Spatial beta diversity for raster — spat.beta • divraster

Calculates spatial beta diversity for taxonomic (TD), functional (FD), and phylogenetic (PD) dimensions. See raster.beta.

Usage

spat.beta(x, tree, filename = "", func = "jaccard", abund = FALSE, ...)

Arguments

x: A SpatRaster with presence-absence data (0 or 1) for a set of species. (This maps to layers in BAT::raster.beta).
tree: It can be a 'data.frame' with species traits or a 'phylo' with a rooted phylogenetic tree. Species names in 'tree' and 'x' must match!
filename: Character. Save results if a name is provided.
func: Character. Distance function for beta diversity calculation. Defaults to "jaccard". Passed to BAT::beta.
abund: Logical. Whether to use abundance data (TRUE) or presence-absence (FALSE). Defaults to FALSE. Passed to BAT::beta.
...: Additional arguments to be passed to internal functions within BAT::raster.beta (e.g., BAT::beta). Note: BAT::raster.beta does not accept a 'neighbour' argument.

Value

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

Examples

# \donttest{
library(terra)
bin1 <- 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"))
spat.beta(bin1)
#> class       : SpatRaster 
#> dimensions  : 8, 8, 4  (nrow, ncol, nlyr)
#> resolution  : 1, 1  (x, y)
#> extent      : 0, 8, 0, 8  (xmin, xmax, ymin, ymax)
#> coord. ref. :  
#> source(s)   : memory
#> names       :    Btotal,     Brepl,    Brich,    Bratio 
#> min values  : 0.4821429, 0.1111111, 0.075000, 0.1582734 
#> max values  : 0.9178571, 0.7285714, 0.609375, 0.8978930 
spat.beta(bin1, traits)
#> class       : SpatRaster 
#> dimensions  : 8, 8, 4  (nrow, ncol, nlyr)
#> resolution  : 1, 1  (x, y)
#> extent      : 0, 8, 0, 8  (xmin, xmax, ymin, ymax)
#> coord. ref. :  
#> source(s)   : memory
#> names       :    Btotal,      Brepl,    Brich,     Bratio 
#> min values  : 0.3237529, 0.03470649, 0.123868, 0.04212794 
#> max values  : 0.8238354, 0.43752776, 0.789129, 0.74179377 
spat.beta(bin1, tree)
#> class       : SpatRaster 
#> dimensions  : 8, 8, 4  (nrow, ncol, nlyr)
#> resolution  : 1, 1  (x, y)
#> extent      : 0, 8, 0, 8  (xmin, xmax, ymin, ymax)
#> coord. ref. :  
#> source(s)   : memory
#> names       :    Btotal,      Brepl,     Brich,    Bratio 
#> min values  : 0.2652022, 0.05756414, 0.1011549, 0.1642921 
#> max values  : 0.5976476, 0.45291494, 0.3969972, 0.7897035 
# }