This is not a proper blog post yet, just my notes.

caffee

R

A good article on passing arguments to R scripts

You can read the docs of commandArgs for more info, but the general use is very simple:

args <- commandArgs(trailingOnly = TRUE)
print(args)  # args is a vector of values

Rscript file.R one two 3

If trailingOnly is set to FALSE, args will contain some other argument values, e.g. “–slave”, “–no-restore”, which are usually not particularly useful and are definitely not provided by the user. trailingOnly set to TRUE will choose only those arugemnts that are provided byt the user.

You can also use optparse package, which lets you provide arguments in a more linux-like way.

library("optparse")
 
option_list = list(
  make_option(c("-o", "--one"), type = "character", default = "first_argument"),
  make_option(c("-t", "--two"), type = "numeric", default = 2)
)
 
opt_parser <- OptionParser(option_list = option_list)
opt <- parse_args(opt_parser)

print(opt)

Rscript file.R --one first_one -t 10

Python

The easiest way:

import sys

print(str(sys.argv))

python3 files.py hi wats up

returns ['files.py', 'hi', 'wats', 'up'].

and a slightly more complicated way:

from argparse import ArgumentParser

parser = ArgumentParser()
parser.add_argument("--one", dest="one")
parser.add_argument("-o", dest="one")
parser.add_argument("--two", dest="two")
args = vars(parser.parse_args())

print(str(args))