Here is simple function to parse unix way of parsing argument from R.

#
#
# EXAMPLE:
# R --test=mydata.csv
#> getopt('test')
#[1] "mydata.csv"

# getting numeric argument
# R --N=123
#> getopt('N',numeric=T)
#[1] 123
#

getopt <- function(argname, numeric = F)
  {
    args <- commandArgs()  
    argexp = sprintf('^--%s=',argname)
    idx <- regexpr(argexp, args);

    ret <- NA
    
    if ( any(idx > 0) )
    { # found matching argument  
    found <- args[idx > 0]
    value <- strsplit(found,"=")
    ret <- unlist(value)[2]
    }

    if ( numeric )
    ret <- as.numeric(ret)

    ret
  }
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cheers, c.okugami