Run RMarkdown with arguments on the command line

问题

I'm trying to run a Rmarkdown file (myfile.Rmd) from the command line terminal. This file needs to take an argument to work. We can use this simple file as an example:

---
title: "Simple example"
output:
  pdf_document: default
---

```{r read_arg, include=FALSE}
args = commandArgs(TRUE)
VAR = args[1]
```

```{r show_var}
VAR
```

So, first of all, is it possible to run a Rmarkdown file by reading arguments as done for Rscripts? I mean, not by reading input files as described in this question.

If so, how can it be done? I hope that the piece of work here used to run a Rmarkdown file worked for me, but it doesn't because of the argument. I'm trying to run something like:

Rscript -e "rmarkdown::render('myfile.Rmd myarg')"

EDIT: But it gives the following error:

Error in tools::file_path_as_absolute(input) : file 'myfile.Rmd_myarg' does not exist Calls: -> setwd -> dirname -> Además: Warning messages: 1: In normalizePath(path, winslash = winslash, mustWork = mustWork) : path[1]="myfile.Rmd myarg": No existe el fichero o el directorio 2: In normalizePath(path, winslash = winslash, mustWork = mustWork) : path[1]="myfile.Rmd_myarg": No existe el fichero o el directorio Ejecución interrumpida

Any ideas? Thank you!

回答1:

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

来源：https://stackoverflow.com/questions/49904943/run-rmarkdown-with-arguments-on-the-command-line

标签

bash

r-markdown