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

In BAT: Biodiversity Assessment Tools

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
)

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.

Value

A SpatRaster object representing dispersion in space.

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)

BAT documentation built on Oct. 11, 2023, 1:07 a.m.