matlabr: a Package to Calling MATLAB from R with system

(This article was first published on  A HopStat and Jump Away » Rbloggers, and kindly contributed to
R-bloggers)     

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

R.matlab

.
It worked for me.
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:

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')

.

have_matlab

: Wrapper for

get_matlab

to return a logical if

matlab

is found.

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

.

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.

rvec_to_matlab

: Takes in a numeric

R

vector 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:

{

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]
/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")
[/code]
[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.