betaDiversity2_speciesRaster: Map turnover in species communities v2

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

Map turnover in species communities v2

Description

Mean community dissimilarity in terms of species composition, phylogeny or traits is calculated for each cell within a circular moving window of neighboring cells.

Usage

betaDiversity2_speciesRaster(x, radius, metric, component = "full")

Arguments

x	object of class speciesRaster.
radius	Radius of the moving window in map units.
metric	choice of metric, see details.
component	which component of beta diversity to use, can be "turnover", "nestedness" or "full"

Details

For each cell, mean dissimilarity is calculated from the focal cell to each of its neighbors.

The following metrics are available. All metrics are based on Sorensen dissimilarity and range from 0 to 1:

• taxonomic

• phylogenetic

• trait

For each metric, the following components can be specified. These components are additive, such that the full metric = turnover + nestedness.

• turnover: species turnover without the influence of richness differences

• nestedness: species turnover due to differences in richness

• full: the combined turnover due to both differences in richness and pure turnover

Trait turnover trait measures the turnover in community trait data. This metric is identical to phylogenetic turnover, but where the phylogeny is replaced with a neighbor-joining tree that is generated from the trait distance matrix.

The following are currently not implemented, but might be in the future: 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.

Value

Returns a raster with mean community dissimilarity for each cell.

Author(s)

Pascal Title

References

Baselga, A. The relationship between species replacement, dissimilarity derived from nestedness, and nestedness. Global Ecology and Biogeography 21 (2012): 1223–1232.

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.

Leprieur, F, Albouy, C, De Bortoli, J, Cowman, PF, Bellwood, DR & Mouillot, D. Quantifying Phylogenetic Beta Diversity: Distinguishing between "True" Turnover of Lineages and Phylogenetic Diversity Gradients. PLoS ONE 7 (2012): e42760–12.

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

tamiasSpRas <- addPhylo_speciesRaster(tamiasSpRas, tamiasTree)
tamiasSpRas <- addTraits_speciesRaster(tamiasSpRas, tamiasTraits)

# taxonomic turnover
beta_taxonomic_turnover <- betaDiversity2_speciesRaster(tamiasSpRas, radius = 70000, 
	metric = 'taxonomic', component = 'turnover')
beta_taxonomic_nestedness <- betaDiversity2_speciesRaster(tamiasSpRas, radius = 70000, 
	metric = 'taxonomic', component = 'nestedness')
beta_taxonomic_full <- betaDiversity2_speciesRaster(tamiasSpRas, radius = 70000, 
	metric = 'taxonomic', component = 'full')

# phylogenetic turnover
beta_phylo_turnover <- betaDiversity2_speciesRaster(tamiasSpRas, radius = 70000, 
	metric = 'phylogenetic', component = 'turnover')
beta_phylo_nestedness <- betaDiversity2_speciesRaster(tamiasSpRas, radius = 70000, 
	metric = 'phylogenetic', component = 'nestedness')
beta_phylo_full <- betaDiversity2_speciesRaster(tamiasSpRas, radius = 70000, 
	metric = 'phylogenetic', component = 'full')

# trait turnover
beta_trait_turnover <- betaDiversity2_speciesRaster(tamiasSpRas, radius = 70000, 
	metric = 'trait', component = 'turnover')
beta_trait_nestedness <- betaDiversity2_speciesRaster(tamiasSpRas, radius = 70000, 
	metric = 'trait', component = 'nestedness')
beta_trait_full <- betaDiversity2_speciesRaster(tamiasSpRas, radius = 70000, 
	metric = 'trait', component = 'full')


colramp <- colorRampPalette(c('blue','yellow','red'))
par(mfrow=c(1,3))
plot(beta_taxonomic_full, col = colramp(100), zlim = c(0,1))
plot(beta_phylo_full, col = colramp(100), zlim = c(0,1))
plot(beta_trait_full, col = colramp(100), zlim = c(0,1))

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