Converting Documents Produced by Sweave
Converting from LaTeX to html
The recommended format for statistical reports to send to collaborators is
pdf produced by
pdflatex.
Sometimes it is necessary to give collaborators a version of a report that can be edited outside of
LaTeX, or to post a report on a web site. Experiments with latex2rtf and hevea have shown that these are not adequate for reports that incorporate advanced features such as latex(describe()) output. One of the most reliable approaches is to use TtH to convert from LaTeX to html.
A linux script is needed to translate Sweave's LaTeX output for use with TtH (thanks to Ben Bolker for providing most of the code). Here are the steps needed to get going.
- As root do the following (the second step is necessary if you are including LaTeX
picture code in documents (as produced by latex.describe) to create the ppmtogif executable)
- apt-get install tth
- apt-get install netpbm
- As user, copy
sweave2html to ~/bin and make sure that ~/bin is in your search path
- Mark this script as executable
To convert your .tex file to html and create all the needed graphics files, do the following.
- Create a
graphics subdirectory in your project directory and have Sweave use it by putting the following command in your .Rnw file: \SweaveOpts{prefix.string=graphics/plot}
- Run Sweave, using for example a script named
Sweave in ~/bin that is marked as executable and contains
#!/bin/sh
echo "Sweave(\"$1.Rnw\")" | R --no-save --no-restore
If you ran Sweave foo next run sweave2html foo
You can also view the output in a browser such as konqueror and copy and paste it into an OpenOffice document and save in a variety of formats including Word. Use Select All and Paste and all graphics and table formats will be preserved.
It is important to give your collaborator all the .pdf files in the graphics directory to use in manuscripts; do not let them use the lower resolution graphs that will be included in the foo.html document. Bundle all the necessary files to send to the collaborator, using for example
zip /tmp/z.zip foo.pdf foo.html *.gif graphics/*.pdf graphics/*.png
E-mail /tmp/z.zip as an attachment.
Using TeX4ht
The TeX4ht package is a comprehensive LaTeX to html convertor. It may be installed easily using apt-get. In one test it performed well (including greek letters and superscripts and LaTeX picture environments) although I did not see how to get postscript or pdf graphics to appear in the final output. Advanced summary.formula.reverse tables are handled nearly perfectly, include those that contain micro dot charts. TeX4ht is used as follows:
htlatex foo.tex # produces foo.html
mk4ht oolatex foo.tex # produces an OpenOffice .sxw file
Note that the tth package has to be installed for htlatex to run completely.
My test of the oolatex option resulted in output that was not as good as running htlatex and opening the resulting .html file in OpenOffice. See StatReport for more information and example output, and note its comment about turning off picture links in the OpenOffice document.
Using OpenOffice Exclusively
The odfWeave package by Max Kuhn can be used to produce reports directly in open document format, and the output can be save in Word format. At present, graphics are somewhat low resolution. Source code is similar to what is used with Sweave. Here is how to run an example (in linux), after installing the odfWeave package and the latest OpenOffice. The file can then be exported to open document or Word format.
R
library(odfWeave)
odfWeave('/usr/local/lib/R/site-library/odfWeave/examples/examples.odt', '/tmp/out.odt')
/tmp/out.odt in OpenOffice Writer. Note: On some systems the correct file name will be /usr/lib/R/site-library/odfWeave/examples/examples.odt.
This approach does not allow you to use the advanced table making capabilities of Hmisc that rely on LaTeX.
Weaving with Raw HTML
Greg Snow has written a document showing how to use raw HTML and the R2HTML package to produce .html reports.
Batch Conversion of Document Formats
cd /tmp
tar zxvf ooconvert-*
# You may need to edit line to change python2.3 to python
sudo chmod a+x ooconvert
sudo mv ooconvert /usr/local/bin or to ~/bin
One-step Conversion of LaTeX Documents to Word
- Install
ooconvert, tth, tex4ht
- Put the following script in
~/bin and chmod +x to make it executable
- Run it by saying
ltx2doc foo to convert foo.tex to foo.doc
mk4ht oolatex $1.tex
rm -f $1.css $1.idv $1.lg $1.tmp $1.4tc $1.xref $1.4ct
ooconvert $1.odt $1.doc
rm $1.odt
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