How to capture bash arguments and dynamically pass them to executable R markdown parameters within the script

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Summary

The goal of this post is to dynamically pass bash arguments to R markdown parameters within a script. This is particularly useful in a cluster environment with the SLURM job manager, where sbatch commands are used to submit bash scripts that set up and run analyses in R.

Root Cause

The root cause of the issue is the inability to capture bash arguments and pass them dynamically to R markdown parameters. The current approach involves specifying static file names as parameters in the executable R code.

Why This Happens in Real Systems

This issue occurs in real systems due to the following reasons:

  • Limited flexibility in passing parameters to R markdown files
  • Inability to capture bash arguments and use them dynamically
  • Static file names are not suitable for large-scale analyses with varying input files

Real-World Impact

The impact of this issue is significant, including:

  • Inefficient use of resources due to the need for manual intervention
  • Limited scalability of analyses due to the static nature of file names
  • Increased error rates due to manual errors in specifying file names

Example or Code

#!/bin/bash
#SBATCH --job-name=pizza
#SBATCH --output=pizza_%j.log
#SBATCH --time=01:00:00
#SBATCH --mem-per-cpu=5G
#SBATCH --partition=linux12h

module load R/4.3.0
filename=$1

Rscript -e "rmarkdown::render('mymarkdownreport.Rmd', params = list(filename = '$filename'))"

How Senior Engineers Fix It

Senior engineers fix this issue by:

  • Capturing bash arguments using $1, $2, etc.
  • Passing the captured arguments to R markdown parameters using Rscript -e
  • Using dynamic file names to improve flexibility and scalability

Why Juniors Miss It

Juniors may miss this solution due to:

  • Lack of experience with bash scripting and R markdown
  • Insufficient understanding of dynamic parameter passing
  • Overreliance on static file names and manual intervention