temp.beta {divraster}

Temporal beta diversity calculation for raster

Description

Calculates temporal beta diversity for taxonomic (TD), functional (FD), and phylogenetic (PD) dimensions. Adapted from beta

Usage

temp.beta(bin1, bin2, tree, filename = "", cores = 1, ...)

Arguments

bin1

A SpatRaster with presence-absence data (0 or 1) for a set of species.

bin2

A SpatRaster with presence-absence data (0 or 1) for a set of species. Species names in 'bin2' and 'bin1' must match!

tree

It can be a 'data.frame' with species traits or a 'phylo' with a rooted phylogenetic tree. Species names in 'tree', 'bin1', and 'bin2' must match!

filename

Character. Save results if a name is provided.

cores

A positive integer. If cores > 1, a 'parallel' package cluster with that many cores is created and used.

...

Additional arguments to be passed passed down from a calling function.

Details

The TD beta diversity partitioning framework we used was developed by Podani and Schmera (2011) and Carvalho et al. (2012) and expanded to PD and FD by Cardoso et al. (2014).

Value

A SpatRaster with beta results (total, replacement, richness difference, and ratio).

References

Cardoso, P. et al. 2014. Partitioning taxon, phylogenetic and functional beta diversity into replacement and richness difference components. - Journal of Biogeography 41: 749–761.

Carvalho, J. C. et al. 2012. Determining the relative roles of species replacement and species richness differences in generating beta-diversity patterns. - Global Ecology and Biogeography 21: 760–771.

Podani, J. and Schmera, D. 2011. A new conceptual and methodological framework for exploring and explaining pattern in presence - absence data. - Oikos 120: 1625–1638.

Hidasi-Neto, J. et al. 2019. Climate change will drive mammal species loss and biotic homogenization in the Cerrado Biodiversity Hotspot. - Perspectives in Ecology and Conservation 17: 57–63.

Examples

library(terra)
bin1 <- terra::rast(system.file("extdata", "ref.tif",
package = "divraster"))
bin2 <- terra::rast(system.file("extdata", "fut.tif",
package = "divraster"))
traits <- read.csv(system.file("extdata", "traits.csv",
package = "divraster"), row.names = 1)
tree <- ape::read.tree(system.file("extdata", "tree.tre",
package = "divraster"))
temp.beta(bin1, bin2)
temp.beta(bin1, bin2, traits)
temp.beta(bin1, bin2, tree)