betaDiversity_speciesRaster: Map turnover in beta diversity

In ptitle/speciesRaster: Generation of SpeciesRaster Object and Calculation of Morphological and Phylogenetic Metrics

Map turnover in beta diversity

Description

Mean community dissimilarity is calculated for each cell within a moving window of neighboring cells.

Usage

betaDiversity_speciesRaster(x, radius = 3, metric, verbose = FALSE)

Arguments

x	object of class speciesRaster.
radius	Radius in terms of number of cells in horizontal and vertical directions from the focal cell to define the moving window.
metric	choice of metric, see details.
verbose	Primarily intended for debugging, print progress to the console.

Details

Sorensen's Beta diversity sorensen is a purely taxonomic measure of turnover.

Phylogenetic Sorensen's Similarity phylosor is a measure of phylogenetic turnover, ranging from 0 to 1. This function returns 1 - phylosor, such that little change in phylogenetic community structure results in values closer to 0.

Range-weighted turnover RWTurnover measures turnover but where taxa are weighted according to the inverse of their range size.

Phylogenetic range-weighted turnover phyloRWTurnover measures turnover in phylogenetic diversity where phylogenetic branches are weighted by the inverse of their geographic distribution.

The radius value defines the number of cells counted out from the focal cell in the horizontal and vertical direction, creating a square window of side = radius * 2 + 1. For each cell, all calculations between the focal cell and a moving window cell are run, and the results are averaged and assigned to that focal cell.

Value

Returns a new speciesRaster object, with mean community dissimilarity for each cell.

Author(s)

Pascal Title

References

Laffan, SW, et al. Range-weighted metrics of species and phylogenetic turnover can better resolve biogeographic transition zones. Methods in Ecology and Evolution 7 (2016): 580-588.

Rosauer, D, Laffan, SW, Crisp, MD, Donnellan, SC, Cook, LG. Phylogenetic endemism: a new approach for identifying geographical concentrations of evolutionary history. Molecular Ecology 18 (2009): 4061-4072.

Examples

library(raster)
tamiasSpRas

beta_taxonomic <- betaDiversity_speciesRaster(tamiasSpRas, radius = 4, metric = 'sorensen')

beta_RW <- betaDiversity_speciesRaster(tamiasSpRas, radius = 4, metric = 'RWTurnover')

tamiasSpRas <- addPhylo_speciesRaster(tamiasSpRas, tamiasTree)
beta_phyloRW <- betaDiversity_speciesRaster(tamiasSpRas, radius = 4, metric = 'phyloRWTurnover')

colramp <- colorRampPalette(c('blue','yellow','red'))
par(mfrow=c(1,3))
plot(beta_taxonomic, col = colramp(100))
plot(beta_RW, col = colramp(100))
plot(beta_phyloRW, col = colramp(100))

ptitle/speciesRaster documentation built on June 11, 2022, 1:35 a.m.