pol2pam: Convert distribution polygons to a presence-absence matrix...

In bamm: Species Distribution Models as a Function of Biotic, Abiotic and Movement Factors (BAM)

Convert distribution polygons to a presence-absence matrix (PAM)

Description

This function takes spatial polygon objects (typically species distribution polygons) and converts them into a presence-absence matrix (PAM) using a rasterization approach at a specified resolution. The function is particularly useful for biodiversity and biogeography analyses.

Usage

pol2pam(poly, taxon_attribute, resolution, polymask = NULL)

Arguments

poly	Spatial polygon object (SpatialPolygonsDataFrame, sf, etc.) containing species or taxon distribution data.
taxon_attribute	Character. The name of the column in 'poly' that contains taxon identifiers (species, genera, etc.).
resolution	Numeric. The resolution for the output raster in coordinate system units (cell size).
polymask	Optional. A spatial polygon object used to mask and crop the resulting raster. If NULL, no masking is applied.

Details

The function works by:

1. Creating a base raster with the specified resolution and extent

2. Splitting polygons by taxon attribute

3. Rasterizing each taxon's distribution using exact extraction

4. Stacking individual rasters into a multi-layer raster

5. Applying optional masking with polymask

6. Converting the raster stack to a PAM using bamm::models2pam

Value

A PAM (Presence-Absence Matrix) object of class 'pam' from the 'bamm' package containing:

• matrix: Presence-absence matrix (1/0) where rows represent grid cells and columns represent taxa

• richness: Richness pattern across grid cells

• sparse: Logical indicating if the matrix is stored in sparse format

• cell_coordinates: Coordinates of each grid cell

Note

This function requires the following packages: raster, exactextractr, purrr, and bamm. The input polygons are converted to SpatialPolygonsDataFrame if they aren't already.

See Also

models2pam, raster, exact_extract

Examples

## Not run: 
# Load required libraries
library(raster)

# Example with sample data
uicn <- readRDS(system.file("extdata/uicn.rds",package = "bamm"))
sudam <- readRDS(system.file("extdata/suam.rds",package = "bamm"))
# Convert to PAM with 0.5 degree resolution
pam_result <- bamm::pol2pam(poly = uicn,
                            taxon_attribute = "binomial",
                            resolution = 0.5,
                            polymask = NULL)

# With masking polygon
pam_masked <- pol2pam(poly = uicn,
                      taxon_attribute = "binomial",
                      resolution = 0.5,
                      polymask = sudam)

## End(Not run)

bamm documentation built on Feb. 4, 2026, 1:07 a.m.