spat.rand {divraster}

Standardized Effect Size (SES) for raster

Description

Calculates the standardized effect size for functional and phylogenetic alpha diversity. See bootspat_str and bootspat_naive

Usage

spat.rand(
  x,
  tree,
  aleats,
  random = c("site", "species", "both", "spat"),
  cores = 1,
  filename = "",
  ...
)

Arguments

x

SpatRaster. A SpatRaster containing presence-absence data (0 or 1) for a set of species.

tree

It can be a 'data.frame' with species traits or a 'phylo' with a rooted phylogenetic tree. Species names in 'tree' and 'x' must match!

aleats

positive integer. A positive integer indicating how many times the calculation should be repeated.

random

character. A character indicating the type of randomization. The currently available randomization methods are "spat", "site", "species" or "both" (site and species).

cores

positive integer. If cores > 1, a 'parallel' package cluster with that many cores is created and used.

filename

character. Output filename.

...

additional arguments to be passed passed down from a calling function.

Value

SpatRaster with Mean, SD, Observed, and SES.

Examples

x <- terra::rast(system.file("extdata", "ref.tif",
package = "divraster"))
traits <- read.csv(system.file("extdata", "traits.csv",
package = "divraster"), row.names = 1)
tree <- ape::read.tree(system.file("extdata", "tree.tre",
package = "divraster"))
spat.rand(x, tree, 3, "site")
spat.rand(x, traits, 3, "site")