MATLAB: How to call functions written in the statistics language, ‘R’, from MATLAB

MATLAB

I have written a program in the statistics language R and I want to call it from MATLAB.

Best Answer

The statistics language, 'R', is not supported in MATLAB; however, the following link contains MATLAB functions on MATLAB Central and File Exchange that may allow communication from MATLAB to R.

<http://www.mathworks.com/matlabcentral/fileexchange/loadFile.do?objectId=5051&objectType=file>

Please note that the files on the MATLAB Central File Exchange are not supported by MathWorks. Questions regarding files from the File Exchange should be directed to the author of the file.

A partial work-around would to use 'system'. In that case one uses syntax similar to:

>> filename = 'Example.R';

>> system([ 'R CMD BATCH --vanilla ' filename])

ans =

Please notice the '0' output, it means that the 'system' command executed successfully. The actual number returned in the case of an unsuccessful run will be the defined by the external command (in this case R).

Further documentation about the use of the function 'system' can be found here:

http://www.mathworks.com/help/matlab/ref/system.html

Related Solutions

MATLAB: Calling R from MATLAB on a Mac

Rscript is a noninteractive variant of the standard R command, designed for just this use.

I've used Rscript with the --vanilla flag successfully from the OS X command line in the past. To use in MATLAB, this is what I'd consider doing.

1. Prepend the following to the top of myscript.R, the program you want to run:

   #! /usr/bin/Rscript

2. From the OS X shell, set the executable bit on your program if it hasn't been done:

   $ chmod u+x myscript.R

3. Now, you're set up to use the system function in MATLAB:

   >> system('~/path_to/myscript.R')

The usual caveats about paths apply.

MATLAB: How to send output from MATLAB to the ‘stdin’ of another program

There are two options for sending output from MATLAB to the stdin of another program:

File-based Input/Output

Use a combination of MATLAB and your system's command line to accomplish your desired workflow.

1. Generate the input for the external program in MATLAB and write it to a file:

>> f = fopen('programInput.txt');
>> fwrite(f, '...');
>> fclose(f);

2. Use the '!' operator (or the 'system' command) to run a shell command to read the file, pipe the file contents to the programs stdin, and write the program stdout to a file.

Windows:

>> !type programInput.txt | myprogram > output.txt

Linux/Mac:

>> !cat programInput.txt | myprogram > output.txt

If you need to process the output of the program in MATLAB you can read the 'output.txt' file into MATLAB.

Use MATLAB support for Python or Java

MATLAB provides support for calling Python and Java libraries from within MATLAB. It is possible to start a process using Python or Java and manipulate the stdin / stdout of the process within MATLAB. Refer to the documentation for Java's ProcessBuilder or Python's subprocess.Popen.

For more information about MATLAB support for Python, refer to the following links:

https://www.mathworks.com/help/matlab/call-python-libraries.html

For more information about MATLAB support for Java, refer to the following links:

https://www.mathworks.com/help/matlab/using-java-libraries-in-matlab.html

Best Answer

Related Solutions

MATLAB: Calling R from MATLAB on a Mac

MATLAB: How to send output from MATLAB to the ‘stdin’ of another program

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