raster.alpha: Maps of alpha diversity (Taxon, Phylogenetic or Functional...

In BAT: Biodiversity Assessment Tools

Maps of alpha diversity (Taxon, Phylogenetic or Functional Diversity - TD, PD, FD).

Description

Observed alpha diversity using rasters of species distributions (presence/absence).

Usage

raster.alpha(layers, tree)

Arguments

layers	A SpatRaster object of species distributions from package terra.
tree	A phylo or hclust object (used only for PD or FD) or alternatively a species x traits matrix or data.frame to build a functional tree.

Details

TD is equivalent to species richness. Calculations of PD and FD are based on Faith (1992) and Petchey & Gaston (2002, 2006), which measure PD and FD of a community as the total branch length of a tree linking all species represented in such community. PD and FD are calculated based on a tree (hclust or phylo object, no need to be ultrametric). The path to the root of the tree is always included in calculations of PD and FD. The number and order of species in layers must be the same as in tree.

Value

A SpatRaster object representing richness in space.

References

Faith, D.P. (1992) Conservation evaluation and phylogenetic diversity. Biological Conservation, 61, 1-10.

Petchey, O.L. & Gaston, K.J. (2002) Functional diversity (FD), species richness and community composition. Ecology Letters, 5, 402-411.

Petchey, O.L. & Gaston, K.J. (2006) Functional diversity: back to basics and looking forward. Ecology Letters, 9, 741-758.

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.alpha(spp)
raster.alpha(spp, tree)

BAT documentation built on May 29, 2024, 7:35 a.m.