Thin an input point layer (e.g., animal telemetry locations) based on a user-specified grid for output to a SDM routine. Set up to use ESRI shapefiles, this can be modified.

pt_thin.R

# Allen Aven November 2015
# Function to thin a point input layer according to an input raster


require(sp)
require(rgdal)
require(raster)
require(dismo)

pt_thin <- function(infile, grid=grid, n_points=5) {
  dsn=dirname(infile)
  layer_name=str_replace(basename(infile), '.shp', '')
  output_layer_name = paste0(layer_name, '_thinned')
  
  # Read the input shapefile
  in_pt <- readOGR(dsn=dsn, layer=layer_name)
  
  # Check for projection agreement between points and grid.  If not, transform points.
  if(!identical(showEPSG(proj4string(grid)), showEPSG(proj4string(in_pt)))) {
    in_pt <- spTransform(in_pt, CRS(proj4string(grid)))
  }
  
  # Thin the points
  thinned_coords <- dismo::gridSample(xy=in_pt, r=grid, n=n_points)
  
  # Handle the output
  out_sp <- data.frame(x=thinned_coords[,1], y=thinned_coords[,2], dataset=output_layer_name)
  coordinates(out_sp) <- data.frame(x=out_sp$x, y=out_sp$y)
  crs(out_sp) <- CRS(proj4string(grid))
  
  # Finally write the resulting shapefile to disk, same directory as input files
  writeOGR(out_sp, dsn=dsn, layer=output_layer_name,
           driver='ESRI Shapefile', overwrite_layer=TRUE)
}