Running R from other software#

Sometimes, authors will provide code that runs R from within, say, Stata or MATLAB. This is equivalent to calling R from the command line, though the specific command line will differ by system.

Warning

If R is calling other software, then consult the other sections in this guide.

The example here works through a specific example where R is called from Stata. Adapt as necessary for other code.

An example#

Stata code calls out to R. This may be done in the following way (partial code)

global r_path "/something/here" //Set path to R program (Adjust this to your local R installation path)
cd "$do_path"
shell "${r_path}/R" --vanilla <"$do_path/Figure1.R"

You need to figure out the path to R on your system.

Shell is not bash!

On Windows, the shell command is not bash. It will call cmd.exe command instead.

The easiest way may be to navigate to where R is usually installed. This would be

  • C:\Program Files\R\

with version-specific subdirectories, e.g.,

  • R-4.4.1

The full path to the R software is then

  • C:\Program Files\R\R-4.4.1\bin\x64\R.exe

So the above would then be (note the forward slashes, not backslashes)

global r_path "C:/Program Files/R/R-4.4.1/bin/x64" //Set path to R program (Adjust this to your local R installation path)
cd "$do_path"
shell "${r_path}/R" --vanilla <"$do_path/Figure1.R"

On macOS, the path to R is usually

  • /Library/Frameworks/R.framework/Resources/bin/R

So the above would then be

global r_path "/Library/Frameworks/R.framework/Resources/bin" //Set path to R program (Adjust this to your local R installation path)
cd "$do_path"
shell "${r_path}/R" --vanilla <"$do_path/Figure1.R"

On Linux, the path to R will depend heavily on the way it was installed. On BioHPC, consult the page. One location might be

  • /programs/R-4.4.2/bin/R

So the above would then be

global r_path "/programs/R-4.4.2/bin" //Set path to R program (Adjust this to your local R installation path)
cd "$do_path"
shell "${r_path}/R" --vanilla <"$do_path/Figure1.R"

Caution#

Always verify that the code actually ran as intended!