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Alternative Method to Calculate Alpha Taxonomic Diversity

Source: R/alpha2.R
spat.alpha2.Rd

Calculates the alpha taxonomic diversity, specifically species richness, for each cell in a SpatRaster object containing species presence-absence data. This function provides a straightforward method to sum the number of species present in each grid cell.

Usage

spat.alpha2(bin, cores = 1, filename = "")

Arguments

bin

A SpatRaster object with multiple layers, where each layer represents a species and cell values are binary (0 for absence, 1 for presence). Species names should correspond to layer names (e.g., names(bin)).

cores

A positive integer (default is 1). If cores > 1, a parallel processing cluster is created using the parallel package to speed up calculations across raster cells.

filename

Character string. Optional path and filename to save the resulting SpatRaster. Supported formats are those recognized by terra::writeRaster (e.g., ".tif", ".grd"). If provided, the SpatRaster will be saved to this file.

Value

A SpatRaster object with a single layer named "Richness". Each cell in this SpatRaster contains the calculated species richness (number of species present). The output SpatRaster will have the same dimensions, resolution, and CRS as the input bin.

Details

This function calculates species richness by summing the presence (value 1) of all species across layers for each individual raster cell. It is an alternative to spat.alpha() when only Taxonomic Diversity (TD) is required, offering a more direct and potentially faster computation for this specific metric. NA values in input cells are ignored during the sum calculation.

Examples

library(terra)

# Load an example SpatRaster with binary presence-absence data
bin_rast <- terra::rast(system.file("extdata", "ref.tif", package = "divraster"))

# Calculate species richness (alpha taxonomic diversity)
richness_map <- spat.alpha2(bin_rast)
richness_map
#> class       : SpatRaster 
#> dimensions  : 8, 8, 1  (nrow, ncol, nlyr)
#> resolution  : 0.125, 0.125  (x, y)
#> extent      : 0, 1, 0, 1  (xmin, xmax, ymin, ymax)
#> coord. ref. : lon/lat WGS 84 (EPSG:4326) 
#> source(s)   : memory
#> name        : Richness 
#> min value   :        2 
#> max value   :        8 

# Plot the resulting richness map
plot(richness_map, main = "Species Richness Map")