range_maps_to_sites(shp, sites, sp_col)

Convert species range maps (shapefiles) to a site × species presence matrix. Sites can be points or hexagons.

spatialcommunity matrix

Args:shp — sf polygon of rangessites — sf points or polygonssp_col — species name column

range_maps_to_sites <- function(shp, sites, sp_col = "SCINAME") {
  if (!requireNamespace("sf", quietly = TRUE)) install.packages("sf")
  library(sf)
  
  # Ensure same CRS
  sites <- st_transform(sites, st_crs(shp))
  
  # For each species, find intersecting sites
  species <- unique(shp[[sp_col]])
  
  mat <- do.call(cbind, lapply(species, function(sp) {
    sp_poly <- shp[shp[[sp_col]] == sp, ]
    presence <- lengths(st_intersects(sites, sp_poly)) > 0
    as.integer(presence)
  }))
  
  colnames(mat) <- species
  rownames(mat) <- seq_len(nrow(sites))
  as.data.frame(mat)
}