R, a powerful statistical computing and graphics language, is widely used for data analysis and visualization. While many users interact with R through its interactive console or integrated development environments (IDEs), there are times when automating tasks or running scripts becomes essential. In this article, we explore various ways to script with R efficiently.
Running R Scripts: `R CMD BATCH` and `Rscript`
R CMD BATCH
If you have an R script file named `foo.R` and you want to run it non-interactively, the `R CMD BATCH` command comes in handy. For example:
R CMD BATCH foo.R
To run it in the background or as a batch job, you can use OS-specific facilities. On Unix-like systems, appending `&` to the command achieves this:
R CMD BATCH foo.R &
Passing Parameters
You can pass parameters to R scripts using additional command-line arguments. For instance:
R CMD BATCH "--args arg1 arg2" foo.R &
Within the script, retrieve these arguments as a character vector:
Sure, here is a Rust snippet:
R
args <- commandArgs(TRUE)Rscript
An alternative front-end for running R scripts is `Rscript`. It simplifies the process of passing arguments:
Rscript foo.R arg1 arg2
Moreover, you can create executable script files using the `Rscript` approach. For instance, create a file named `runfoo`:
#! /path/to/Rscript
args <- commandArgs(TRUE)
# ... R code ...
q(status=<exit status code>)
Make it executable:
chmod 755 runfoo
Now, you can invoke it with different arguments:
./runfoo arg1 arg2
Dynamic Path to Rscript
To avoid hardcoding the path to `Rscript`, consider using:
#! /usr/bin/env Rscript
Input Considerations
When scripting, consider the source of input. If you read from stdin, keep in mind that `stdin()` in R scripts refers to the script file itself. To read from the process's stdin, use "stdin" as a file connection:
R
chem <- scan("stdin", n=24)Executable Script Files
Another approach, suggested by François Pinard, involves using a here document:
#!/bin/sh
# [environment variables can be set here]
R --no-echo [other options] <<EOF
# R program goes here...
EOF
Be cautious with stdin() references in this approach.
Short Scripts with `Rscript -e`
For short scripts, you can use the `-e` flag with `Rscript` to pass the script directly on the command line:
Rscript -e "print('Hello, R!')"
In conclusion, scripting with R provides flexibility and automation for various tasks. Whether using `R CMD BATCH` or `Rscript`, understanding these options allows users to choose the approach that best fits their needs.
