pam builds geographic presence-absence matrices (PAMs) from species range polygons stored as terra::SpatVector objects.
A PAM is a sites-by-species binary table: rows are grid cells, columns are species, and each entry is 1 (present) or 0 (absent). PAMs are a foundational data structure in macroecology and biogeography for computing species richness, range-diversity plots, co-occurrence analysis, and conservation prioritisation.
Installation
# Install from GitHub
# install.packages("remotes")
remotes::install_github("alrobles/PAM")Quick Start
library(pam)
# Load example data: Rodentia of Mexico
shp <- get_rodentia_mexico()
# Build PAM at 1-degree resolution
pam_result <- get_geo_pam(shp, res = 1)
head(pam_result)
#> # A tibble: 6 × 42
#> x y Chaetodipus arenarius ...
#> <dbl> <dbl> <dbl>
#> 1 -118. 23.5 0
#> ...Main Functions
| Function | Description |
|---|---|
get_geo_pam() |
Build a PAM from a SpatVector at a given resolution |
get_rodentia_mexico() |
Example data: rodent ranges for Mexico |
get_world_pca() |
WorldClim bioclimatic PCA raster (2 layers) |