How to Read Command Line Parameters from an R Script?
Last Updated :
06 Jun, 2024
Reading command line parameters in an R script is essential for creating flexible and reusable scripts that can handle different inputs without modifying the code. This is particularly useful for automation and batch-processing tasks. This article will guide you through the process of reading command line parameters in an R Programming Language script using base R functions and external packages.
Using Base R Functions
In base R, command line arguments can be accessed using the commandArgs() function. This function retrieves the command line arguments passed to the R script. Here's how you can use it:
R
# save this script as script.R
# Read command line arguments
args <- commandArgs(trailingOnly = TRUE)
# Check if arguments are provided
if (length(args) == 0) {
stop("No arguments provided")
}
# Print the arguments
print(args)
# Example: Access individual arguments
arg1 <- args[1]
arg2 <- args[2]
# Print individual arguments
cat("Argument 1:", arg1, "\n")
cat("Argument 2:", arg2, "\n")
Output:
character(0)
Argument 1: NA
Argument 2: NA
Run the Script from the Command Line
Open your terminal or command prompt and navigate to the directory where your script. R is located. Run the script with arguments:
R
Rscript script.R arg1_value arg2_value
Output:
[1] "10" "Hello World"
Argument 1: 10
Argument 2: Hello World
Using the optparse Package
The optparse package provides a more structured way to handle command line arguments, similar to the argparse module in Python. This package allows you to define options and parse arguments with more control and clarity.
First, you need to install the optparse package if you haven’t already:
install.packages("optparse")
Using optparse to Handle Command Line Arguments
R
# save this script as script_optparse.R
# Load the optparse package
library(optparse)
# Define options
option_list <- list(
make_option(c("-n", "--number"), type = "integer", default = 0,
help = "an integer number", metavar = "NUMBER"),
make_option(c("-m", "--message"), type = "character", default = "default message",
help = "a string message", metavar = "MESSAGE")
)
# Create the parser object
opt_parser <- OptionParser(option_list = option_list)
# Parse the arguments
opt <- parse_args(opt_parser)
# Access the arguments
cat("Number:", opt$number, "\n")
cat("Message:", opt$message, "\n")
Output:
Number: 10
Message: Hello World
Using the argparse Package
Another popular package for parsing command line arguments is argparse, which provides functionality similar to Python’s argparse module.
install.packages("argparse")
Using argparse to Handle Command Line Arguments
R
# Load the argparse package
library(argparse)
# Create a parser object
parser <- ArgumentParser(description = "Process some integers and a message.")
# Define arguments
parser$add_argument("-n", "--number", type = "integer", default = 0,
help = "an integer number")
parser$add_argument("-m", "--message", type = "character", default = "default message",
help = "a string message")
# Parse the arguments
args <- parser$parse_args()
# Access the arguments
cat("Number:", args$number, "\n")
cat("Message:", args$message, "\n")
Output:
Number: 10
Message: Hello World
Conclusion
Reading command line parameters in an R script can be achieved using base R functions or more advanced packages like optparse and argparse. Here’s a quick recap:
- Using Base R: Utilize commandArgs(trailingOnly = TRUE) to read raw command line arguments.
- Using optparse: Define and parse arguments with more control and structure.
- Using argparse: Similar to optparse, but inspired by Python’s argparse module.
Each method has its use cases, with base R being suitable for simpler scripts and optparse/argparse providing more advanced features for complex scenarios. By understanding these methods, you can create flexible and powerful R scripts that handle a variety of input scenarios efficiently.
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