Dear Group,
I have made significant improvements to our Sweave template, have made
the template self-contained (i.e., you can run it yourself and it will
find the datasets it needs), and have included the output pdf file.
This is at http://biostat.mc.vanderbilt.edu/SweaveTemplate . You will
see in the pdf file the enhancements in how R code is pretty-printed,
and I have added an example where some R function output is suppressed
from the listing that Sweave typesets. The new template also suggests
how to auto-document the computing environment at the end of the report,
and how to properly reference R and add-on packages. Figures are
centered (but not as nicely as Marc Schwartz' approach) and better
defaults are used for axis label and tick mark label positioning.
Thanks to Romain Francois for providing the trick of suppressing parts
of R output (replacing it with ...) and Peter Ruckdeschel for his
excellent SweaveListingUtils package. Suggestions for further
improvements are welcomed.
Frank
--
Frank E Harrell Jr Professor and Chair School of Medicine
Department of Biostatistics Vanderbilt University
Frank, Your template is very interesting. The "pretty-ifing" of the left arrow and tilde in the input chunk has the unfortunate side-effect of making the code non-paste-able into R. I seem to recall that your reports used to include the latex source code as an appendix. Maybe one option could be to include an appendix with the results of Stangle applied to the .Rnw file, formatted as plain text. This would create a concise collection of all the necessary code to reproduce the results. Just brainstorming here.... Kevin Wright On Sun, Jun 14, 2009 at 11:29 PM, Frank E Harrell Jr < f.harrell@vanderbilt.edu> wrote:> Dear Group, > > I have made significant improvements to our Sweave template, have made the > template self-contained (i.e., you can run it yourself and it will find the > datasets it needs), and have included the output pdf file. This is at > http://biostat.mc.vanderbilt.edu/SweaveTemplate . You will see in the pdf > file the enhancements in how R code is pretty-printed, and I have added an > example where some R function output is suppressed from the listing that > Sweave typesets. The new template also suggests how to auto-document the > computing environment at the end of the report, and how to properly > reference R and add-on packages. Figures are centered (but not as nicely as > Marc Schwartz' approach) and better defaults are used for axis label and > tick mark label positioning. > > Thanks to Romain Francois for providing the trick of suppressing parts of R > output (replacing it with ...) and Peter Ruckdeschel for his excellent > SweaveListingUtils package. Suggestions for further improvements are > welcomed. > > Frank > -- > Frank E Harrell Jr Professor and Chair School of Medicine > Department of Biostatistics Vanderbilt University > > ______________________________________________ > R-help@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide > http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. >[[alternative HTML version deleted]]
Frank E Harrell Jr wrote:> > Dear Group, > > I have made significant improvements to our Sweave template, have made > the template self-contained (i.e., you can run it yourself and it will > find the datasets it needs), and have included the output pdf file. > This is at http://biostat.mc.vanderbilt.edu/SweaveTemplate . You will > see in the pdf file the enhancements in how R code is pretty-printed, > and I have added an example where some R function output is suppressed > from the listing that Sweave typesets. The new template also suggests > how to auto-document the computing environment at the end of the > report, and how to properly reference R and add-on packages. Figures > are centered (but not as nicely as Marc Schwartz' approach) and better > defaults are used for axis label and tick mark label positioning. > > Thanks to Romain Francois for providing the trick of suppressing parts > of R output (replacing it with ...) and Peter Ruckdeschel for his > excellent SweaveListingUtils package. Suggestions for further > improvements are welcomed. > > FrankThanks to some feedback from Philippe Grosjean today, I managed to make some progress on highlight. I posted the result of the template using both systems here: http://addictedtor.free.fr/misc/sweave/ -- Romain Francois Independent R Consultant +33(0) 6 28 91 30 30 http://romainfrancois.blog.free.fr