CODEWITHSUNDEEP
rlinuxshellparameter-passing
ritz
ritz

Reputation: 107

How to introduce the Shell variable to R script?

I'd like to run a R Script within a Shell Script, which is not a problem to me:

Example:

#!/bin/bash
_input_file=$1
_output_file=$2
some shell script...
........
Rscript R.r >"_output_file"          #call R script

My Problem is I'd like to define a variable (_output_file) within my Shell Script to assign to my R Script. _output_file contain path and folder name of output.

R script :

#!/usr/bin/env Rscript
x <- read.csv(_output_file,"/results/abc.txt", header=F)
library(plyr)
.....
.........

So I would like the call variable (_output_file) and its path to be able to read abc.txt file. So,how to introduce the Shell variable to R script?

Upvotes: 4

Views: 2271

Answers (1)

Tung
Tung

Reputation: 28441

This is how I usually do it

Shell script file

#!/bin/bash

_input_file=$1
_output_file=$2

# preprocessing steps

# run R.r script with ${_output_file} parameter
Rscript --vanilla R.r ${_output_file} 

echo
echo "----- DONE -----"
echo

exit 0

R.r file

### Ref links
# http://tuxette.nathalievilla.org/?p=1696
# https://swcarpentry.github.io/r-novice-inflammation/05-cmdline/

# get the input passed from the shell script
args <- commandArgs(trailingOnly = TRUE)
str(args)
cat(args, sep = "\n")

# 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 {
  print(paste0("Arg input:  ", args[1]))
}

# use shell input
file_to_read <- paste0(args[1], "/results/abc.txt")
print(paste0("Input file:  ", file_to_read))
df <- read.csv(file_to_read, header = F)

# check 
head(df)
summary(df)

library(plyr)

# do something here

Upvotes: 3

Related Questions