Re: [R] Truncated R output in Sweave

[Romain Francois]

Frank E Harrell Jr wrote:

Romain Francois wrote:

Frank E Harrell Jr wrote:

Dear Colleagues:

In producing a book or a handout I sometimes cut out a large part of the printed output of an R function, substituting ... for that chunk. Deleting non-essential output saves paper. It would be nice to have a capability in Sweave to allow the user to specify a starting and an ending regular expression that would identify consecutive lines of output to replace with ..., without showing the extra code required to do this to the user. I would want the LaTeX output, other than the omission, to appear the same as if the section were not omitted. Does anyone have an idea of how to do this elegantly?

Hello,



\documentclass[a4paper]{article}
\begin{document}
<<aa,eval=FALSE,echo=T>>=
rnorm( 200 )
<<echo=F>>=
txt <- capture.output( {
<<aa>>
   } )
if( length(txt) > 10 ){
   txt <- c( txt[1:10], "..." )
}
cat( txt, sep = "\n" )
@
\end{document}

You could use the same trick that is sometimes used to embed lattice calls into print calls (see the grid vignette for example)

Thank you Romain - I did not know of that construct.

By the way I just discovered the SweaveListingUtils package by Peter Ruckdeschel (on CRAN), which produces beautifully printed R code in Sweave code chunks. I put some info about it at http://biostat.mc.vanderbilt.edu/SweaveTemplate which has our Sweave template for statistical reports.

You might also be interested by the driver that comes with the highlight package (not yet on cran though, but the r-forge version is stable enough).

 > install.packages("highlight", repos="http://R-Forge.R-project.org";)
 > require( highlight )
 > Sweave( file, driver = HighlightWeaveLatex() )

Interesting. What would be the corresponding batch file command to achieve this? I like to run R CMD Sweave my.Rnw.

I have this as Hweave in my ${R_HOME}/bin directory:

#!/bin/env Rscript

args <- commandArgs( TRUE )
if( length( args ) < 1 ){
       stop( "need at least the file name" )
}
require( utils )
require( highlight, lib.loc = "~/.R/library" )
Sweave( args[1], driver = HighlightWeaveLatex() )

so that I can just do :

$ R CMD Hweave test.Rnw

And would you mind giving a very brief comparison of the two highlighting approaches regarding the LaTeX output?

highlight works with no modification on the sweave input file.

SweaveListingUtils depends on listings and is basically based on a list of keywords that it recognizes. highlight uses the R parser (or a slightly modified version of it) to identify the syntactic meaning of each token in the code. This gives you more control about how you want to code to be highlighted. It also uses true type font everywhere which I find more pleasing than what listings produces, it is a matter of taste I suppose.

Thanks!
Frank

*||*

Thanks
Frank

--
Romain Francois
Independent R Consultant
+33(0) 6 28 91 30 30
http://romainfrancois.blog.free.fr

test-listings.pdf
Description: Adobe PDF document

test-highlight.pdf
Description: Adobe PDF document

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