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02_functions.md

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using R to write a MATLAB function file

I want to create MATLAB function files from R to support the reproducibility of MATLAB course materials written in R Markdown.

The idea is to:

  • write the lines of a MATLAB user-defined function as a R string
  • in R, write those lines to a text file function.m
  • eventually write a single R script that creates all my commonly used m-functions that I can source() from any Rmd

In MATLAB R2016b or later, multiple functions can be defined in a single script. However, my current plan is to create separate m-files for each function.

managing files

I use relative file paths with respect to the RStudio Project working directory. My examples require a file structure that includes:

project\
  |-- derived\
  |-- results\
  |-- scripts\
  `-- project.Rproj

getting started

Create an Rmd script and save it to the scripts/ directory.

library(knitr)
opts_knit$set(root.dir = "../")

Packages.

library(readr)
library(reach)
library(R.matlab)

Executed only if a MATLAB issues a path warning.

# set path
m_script <- "pathstr = [cd]; 
  addpath(genpath(pathstr), '-end'); 
  savepath;" 
reach::runMatlabCommand(m_script)

write_sys()

My test-case MATLAB function, write_sys.m, writes a system transfer function to a text file. The function is based on a code chunk from the exploratory Bode plot tutorial.

I formulate formulate these lines as a MATLAB function in a string in the Rmd script. Use cat() to write the lines to a text file with a .m suffix in the derived/ directory.

# write_sys.m
function_lines <- "
function write_sys(sys, filepath)
  fid = fopen(filepath, 'wt');
  sys_string = evalc('sys');
  fprintf(fid, sys_string);
  fclose(fid);
end
"# end lines
cat(function_lines, file = 'derived/write_sys.m',
    sep = '\n', append = FALSE)

The arguments are:

  • sys the result of the MATLAB tf() function
  • filepath the relative path and filename to be written

The scripts/ directory should include this Rmd script. The derived/ directory should have the m-file we just made.

test the function

I'll create a transfer function for a first-order system and include the new function call, writing the transfer function to the results/ directory.

m_script <- "% assign parameters
K  = 1;
wb = 0.5;

% create the transfer function 
n = K;
d = [1/wb  1];
sys = tf(n, d);

% write sys to txt
write_sys(sys, 'results/sys02.txt')
"

Then execute the m-file.

# run the m-file
reach::runMatlabCommand(m_script)
Sys.sleep(12)

Examine the results.

# read the lines saved by the function 
sys <- read_lines('results/sys02.txt', skip = 3, n_max = 3)

# print to the document
cat(sys, sep = "\n")
     1
  -------
  2 s + 1

coda

session info

library(devtools)
session_info()
 setting  value                       
 version  R version 3.3.1 (2016-06-21)
 system   x86_64, mingw32             
 ui       RStudio (0.99.902)          
 language (EN)                        
 collate  English_United States.1252  
 tz       America/New_York            
 date     2016-11-06                  

 package     * version date       source                                 
 assertthat    0.1     2013-12-06 CRAN (R 3.2.1)                         
 devtools    * 1.12.0  2016-06-24 CRAN (R 3.3.1)                         
 digest        0.6.10  2016-08-02 CRAN (R 3.3.1)                         
 evaluate      0.10    2016-10-11 CRAN (R 3.3.1)                         
 htmltools     0.3.5   2016-03-21 CRAN (R 3.3.0)                         
 knitr       * 1.14.15 2016-11-03 Github (yihui/knitr@56faff4)           
 magrittr      1.5     2014-11-22 CRAN (R 3.2.1)                         
 memoise       1.0.0   2016-01-29 CRAN (R 3.2.3)                         
 png           0.1-7   2013-12-03 CRAN (R 3.3.0)                         
 R.matlab    * 3.6.1   2016-10-20 CRAN (R 3.3.1)                         
 R.methodsS3   1.7.1   2016-02-16 CRAN (R 3.2.3)                         
 R.oo          1.20.0  2016-02-17 CRAN (R 3.2.3)                         
 R.utils       2.4.0   2016-09-14 CRAN (R 3.3.1)                         
 Rcpp          0.12.7  2016-09-05 CRAN (R 3.3.1)                         
 reach       * 0.3.0   2015-10-17 Github (schmidtchristoph/reach@f503d44)
 readr       * 1.0.0   2016-08-03 CRAN (R 3.3.1)                         
 rmarkdown   * 1.1     2016-10-16 CRAN (R 3.3.1)                         
 rsconnect     0.4.3   2016-05-02 CRAN (R 3.3.0)                         
 rstudioapi    0.6     2016-06-27 CRAN (R 3.3.1)                         
 stringi       1.1.2   2016-10-01 CRAN (R 3.3.1)                         
 stringr     * 1.1.0   2016-08-19 CRAN (R 3.3.1)                         
 tibble        1.2     2016-08-26 CRAN (R 3.3.1)                         
 withr         1.0.2   2016-06-20 CRAN (R 3.3.1)                         
 yaml          2.1.13  2014-06-12 CRAN (R 3.2.1)

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