Re: [R] [slightly off topic] Sweave with markdown
Thank you all, I think I have a good list of options now. The best suited to my personal taste seems to be the Brew package, which I completely overlooked until I looked at the source examples. If I can persuade my text editor (textmate) to recognize the markup and also execute the R chunks, I'll have my dream workflow: a single text file with both text (in a lightweight, email friendly markup), and the R commands together. The MultiMarkdown extension allows me to convert the brewed file into whatever output one could wish for: LaTeX, Html, pdf, rtf,... I'll probably be using the html conversion for routine work, and the LaTeX one when a clean printed version is needed. The use of dev.copy or some similar command should make easy the creation of both bitmap and vector versions of the graphs if needed. Thanks again everyone! baptiste On 23 May 2008, at 13:30, Gabor Grothendieck wrote: You could check out the brew package: https://stat.ethz.ch/pipermail/r-packages/2007/000327.html On Fri, May 23, 2008 at 4:37 AM, baptiste Auguié [EMAIL PROTECTED] wrote: DeaR list, Has anyone tried to mix the Sweave paradigm with the Markdown[*] (and co.) syntax? Would this be hard to implement? My tiny understanding of Sweave is that one can define new drivers for the text part, while some functions that deal with the R code would not require any modification. Here's the reason I'm interested in Mardown for a driver. I've been orbiting around Sweave for several weeks, and while I understand the great value of this literate programming, I'm a bit put off by the technical aspect. I'm a LateX user, and a R user (you'd have guessed, albeit fairly novice), so the problem is not to get it working (i got some writings done with Sweave), but more of getting an efficient workflow. I find the LaTeX commands overly intruding in the middle of my R source code, plus the relatively slow compilation of latex makes it quite impractical for quick studies ( I once spent 20 minutes trying to get the graph to be at a sensible scale on the page). As an alternative, I'm resorting to having a folder per study (I'm physicist, doing data analysis for optical spectroscopy), with one R file per analysis and a text file to keep track of the experimental conditions. When the data is really important / interesting, I've also tried to write a package: great for storing the data, functions and commands in a consistent manner (this works fine, but it cannot be a solution for quick trial experiments. Also, the figures cannot be included in the html doc as far as I know.) I was considering some alternatives to Sweave, namely R2HTML and odfWeave, but in the former the source syntax is no less disturbing than LaTeX (although the zero compilation time is a plus), while for the latter I do not have a decent compatible editor (on a Mac, I tried Openoffice and Abiword but the fonts look like my handwriting for some obscure reason). Maybe I'll give it another shot at some stage, I just usually prefer plain text files. Any input welcome, Baptiste [*]: http://en.wikipedia.org/wiki/Markdown _ Baptiste Auguié Physics Department University of Exeter Stocker Road, Exeter, Devon, EX4 4QL, UK Phone: +44 1392 264187 http://newton.ex.ac.uk/research/emag http://projects.ex.ac.uk/atto __ 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. _ Baptiste Auguié Physics Department University of Exeter Stocker Road, Exeter, Devon, EX4 4QL, UK Phone: +44 1392 264187 http://newton.ex.ac.uk/research/emag http://projects.ex.ac.uk/atto __ 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.
