Articles about R - mpastell.com

Create odf, pdf and html report from a single Sweave document

2010-03-24T22:00:00Z

A lot of us know about Sweave and Latex and they work very well in creating elegant dynamic reports from R computation. However, sometimes we would like to also produce a word processing document for a colleague or a html version of the same report. Now there are tools for producing these like odfWeave. But wouldn't it be nice to get all of the output formats from the source document with same mark up?

Today I'm going to write about a good option how to get a nice looking odf, pdf and html report from the same source: ascii package with reStructuredText (reST) markup. reStructuredText is a simple plain text mark up that can be converted to several formats using the Python Docutils. It is simpler to write than Latex and it also the syntax that is used in Sphinx documents. The ascii package has a Sweave driver for weaving R code from documents written with reST and some other mark up languages as well. I have created a simple example document ascii-example.Rnw, which demonstrates the capabilities of the combination. The source file is a Sweave document with reST mark up instead of Latex. I had to make small modifications to the in ReST driver in ascii package to get this example to work¹ (download it here: newRest.R). I then processed the example with the new driver in R:

> library(ascii)
> source('newRest.R')
> ReST('ascii-example.Rnw')

Weaving produced this ascii-example.rst reST document which I then converted to odf, html, pdf with pdflatex and pdf with rst2pdf using:

rst2odt ascii-example.rst ascii-example.odt
rst2html ascii-example.rst ascii-example.html
rst2latex ascii-example.rst ascii-example.tex && pdflatex ascii-example.tex
rst2pdf ascii-example.rst

And here are the results: odt, html, pdf from latex and pdf from rst2pdf. You'll need to have Docutils and odtwriter for the conversion.

I have used the default options, but there are a lot options that can be passed to the docutils writers to customize the output, such as custom stylesheets. The image format in the pdfs is not optimal, but in can be changed with the "res" option in code chunk or you can also choose to use pdf format instead of jpg, but then it won't show up in html documents. I think using reST with ascii package is a good option for producing reports and tutorials in multiple output formats. That is also because I'm already familiar with reST directives and also use Sphinx for other purposes too. The reST syntax is also very fast to learn and I think it is definitely worth exploring. I also recommend using Sphinx if you only want to get html and pdf output, because it has more directives than plain reST e.g. math support.

I changed the driver to output code chunks in reST literal environment :: instead of .. codeblock:: r, because the codeblock directive is not supported in odt conversion and very poorly supported in latex conversion. ↩

Python in Sweave document

2010-02-08T22:00:00Z

Modifications to the custom driver:
Example usage

Lately I have been using a lot of Python for signal processing and I quite like SciPy. However, I have been missing something like Sweave, which is great literate programming environment for R. Today I managed to look a bit more into it and found this hack on how to use Python code in Sweave document by Romain Francois. However, I wanted to be able to catch the input as well as output so I made a small changes to his Sweave Driver.

Modifications to the custom driver:

driver <- RweaveLatex() 
runcode <- driver$runcode

driver$runcode <- function(object, chunk, options){ 
  if( options$engine == "python")
    { driver$writedoc( object, c("\\\\begin{verbatim}", chunk,
    "\\\\end{verbatim}", "\\\\begin{python}", chunk,"\\\\end{python}") ) }
  else{ runcode( object, chunk, options ) 
  } 
}

The driver now catches the input in verbatim environment (which can be easily changed to listings) and the output to python environment. The tex document can then be processed with the python latex package to evaluate the python expressions. Tho use the driver you need to put the option "engine="python" in your code chunks.

Example usage

My example is python code that calculates and plots the frequency response of a moving average filter. Here is the code in the Sweave document ma.Rnw. Process the file in R using the custom driver above:

Sweave( "ma.Rnw", driver = driver)

It should produce ma.tex. Then run latex (make sure you have the python package installed):

pdflatex -shell-escape ma.tex

Which should then in turn output this ma.pdf file.

