Recommendations for developing Sweave documents

Question

I'm looking to streamline my Sweave document creation, and I'd like to hear about people's current setups. I feel like the holy grail goes something like this:

Editing Rnw code on one half of the screen
Single keybinding compiles Sweave document and runs pdflatex
View PDF on the other half of the screen; once compiled, PDF is refreshed and centered around the portion of the document you're editing
If compilation has errors, replace the PDF with the results of the compilation (e.g. latex errors or Sweave errors)

I am guessing/hoping that the solution is part Emacs/ESS combined with some code for the Emacs profile and/or a nice Makefile. But I would really like to hear about everybody's preferred way of creating Sweave and/or Latex documents.

score 9 · Accepted Answer · answered Sep 04 '09 at 15:17

A few other R users I talked to use a 'one-directory-per-project' setup, and a simple Makefile. As you suspected, that works well with Emacs/ESS.

I tend to just call a simple shell script sweave which I wrote before before 'R CMD Sweave' was added (as I find re-creating or copying the Makefile unappealing, YMMV). I also use Emacs and an auto-refreshing pdf viewer (like okular or kpdf). Emacs23 can preview pdf files directly too but I have yet to switch my work flow to that.

edd@ron:~$ cat bin/sweave
#!/bin/bash -e

function errorexit () {
    echo "Error: $1"
    exit 1
}

function filetest () {
    if [ ! -f $1 ]; then
       errorexit "File $1 not found"
    fi
    return 0
}


if [ "$#" -lt 1 ]; then
    errorexit "Need to specify argument file"
fi


BASENAME=$(basename $1 .Rnw)

RNWFILE=$BASENAME.Rnw
filetest $RNWFILE
echo "library(tools); Sweave(\"$RNWFILE\")" \
      | R --no-save --no-restore --slave

LATEXFILE=$BASENAME.tex
filetest $LATEXFILE && pdflatex $LATEXFILE

score 6 · Answer 2 · answered Sep 04 '09 at 18:59

6

You can do everything that you suggest there with the StatET plugin for Eclipse. That's what I use for Sweave development; it understands both latex and R very well, including syntax highlighting, etc.

You can get it here: http://www.walware.de/goto/statet.

Longhow Lam has written a nice guide: http://www.splusbook.com/Rintro/R_Eclipse_StatET.pdf.

http://www.statalgo.com/?p=93

answered Sep 04 '09 at 18:59

Shane

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I agree. Sweave, StatET, and Eclipse work well together. I wrote a post describing one way of configuring Sweave with Eclipse http://bit.ly/adfhZ1 – Jeromy Anglim Feb 23 '10 at 07:49
(splusbook link is broken. however I googled it and the following, seemingly equivalent, alternative, worked for me: http://www.splusbook.com/RIntro/R_Eclipse_StatET.pdf) – isomorphismes Sep 08 '11 at 21:39

Sharpie · Answer 3 · 2011-07-02T00:20:07.840

6

I use TeXShop on OS X to produce all of my LaTeX and Sweave reports. For me, a new compilation pipeline is as simple as adding a file, called Sweave.engine to ~/Library/TeXShop/Engines/ which contains the following:

#!/usr/bin/env Rscript
args <- commandArgs(T)

fname <- strsplit(args[1],'\\.')[[1]][2]

Sweave(paste(fname,'Rnw',sep='.'))

system(paste('pdflatex',paste(fname,'tex',sep='.')))

Sweave is now a selectable method of compiling a document inside TeXShop. I can set it to be the default for a document by adding the following TeX hash-bang to the top of the file:

% !TEX TS-program = Sweave

Hitting Cmd-T will typeset the document- the pdf automatically pops up in a separate window. TeXShop also incorporates SyncTeX technology so a Cmd-Click in the Rnw source will highlight the corresponding output in the PDF window and a Cmd-Click in the PDF window will highlight the corresponding input in the Rnw source.

TeXShop is mac-only but a great Qt/poppler-based clone, TeXworks, is available for Linux, Windows and Mac and supports many of the same features-- including TeX hash-bangs and SyncTeX. TeXworks has reached a level of maturity where it is included in version 2.8 of the MikTeX package for Windows.

edited Jul 02 '11 at 00:20

answered Sep 24 '09 at 01:09

Sharpie

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I like the direct use of Rscript! So many solutions invoke a shell to invoke R... For the record, the `strsplit` and `paste` for handling filename extensions is not necessary - both `Sweave` and `pdflatex` automatically add the extension. – Dav Clark Feb 11 '11 at 02:14
I think it was necessary at the time I wrote that post as TeX Shop passed the whole filename, `File.Rnw` to the engine. `Sweave` would be fine with it, but `pdflatex` would choke. – Sharpie Feb 11 '11 at 05:29
So - you say you have cmd-click between your .Rnw and .pdf files. Did you have to jump through these hoops also: http://cameron.bracken.bz/synctex-with-sweavepgfsweave-in-texshoptexworks – Dav Clark Jul 01 '11 at 23:54
No I didn't--so the SyncTeX support is probably a bit off. But I tend to write a lot of small Sweave chunks rather than bit ones, so SyncTeX lands me "in the ballpark" where I don't notice the issues associated with not using concordance. – Sharpie Jul 02 '11 at 00:18

score 3 · Answer 4 · answered Sep 10 '11 at 06:59

Try RStudio.

I have been a fan of Emacs and TeXShop as mentioned in previous answers.

However, Rstudio is starting to win me over. It is a rapidly-improving dedicated IDE for R. Definitely worth checking out.

I still love doing certain R-only development tasks in the standard R IDE for mac. But for Sweave documents and some associated R devel at the same time, RStudio wins. It works with virtually zero tweaking. I'm not sure about the PDF-related features in the latter half of the original question.

Kevin Wright · Answer 5 · 2012-02-20T17:04:45.170

2

One thing that has saved me some time is the 'auto-insert' mode in emacs. I have it set up so that each time I open a new .rnw file, emacs automatically sets up a basic document template and all I need to do is start writing my report.

Update: I've switched away from auto-insert. Now I use the "template.el" approach.

edited Feb 20 '12 at 17:04

answered Nov 03 '09 at 15:54

Kevin Wright

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score 1 · Answer 6 · answered Sep 05 '09 at 09:53

I use the "one-directory-per-project" and Makefile approach as well. I also include commands to create output in HTML, which can then be converted to OOo and MS Word, using tth. This is important for me since a lot of my collaborators are MS Office users and are resistant to using the PDF output. I learned a lot about how to do this from Frank Harrell's twiki at Vanderbilt.

Personally I use gvim as my editor of choice and running make from there is quite simple, as it is from Emacs.

Recommendations for developing Sweave documents

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