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:
- I didn’t take the time to learn
- It worked for me.
- I wrote a package to wrap the options Mandy described:
matlabr: Wrapping together system calls to MATLAB
matlabr package is located in GitHub and you can install it with the following command:
It has a very small set of functions and I will go through each function and describe what they do:
get_matlab: Mostly internal command that will return a character string that will be passed to
matlabis 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
have_matlab: Wrapper for
get_matlabto return a logical if
run_matlab_script: This will pass a
.mfile 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
run_matlab_code: This takes a character vector of MATLAB code, ends lines with
;, writes it to a temporary
.mfile, and then runs
run_matlab_scripton the temporary
rvec_to_matlab: Takes in a numeric
Rvector and creates a MATLAB column matrix.
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:
}. It then stacks these cells into a “matrix” of cells.
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
z (scalars) and a matrix named
a and then save
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
First off, we see that
test.txt indeed was written to disk.
file.exists("test.txt")  TRUE
We can read in the
test.txt from using
output = readLines(con = "test.txt") print(output)  " 1.0000000e+01"  " 1.0000000e+00 2.0000000e+00 3.0000000e+00"  " 4.0000000e+00 5.0000000e+00 6.0000000e+00"  " 7.0000000e+00 8.0000000e+00 1.0000000e+01"  " 3.0000000e+01"
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.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
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.