models2pam {bamm}

models2pam: Converts binary rasters to a PAM

Description

Function to convert binary raster models to a Presence Absences Matrix.

Usage

models2pam(
  mods_stack,
  return_coords = FALSE,
  sparse = TRUE,
  parallel = FALSE,
  ncores = 2
)

Arguments

mods_stack

A raster stack containing binary models of each species in the community.

return_coords

Logical. If TRUE the pam will be returned with coordinates in the first two columns.

sparse

Logical. If TRUE the PAM will be returned as a sparse matrix.

parallel

Logical. If TRUE computations will be done in parallel

ncores

Integer. Number of cores to run the parallel process.

Details

For more information about PAM see Soberon and Cavner (2015).

Value

A presence-absence matrix (PAM).

Author(s)

Luis Osorio-Olvera & Jorge Soberón

References

Soberon J, Cavner J (2015). “Indices of Biodiversity Pattern Based on Presence-Absence Matrices: A GIS Implementation.” Biodiversity Informatics, 10, 22–34..

Examples

lagos_path <- system.file("extdata/conejos",
                          package = "bamm")
enm_path <- list.files(lagos_path,
                       pattern = ".tif",
                       full.names = TRUE)[1:10]
en_models <- raster::stack(enm_path) >0.01
pam <- bamm::models2pam(en_models,
                        return_coords=TRUE,
                        sparse=FALSE,
                        parallel=FALSE,ncores=2)
head(pam)