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
)

Arguments

layers

A Raster* object of species distributions (typically a multi-layer type: RasterStack or RasterBrick).

tree

An hclust or phylo object representing a phylogenetic or functional tree. One of tree or distance must be provided.

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.

Value

A raster object representing dispersion in space.

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).

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

Run this code

# NOT RUN {
sp1 <- raster::raster(matrix(c(NA,1,1,1,1,0,0,0,0), nrow = 3, ncol = 3, byrow = TRUE))
sp2 <- raster::raster(matrix(c(0,0,0,0,1,1,1,1,1), nrow = 3, ncol = 3, byrow = TRUE))
sp3 <- raster::raster(matrix(c(0,0,0,1,1,1,0,0,0), nrow = 3, ncol = 3, byrow = TRUE))
spp <- raster::stack(sp1, sp2, sp3)
tree <- hclust(dist(c(1:3), method="euclidean"), method="average")
raster.dispersion(spp, tree)
# }

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