ESS on Mac OS X

2009-11-24T22:00:00Z

One of the search terms that bring people frequently to my site is "install ESS on Mac OS X" or something like that. As it turns out installing ESS on OS X is really easy, but Google search does not really bring up good instructions. There are at least two easy options:

Use Aquamacs, it comes bundled with ESS
Use Carbon Emacs, it also comes with ESS, but you need to add the line (require 'ess-site) to your .emacs file in your home directory in order to enable it.

That's it!

MATLAB style stem plot with R

2009-09-10T21:00:00Z

Recently I wanted to plot an impulse response function with R and missed the MATLAB style stem plot for doing it. I couldn't find an R function for it with a quick Google search so I made my own. So here is the function and a small example:

#The function
stem <- function(x,y,pch=16,linecol=1,clinecol=1,...){
if (missing(y)){
    y = x
    x = 1:length(x) }
    plot(x,y,pch=pch,...)
    for (i in 1:length(x)){
       lines(c(x[i],x[i]), c(0,y[i]),col=linecol)
    }
    lines(c(x[1]-2,x[length(x)]+2), c(0,0),col=clinecol)
}

#An example
x <- seq(0, 2*pi, by = 0.2)
par(mfrow = c( 2, 1))
stem(x, sin(x), main = 'Default style')
stem(x, sin(x) ,main='With MATLAB colors', col= 4, linecol= 4, clinecol= 2)

R 64 bit on Mac OSX with ESS

2009-08-05T21:00:00Z

Compiling
Getting ESS to work

The current R version comes also with a 64-bit version so its not necessary to compile it from source anymore, but you do need to tell ESS how to use the 64bit version

So today I compiled 64 bit R 2.91 on Mac OS X 10.5.7 in order to get maximum speed for my analyses. The speed increase I got was 15-25 %, when I ran some tests with matrix calculation and intensive loops. Note that you can also download optimized binaries from http://r.research.att.com/, although they are not the latest version. It took me some effort and googling to get it done so I'm going to post the instructions here, so that I know how to do it next time and I hope that it also benefits others. After I got the installation done I ran into a problem getting ESS to recognize my 64 bit version, but I managed to solve that as well. So here is how I did it:

Compiling

First I installed the necessary developer tools from http://r.research.att.com/tools/. I already had gcc 4.2 from apple so installed gfortran and libreadline readline-5.2-1-quad.tar.gz. Readline is a precompiled binary and you extract is using

sudo tar fvxz readline-5.2-1-quad.tar.gz -C /

After installing the depencies I extracted R-2.9.1.tar.gz downloaded from cran and executed configure in the extracted directory with the following options (a bit modified from http://r.research.att.com/building.html):

./configure SHELL='/bin/bash' r_arch=x86_64 \
CC='gcc -arch x86_64 -std=gnu99' CXX='g++ -arch x86_64' \
OBJC='gcc -arch x86_64' F77='gfortran -arch x86_64' \
FC='gfortran -arch x86_64' --with-system-zlib --with-blas='-framework vecLib' \
--with-lapack --host=x86_64-apple-darwin9.7.0 --build=x86_64-apple-darwin9.7.0

After running "make" and "make install" I had a working installation that can be started using:

R --arch x86_64

Just running R tries to run 32 bit version of R which I don't have, so I made an alias R='R--arch=x86_64' to .profile and R starts form terminal with just the familiar R.

Getting ESS to work

Ok, all was well so far but then I discovered that ESS can't find R anymore, because it is trying to execute the 32 bit version and doesn't work. So after looking at the ESS source I discovered that you can modify R startup options in the file "essd-r.el". I use Carbon Emacs, but this methods should work with other Emacs variants. If you are wondering how to install ESS on OS X have a look at this post. First give yourself a permission to modify the file:

chmod u+w essd-r.el

Then open it and look for a line that says:

inferior-R-args " " ; add space just in case

And chance it to:

inferior-R-args "--arch x86_64 " ; add space just in case

Thats it, you should now have a working ESS set up with a 64 bit R!