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Commit 34e925e3 authored by Maria Voigt's avatar Maria Voigt
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adding optparse logic to abundance pred script

parent 1e799056
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......@@ -23,20 +23,76 @@ suppressPackageStartupMessages(library(optparse))
cl <- makeForkCluster(outfile = "")
registerDoParallel(cl)
print(paste(Sys.time(), "0. start run"))
#-----------------------------#
# command line option parsing #
#-----------------------------#
option_list <- list (
make_option(c("-i", "--input-directory"), dest = "input_directory",
type = "character", help = "directory with input files",
metavar = "/path/to/input-dir"),
make_option(c("-indir-pred", "--predictor-input-directory"),
dest = "pred_input_directory", type = "character",
help = "directory with predictor input files",
metavar = "/path/to/pred_input-dir"),
make_option(c("-o", "--output-directory"), dest = "output_directory", type = "character", help = "directory with output files", metavar = "/path/to/output-dir"),
make_option("--year-to-predict",
dest = "year_to_predict",
type = "integer",
help = "year of the survey years (1994:2015) to predict abundance to",
metavar = "2015")
)
options <- parse_args(OptionParser(option_list=option_list))
# sanity checks
if (is.null(options$input_directory)) {
stop("input directory not specified, check --help")
}
if (is.null(options$pred_input_directory)) {
stop("input directory not specified, check --help")
}
if (is.null(options$output_directory)) {
stop("output directory not specified, check --help")
}
year_to_predict_possibilities <- c(1999:2015)
if (!(options$year_to_predict %in% year_to_predict_possibilities)) {
stop(paste("the year to predict to year must be between",
min(year_to_predict_possibilities),
"and", max(year_to_predict_possibilities)))
}
# input directory
indir <- options$input_directory
print(paste("indir", indir))
# input directory
indir_predictors <- options$pred_input_directory
print(paste("indir_predictors", indir_predictors))
# directory in which output is written
outdir <- options$output_directory
print(paste("outdir", outdir))
year_to_predict <- as.numeric(options$year_to_predict )
print(paste("year to predict " , year_to_predict))
#------------------------#
# command line arguments #
#------------------------#
print(paste(Sys.time(), "0. start run"))
args <- commandArgs(trailingOnly = TRUE)
print(paste("args", args))
indir <- args[1]
print(paste("indir ", indir))
outdir <- args[2]
print(paste("outdir ", outdir))
indir_predictors <- args[3]
print(paste("indir predictors", indir_predictors))
year_to_predict <- as.numeric(args[4])
print(paste("year " , year_to_predict))
indir_fun <- "~/orangutan_density_distribution/src/functions/"
crs_aea <- "+proj=aea +lat_1=7 +lat_2=-32 +lat_0=-15 +lon_0=125 +x_0=0
......
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