R Markdown & the Shell

Running R in batch mode on Linux

http://www.cureffi.org/2014/01/15/running-r-batch-mode-linux/

http://www.rexamples.com/8/How%20to%20run%20the%20code

Run a bash script from an R script

https://stackoverflow.com/questions/11395217/run-a-bash-script-from-an-r-script

https://bash-intro.rsquaredacademy.com/r-command-line.html

Run RMarkdown with arguments on the command line

Adding the myarg object as a parameter is the way to go:

Rscript -e "rmarkdown::render('example.Rmd',params=list(args = myarg))"

And then add the parameter to your Rmd file:

---
title: "Simple example"
output:
  pdf_document: default
params:
  args: myarg
---

Documentation on parameterized reports here: https://rmarkdown.rstudio.com/developer_parameterized_reports.html

https://rmarkdown.rstudio.com/