library(optparse)

# ------------------------------------------------------------------------------
# defaults
# ------------------------------------------------------------------------------

default.ncores <- 32
default.typp <- "shp"
# ------------------------------------------------------------------------------
# parsing arguments
# ------------------------------------------------------------------------------

options <- list (

	make_option(
		opt_str = c("-c", "--cores"),
		dest    = "ncores",
		type    = "integer",
		default = default.ncores,
		help    = paste0("number of CPU cores to use, defaults to ", default.ncores),
		metavar = "4"
	),
	
	make_option(
	  opt_str = c("-t", "--typp"),
	  dest    = "typp",
	  type    = "character",
	  default = default.typp,
	  help    = "Which data type? raster or shp",
	  metavar = "4"
	)
)

parser <- OptionParser(
       usage       = "Rscript %prog [options] data dt_beals header output",
       option_list = options,
       description = "\nan awesome R script",
       epilogue    = "use with caution, the awesomeness might slap you in the face!"
)

cli <- parse_args(parser, positional_arguments = 4)

# ------------------------------------------------------------------------------
# assign a few shortcuts
# ------------------------------------------------------------------------------

x.shp     	   <- cli$args[1]
myfunction  	 <- cli$args[2]
output  	     <- cli$args[3]
toextract   	 <- cli$args[4]
typp           <- cli$options$ncores
ncores   	     <- cli$options$ncores


# ------------------------------------------------------------------------------
# actual program
# ------------------------------------------------------------------------------

source("A98_PredictorsExtract.R")

PredExtr( x.shp, myfunction, output, toextract, typp, ncores)