Example script content:
#!/usr/bin/env Rscript
args <- commandArgs(trailingOnly = TRUE)
rnorm(n=as.numeric(args[1]), mean=as.numeric(args[2]))
Invoke the script:
$ Rscript myScript.R 5 100
Obviously, this creates a string vector args which contains the entries 5 and 100
General usage:
Rscript [options] [-e expr [-e expr2 ...] | file] [args]
Handling mising arguments:
# test if there is at least one argument: if not, return an error
if (length(args)==0) {
stop("At least one argument must be supplied (input file).n", call.=FALSE)
} else if (length(args)==1) {
# default output file
args[2] = "out.txt"
}
For storing helpful information about what types of parameters are expected etc., the optparse package is the way to go. Eric Minikel has a great example. Below is a shorter summary:
#!/usr/bin/env Rscript
library("optparse")
option_list = list(
make_option(c("-f", "--file"), type="character", default=NULL,
help="dataset file name", metavar="character"),
make_option(c("-o", "--out"), type="character", default="out.txt",
help="output file name [default= %default]", metavar="character")
);
opt_parser = OptionParser(option_list=option_list);
opt = parse_args(opt_parser); # list with all the arguments sorted by order of appearance in option_list
Arguments can be called by their names; here: opt$file and opt$out:
## program...
df = read.table(opt$file, header=TRUE)
num_vars = which(sapply(df, class)=="numeric")
df_out = df[ ,num_vars]
write.table(df_out, file=opt$out, row.names=FALSE)