matlabr: a Package to Calling MATLAB from R with system

In my research, I primarily use R, but I try to use existing code if available. In neuroimaging and other areas, that means calling MATLAB code. There are some existing solutions for the problem of R to MATLAB: namely the R.matlab package and the RMatlab package (which can call R from MATLAB as well). I do not use thse solutions usually though.

Previously, Mandy Mejia wrote “THREE WAYS TO USE MATLAB FROM R”. Option 2 is about how to use R.matlab, and Mandy gives and example with some cod. She also describes in Options 1 and 3 how to use the system command to call MATLAB commands.

I like this strategy options because:

  1. I didn’t take the time to learn R.matlab.
  2. It worked for me.
  3. I wrote a package to wrap the options Mandy described: matlabr.

matlabr: Wrapping together system calls to MATLAB

The matlabr package is located in GitHub and you can install it with the following command:

devtools::install_github("muschellij2/matlabr")

It has a very small set of functions and I will go through each function and describe what they do:

  1. get_matlab: Mostly internal command that will return a character string that will be passed to system. If matlab is in your PATH (bash variable), and you are using R based on the terminal, the command would return "matlab". If MATLAB is not in your PATH or using a GUI-based system like RStudio, you must set options(matlab.path='/your/path/to/matlab').
  2. have_matlab: Wrapper for get_matlab to return a logical if matlab is found.
  3. run_matlab_script: This will pass a .m file to MATLAB. It also wraps the command in a try-catch statement in MATLAB so that if it fails, it will print the error message. Without this try-catch, if MATLAB errors, then running the command will remain in MATLAB and not return to R.
  4. run_matlab_code: This takes a character vector of MATLAB code, ends lines with ;, writes it to a temporary .m file, and then runs run_matlab_script on the temporary .m file.
  5. rvec_to_matlab: Takes in a numeric R vector and creates a MATLAB column matrix.
  6. rvec_to_matlabclist: Takes in a vector from R (usually a character vector) and quotes these strings with single quotes and places them in a MATLAB cell using curly braces: { and }. It then stacks these cells into a “matrix” of cells.

Setting up matlabr

Let’s set up the matlab.path as I’m running in RStudio:

library(matlabr)
options(matlab.path = "/Applications/MATLAB_R2014b.app/bin")
have_matlab()

The result from have_matlab() indicates that the matlab command can be called.

Let’s write some code to test it

Here we will create some code to take a value for x, y, z (scalars) and a matrix named a and then save x, a, z to a text file:

code = c("x = 10", 
         "y=20;", 
         "z=x+y", 
         "a = [1 2 3; 4 5 6; 7 8 10]",
         "save('test.txt', 'x', 'a', 'z', '-ascii')")
res = run_matlab_code(code)
/var/folders/1s/wrtqcpxn685_zk570bnx9_rr0000gr/T//RtmpHnOinq/file2f8352c04937.m

Output

First off, we see that test.txt indeed was written to disk.

file.exists("test.txt")
[1] TRUE

We can read in the test.txt from using readLines:

output = readLines(con = "test.txt")
print(output)
[1] "   1.0000000e+01"                                
[2] "   1.0000000e+00   2.0000000e+00   3.0000000e+00"
[3] "   4.0000000e+00   5.0000000e+00   6.0000000e+00"
[4] "   7.0000000e+00   8.0000000e+00   1.0000000e+01"
[5] "   3.0000000e+01"                                

Conclusions

matlabr isn’t fancy and most likely has some drawbacks as using system can have some quirks. However, these functions have been helpful for me to use some SPM routines and other MATLAB commands while remaining “within R“. R.matlab has a better framework, but it may not be as straightforward for batch processing. Also matlabr has some wrappers that will do a try-catch so that you don’t get stuck in MATLAB after calling system.

Let me know if this was helpful or if you have ideas on how to make this better. Or better yet, give a pull request.

Advertisements

8 thoughts on “matlabr: a Package to Calling MATLAB from R with system

  1. Pingback: R and Matlab | Ryo Eng ®

  2. Thank you. I am using a windows 8 PC. I tried to implement the example code you provided. But got the error message. My code and output are as follows:

    library(matlabr)
    options(matlab.path = “C:/Program Files/MATLAB/R2013a/bin”)
    have_matlab()

    (It returns True)

    code = c(“x = 10”,
    “y=20;”,
    “z=x+y”,
    “a = [1 2 3; 4 5 6; 7 8 10]”,
    “save(‘test.txt’, ‘x’, ‘a’, ‘z’, ‘-ascii’)”)
    res = run_matlab_code(code)

    (The error output is
    Warning messages:
    1: running command ‘which matlab’ had status 127
    2: running command ‘which matlab’ had status 127
    3: running command ‘C:/Program Files/MATLAB/R2013a/bin/matlab -nodesktop -nosplash -nodisplay -r “try, run(‘C:\Users\Hairong\AppData\Local\Temp\RtmpSWfZiq\file12083a713ba8.m’); catch err, disp(err.message); exit(1); end; exit(0);”‘ had status 127 )

    file.exists(“test.txt”)

    (output is False)

    Can you please check out what caused that if you have time?
    Thanks,
    Hairong

    • Sorry for the late reply, had to get a windows box up and running with matlab.

      Please reinstall matlabr using:
      devtools::install_github(“muschellij2/matlabr”)

      ##############################
      #Test code
      ##############################
      library(matlabr)
      options(matlab.path=’C:\\Program Files\\MATLAB\\R2015b\\bin’)
      verbose = TRUE
      code = c(“x = 10;”,
      “save(‘C:\\Users\\Windows7\\Desktop\\test.txt’, ‘x’, ‘-ascii’)”)
      run_matlab_code(code)

      Now, the matlab command window will come up and run, but the R command returns the result as 0 if it can send the command. This isn’t ideal b/c R won’t wait for matlab to finish. I haven’t figured this out on a windows machine, and is likely a byproduct of me using the system command.

      I hope that helps, albeit a non-complete answer.

  3. Hi, i am running matlab code to get genbank file, however i cannot get the txt file. Please explain to me. Thank you.

    devtools::install_github(“muschellij2/matlabr”, force = TRUE)
    library(matlabr)
    options(matlab.path = “C:/Program Files/MATLAB/R2016b/bin”)
    have_matlab()
    run_matlab_script(hiv.mat)
    code = c(“hiv=getgenbank(‘NC_001802′,’SequenceOnly’,true);”,
    “save(‘hiv.txt’, ‘hiv’, ‘-ascii’)”)
    res = run_matlab_code(code)
    file.exists(“hiv.txt”)
    #system(“matlab -nodisplay -r ‘stuff; to; do; in; matlab;'”)
    #set a variable in R and save in a csv file
    output = readLines(con = “hiv.txt”)
    print(output)

      • This is my output

        > have_matlab()
        [1] TRUE

        > res = run_matlab_code(code)
        C:\Users\user\AppData\Local\Temp\RtmpIZ8QUH\file119c41bd3090.m

        > file.exists(“hiv.txt”)
        [1] FALSE

        > output = readLines(con = “hiv.txt”)
        Error in file(con, “r”) : cannot open the connection
        In addition: Warning message:
        In file(con, “r”) : cannot open file ‘hiv.txt’: No such file or directory

Leave a Reply

Fill in your details below or click an icon to log in:

WordPress.com Logo

You are commenting using your WordPress.com account. Log Out / Change )

Twitter picture

You are commenting using your Twitter account. Log Out / Change )

Facebook photo

You are commenting using your Facebook account. Log Out / Change )

Google+ photo

You are commenting using your Google+ account. Log Out / Change )

Connecting to %s