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Build a Presence-Absence Matrix from Species Range Polygons

Source: R/get_geo_pam.R
get_geo_pam.Rd

Rasterizes a set of species range polygons onto a regular grid and returns a sites-by-species presence-absence matrix (PAM) as a tibble.

Usage

get_geo_pam(shp, res = 0.5, ...)

Arguments

shp

A SpatVector with a sciname attribute column identifying each species.

res

Numeric. Grid cell size in the same units as the coordinate reference system of shp (typically decimal degrees). Default 0.5.

...

Additional arguments passed to rasterize.

Value

A tibble with columns x, y (cell centroids) followed by one column per species containing 1 (present) or 0 (absent).

Examples

# \donttest{
# A small, fully local example: two square ranges, no download needed
square <- function(x0, y0, size = 2) {
  m <- matrix(c(x0, y0, x0 + size, y0,
                x0 + size, y0 + size, x0, y0 + size),
              ncol = 2, byrow = TRUE)
  terra::vect(m, type = "polygons", crs = "EPSG:4326")
}
ranges <- rbind(square(0, 0), square(2, 2))
ranges$sciname <- c("species_a", "species_b")
pam <- get_geo_pam(ranges, res = 1)
head(pam)
#> # A tibble: 6 × 4
#>       x     y species_a species_b
#>   <dbl> <dbl>     <dbl>     <dbl>
#> 1   0.5   0.5         1         0
#> 2   0.5   1.5         1         0
#> 3   1.5   0.5         1         0
#> 4   1.5   1.5         1         0
#> 5   2.5   2.5         0         1
#> 6   2.5   3.5         0         1

# The packaged example data are downloaded on demand, so guard for
# machines without network access (the function returns a character
# string instead of a SpatVector when the server is unreachable)
shp <- get_rodentia_mexico()
if (!is.character(shp)) {
  pam_mex <- get_geo_pam(shp, res = 1)
  head(pam_mex)
}
#> # A tibble: 6 × 27
#>       x     y `Orthogeomys grandis` `Peromyscus gambelii` Reithrodontomys fulv…¹
#>   <dbl> <dbl>                 <dbl>                 <dbl>                  <dbl>
#> 1 -117.  32.0                     0                     0                      0
#> 2 -116.  30.0                     0                     0                      0
#> 3 -116.  31.0                     0                     0                      0
#> 4 -116.  32.0                     0                     0                      0
#> 5 -115.  30.0                     0                     0                      0
#> 6 -115.  32.0                     0                     0                      0
#> # ℹ abbreviated name: ¹​`Reithrodontomys fulvescens`
#> # ℹ 22 more variables: `Reithrodontomys megalotis` <dbl>,
#> #   `Sciurus alleni` <dbl>, `Sciurus niger` <dbl>, `Sigmodon alleni` <dbl>,
#> #   `Sigmodon arizonae` <dbl>, `Sigmodon hirsutus` <dbl>,
#> #   `Sigmodon hispidus` <dbl>, `Sigmodon leucotis` <dbl>,
#> #   `Sigmodon mascotensis` <dbl>, `Sigmodon ochrognathus` <dbl>,
#> #   `Sigmodon planifrons` <dbl>, `Sigmodon toltecus` <dbl>, …
# }