BAT (version 2.9.6)

raster.dispersion: Maps of phylogenetic/functional dispersion of species or individuals.

Description

Average dissimilarity between any two species or individuals randomly chosen in a community using rasters of species distributions (presence/absence or abundance).

Usage

raster.dispersion(
  layers,
  tree,
  distance,
  func = "originality",
  abund = FALSE,
  relative = FALSE
)

Value

A SpatRaster object representing dispersion in space.

Arguments

layers

A SpatRaster object of species distributions from package terra.

tree

A phylo or hclust object or alternatively a species x traits matrix or data.frame to build a functional tree.

distance

A dist object representing the phylogenetic or functional distance between species.

func

Calculate dispersion using originality (default), uniqueness or contribution.

abund

A boolean (T/F) indicating whether dispersion should be calculated using individuals (T) or species (F).

relative

A boolean (T/F) indicating whether dispersion should be relative to the maximum distance between any two species in the tree or distance matrix.

Details

If abundance data is used and a tree is given, dispersion is the quadratic entropy of Rao (1982). If abundance data is not used but a tree is given, dispersion is the phylogenetic dispersion measure of Webb et al. (2002). Note that cells with less than two species cannot have dispersion values.

References

Rao, C.R. (1982) Diversity and dissimilarity coefficients: a unified approach. Theoretical Population Biology, 21: 24-43.

Webb, C.O., Ackerly, D.D., McPeek, M.A. & Donoghue, M.J. (2002) Phylogenies and community ecology. Annual Review of Ecology and Systematics, 33: 475-505.

Examples

sp1 <- terra::rast(matrix(c(NA,1,1,1,1,0,0,0,0), nrow = 3, ncol = 3, byrow = TRUE))
sp2 <- terra::rast(matrix(c(0,0,0,0,1,1,1,1,1), nrow = 3, ncol = 3, byrow = TRUE))
sp3 <- terra::rast(matrix(c(0,0,0,1,1,1,0,0,0), nrow = 3, ncol = 3, byrow = TRUE))
spp <- c(sp1, sp2, sp3)
tree <- hclust(dist(c(1:3), method="euclidean"), method="average")
tree$labels = c("Sp1", "Sp2", "Sp3")
names(spp) = tree$labels
raster.dispersion(spp, tree)