Rmd file which sources an R script which sources another R script

Question

To make my code modular, I wrote a R script for plotting data, which invokes an R script to prepare the data (to be plotted):

The document.Rmd file contains a line source('./R/customPlot.R') and this script in turns contains a line source('./prepareData.R').

Running the document.Rmd gives me an error message that ./prepareData.R was not found, which could easily be fixed by changing the line in the script customPlot.R to source('./R/prepareData.R).

In this case, however, I could no longer just run customPlot.R on it's own to visually check its output.

My folder structure looks like this:

project/
  Rmd/
    document.Rmd   # calls source('./R/customPlot.R')
  R/
    customPlot.R   # calls source('./prepareData.R')
    prepareData.R

By searching the web, I learned that generating a package of my code might be a possible solution. Although my project is a bit larger, I wanted to ask whether it's worth the overhead. After all, the majority of files in my project are data and actually few of them are code.

R has no good built-in solution for this. Consider using a modern module system, via [‘box’](https://klmr.me/box). — Konrad Rudolph, Jul 04 '23 at 09:44

score 1 · Answer 1 · answered Jul 04 '23 at 09:38

1

Heh, interesting...

The solution might be with here::here() function, like:

project/
  Rmd/
    document.Rmd  
      #'
      source(file = "../R/1.R")
      #'
  R/
    customPlot.R
      #' 
      source(file =  paste0(here::here(), "/R/prepareData.R"))
      #'
    prepareData.R

answered Jul 04 '23 at 09:38

Grzegorz Sapijaszko

1,913
1
5
12

Thanks, this is already helpful. Best would of course be a solution without additional dependencies. – NicolasBourbaki Jul 04 '23 at 10:08
Then move .Rmd to `project` folder, out of `Rmd` subfolder. The thing is, RStudio projects uses their `project` folder as main/base folder... – Grzegorz Sapijaszko Jul 04 '23 at 10:44
Yes, that's a possibility, although it would make the code organization a bit less obvious. – NicolasBourbaki Jul 04 '23 at 11:00
Unfortunately this only works if the user runs the code from the working directory `project/`, i.e. it’s not robust. – Konrad Rudolph Jul 04 '23 at 11:09

Rmd file which sources an R script which sources another R script

1 Answers1