[R] [slightly off topic] Sweave with markdown
DeaR list, Has anyone tried to mix the Sweave paradigm with the Markdown[*] (and co.) syntax? Would this be hard to implement? My tiny understanding of Sweave is that one can define new drivers for the text part, while some functions that deal with the R code would not require any modification. Here's the reason I'm interested in Mardown for a driver. I've been orbiting around Sweave for several weeks, and while I understand the great value of this literate programming, I'm a bit put off by the technical aspect. I'm a LateX user, and a R user (you'd have guessed, albeit fairly novice), so the problem is not to get it working (i got some writings done with Sweave), but more of getting an efficient workflow. I find the LaTeX commands overly intruding in the middle of my R source code, plus the relatively slow compilation of latex makes it quite impractical for quick studies ( I once spent 20 minutes trying to get the graph to be at a sensible scale on the page). As an alternative, I'm resorting to having a folder per study (I'm physicist, doing data analysis for optical spectroscopy), with one R file per analysis and a text file to keep track of the experimental conditions. When the data is really important / interesting, I've also tried to write a package: great for storing the data, functions and commands in a consistent manner (this works fine, but it cannot be a solution for quick trial experiments. Also, the figures cannot be included in the html doc as far as I know.) I was considering some alternatives to Sweave, namely R2HTML and odfWeave, but in the former the source syntax is no less disturbing than LaTeX (although the zero compilation time is a plus), while for the latter I do not have a decent compatible editor (on a Mac, I tried Openoffice and Abiword but the fonts look like my handwriting for some obscure reason). Maybe I'll give it another shot at some stage, I just usually prefer plain text files. Any input welcome, Baptiste [*]: http://en.wikipedia.org/wiki/Markdown _ Baptiste Auguié Physics Department University of Exeter Stocker Road, Exeter, Devon, EX4 4QL, UK Phone: +44 1392 264187 http://newton.ex.ac.uk/research/emag http://projects.ex.ac.uk/atto __ 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.
Re: [R] [slightly off topic] Sweave with markdown
You could check out the brew package: https://stat.ethz.ch/pipermail/r-packages/2007/000327.html On Fri, May 23, 2008 at 4:37 AM, baptiste Auguié [EMAIL PROTECTED] wrote: DeaR list, Has anyone tried to mix the Sweave paradigm with the Markdown[*] (and co.) syntax? Would this be hard to implement? My tiny understanding of Sweave is that one can define new drivers for the text part, while some functions that deal with the R code would not require any modification. Here's the reason I'm interested in Mardown for a driver. I've been orbiting around Sweave for several weeks, and while I understand the great value of this literate programming, I'm a bit put off by the technical aspect. I'm a LateX user, and a R user (you'd have guessed, albeit fairly novice), so the problem is not to get it working (i got some writings done with Sweave), but more of getting an efficient workflow. I find the LaTeX commands overly intruding in the middle of my R source code, plus the relatively slow compilation of latex makes it quite impractical for quick studies ( I once spent 20 minutes trying to get the graph to be at a sensible scale on the page). As an alternative, I'm resorting to having a folder per study (I'm physicist, doing data analysis for optical spectroscopy), with one R file per analysis and a text file to keep track of the experimental conditions. When the data is really important / interesting, I've also tried to write a package: great for storing the data, functions and commands in a consistent manner (this works fine, but it cannot be a solution for quick trial experiments. Also, the figures cannot be included in the html doc as far as I know.) I was considering some alternatives to Sweave, namely R2HTML and odfWeave, but in the former the source syntax is no less disturbing than LaTeX (although the zero compilation time is a plus), while for the latter I do not have a decent compatible editor (on a Mac, I tried Openoffice and Abiword but the fonts look like my handwriting for some obscure reason). Maybe I'll give it another shot at some stage, I just usually prefer plain text files. Any input welcome, Baptiste [*]: http://en.wikipedia.org/wiki/Markdown _ Baptiste Auguié Physics Department University of Exeter Stocker Road, Exeter, Devon, EX4 4QL, UK Phone: +44 1392 264187 http://newton.ex.ac.uk/research/emag http://projects.ex.ac.uk/atto __ 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. __ 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.
Re: [R] [slightly off topic] Sweave with markdown
On Fri, May 23, 2008 at 4:37 AM, baptiste Auguié [EMAIL PROTECTED] wrote: (although the zero compilation time is a plus), while for the latter I do not have a decent compatible editor (on a Mac, I tried Openoffice and Abiword but the fonts look like my handwriting for some obscure reason). Maybe I'll give it another shot at some stage, I just usually prefer plain text files. Try using NeoOffice or the development version of OpenOffice. The new version (3.0) of OpenOffice is better integrated into OS X and should probably do the trick http://download.openoffice.org/3.0beta/ It is beta, but it has been pretty stable for me. Max __ 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.
