_alg = "bootspat_str",
                      spat_alg_args = list(rprob = NULL,
                                           rich = NULL,
                                           fr_prob = NULL),
                      aleats = 2)
terra::plot(tses)