gdalPolygonize.R

## 
## this snippet loops through a directory with rasters and crates polygons
## using a call to gdal_polygonize.py 
## (for Mac, with kynchaos GDAL framework)
## 

# make sure to not mess up the paths here!
setwd("root/dir")
indir <- "rasterdir-ending-with-slash/"
outdir <- "polydir-ending-with-slash/" 
pth <- "/path/to/gdal_polygonize.py"

# let's do it
infiles <- list.files(indir)
outfiles <- sub(".asc", ".shp", infiles) # or replace .asc with .tif
dir.create(file.path(".", outdir), showWarnings = FALSE)
sapply(1:length(infiles), function(i) 
  system(paste(pth, paste0(indir, infiles[i]), "-f 'ESRI Shapefile'", paste0(outdir, outfiles[i]))))