To do the job you need at a basic understanding (or a desire to learn) the following:

• Git/Github
• Sweave
• LaTeX
• Make
• R (duh :p)

Compensation includes:

• Undying glory
• The respect of your peers
• Self satisfaction
• A high-five from me if we ever meet in person!

If you are interested in the job please contact me at cameron[dot]bracken[at]gmail[dot]com

R development in TextMate is great with the R bundle. Unfortunately the R bundle does not support highlighting of roxygen documentation by default. That was always a sticking point for me switching to roxygen because TextMate has really nice highlighting for Rd files.

So I hacked on the syntax file to get at least some preliminary highlighting of stuff after roxygen comments (#'). The file is in a gist over at github. It doesn’t yet work quite as well as I would like but it is better than nothing. In particular, highlighting of R code in examples does not work. Contributions/additions are welcome.

You must have must have the R bundle installed. The easiest way to install is to open the bundle editor (“Bundles” > “Bundle Editor” > “Show Bundle Editor”) and copy this file over the R syntax file from the R bundle. Then “Reload Bundles” or restart TextMate.

You may need to install the R bundle first if you have not already:

Then either reload the bundles or restart TextMate to get the bundle activated.

Unfortunately all that goes out the window when using Sweave. Fortunately we can make it work! By that I mean it is possible to sync beween a pdf and the .Rnw source file. We need three things:

1. Add the concordance option when compiling with Sweave. That means add the line \SweaveOpts{concordance=T} to the top of your document after loading the Sweave style file.

2. Enable synctex with the --synctex=1 flag when compiling the tex file.

3. From the patchDVI (sweavesearch project on R-Forge), you need to use the patchSynctex function. This package is not available on CRAN afaik so you should install it from source from R-Forge:

   install.packages("patchDVI", repos="http://R-Forge.R-project.org")

Here is an example file for either Sweave or pgfSweave:

Here is a script to compile:

say you name it runSweave.sh, then call it

A much easier way would be to set up an engine in TeXShop or a custom “processing tool” in TeXWorks. There is a function in the patchDVI package called SweavePDF that should do the same thing but I have not tried it.

After all the compiling and patching of the synctex file is done, try right clicking and selecting ‘Sync’ in TeXShop or ‘Jump to PDF’ in TeXWorks, and everything should work! NOTE: I dont use TeXWorks so I haven’t gotten it to work but others have reported it does.

As for pgfSweave, the current version does not correctly output concordance information. But a patch enables proper concordance support (thanks aecay!). The next version of pgfSweave should have this working. To compile with pgfSweave, it is pretty much the same:

WARNING: This could be very slow if your graphic is complex

1. PGF 2.10 is required! This has been out for some months now but many LaTeX distros are notoriously slow at updating, so you may need to update manually.
2. Backward compatibility may break with some documents who still have the \pgfrealjobname hardcoded or who use the tex.driver option.
3. A new workflow is required to compile documents (it includes make), this is outlined in the vignette.
4. You can use all the nifty features in the TikZ externalization library, see the TikZ/PGF manual for more details.
5. Most importantly it is faster!

There are a boat load of other changes and new features, I think you like it, check them out:

• The pesky Rplots.pdf file is not generated anymore
• Brand new vignette by Hans Ekbrand on the use of pgfSweave with large data sets based on this site.
• New example on using caching by Yihui Xie
• Reusing code chunks now works as expected
• Inline comments are now preserved when tidy=T (thanks to changes in the formatR)

Please see the NEWS file for the full list sicce version 1.1.0.

I am also now working on the next version of pgfSweave to be version 1.2. This version will make some considerable changes to improve efficiency, namely

• Scrap the “old” externalization (\beginpgfgraphicnamed) in favor of the tikz external library (\tikzexternalize) which will allow for parallel compilation of external graphics
• Improve recognition of changes to plotting chunks for efficiency
• Fix centering of \include‘d images and highlighted output
• Improve upon the package load time
• Spif up the command line interface with some new options

The main new features are:

• Automatic code highlighting via the highlight package. This can be turned off with the highlight option.
• “Tidying” of source code output via the tidy option.
• Access to tikzDevice sanitization through a code chunk option sanitize
• Automatic addition of the \pgfrealjobname command if it does not exist similarly to the addition of the \usepackage{Sweave} line.
• Setting tex.driver=latex will now (in addition to working) generate an eps file

And of course bug fixes:

• Fixes for bunches of issues related to the changes in Sweave in R 2.12. I think these issues are now resolved (fingers crossed)
• keep.source actually works now.

See the NEWS file for the complete list of changes and the vignette for information on now to use the new options.

I created a css file that kills the sidebar and some other things:

• Inbox spans full screen
• Extra attachment icons
• No ads
• Messages span whole screen
• No footer

Please hack away. This script has pieces cobbled from various user scripts and extensions, I am really sorry but I don’t remember all my sources, please call me out on that.

Get it here.

UPDATE: Gmail changed some things, so I updated the css file fo fix some weirdness. It also now works with viewing contacts!

Say you named it test-pgf-version.tex. Then:

should display the version number. I happen to need to do this from R so using similar logic:

which accomplishes the same task as the second line above.

• Unlabeled code chunks are now allowed.
• The correct version of PGF is now checked for on startup. If the version is < 2.00, the package will fail to load.

http://cran.r-project.org/web/packages/pgfSweave/index.html

Incidentally, if you want to add files to TEX Live for one particular user, install them in a similar tree ~/Library/texmf where ~/Library is the Library folder in that user’s home directory. The folder texmf and other folders for the tree will have to be created. For instance, TEX will find any file in ~/Library/texmf/tex or a subfolder of this location, LATEX will find any file in ~/Library/texmf/tex/latex or a subfolder of this location, and BibTEX will find any .bib file in ~/Library/texmf/bibtex/bib or a subfolder of this location, and any .bst file in ~/Library/texmf/bibtex/bst or a subfolder of this location. It is not necessary to use texhash when adding files to this local tree.

http://cran.r-project.org/web/packages/pgfSweave/index.html

The pgfSweave R package is about speed and style of graphics. For speed, the package provides capabilities for “caching” graphics generated with Sweave on top of the caching funcitonality of cacheSweave. For style the pgfSweave package facilitates the integration of R graphics with LaTeX reports through the tikzDevice package and eps2pgf utility. With these tools, figure labels are converted to LaTeX strings so they match the style of the document and the full range of LaTeX math symbols/equations are available.

The backbone of pgfSweave is a a new driver for Sweave (pgfSweaveDriver). The driver provides new chunk options tikz, pgf and external on top of the cache option provided by cacheSweave.

This package started as a fork (hack) of cacheSweave to suit our own narrow purposes and has since become a valuable tool for much of our own work. We hope you will find it useful as well.

-Cameron Bracken and Charlie Sharpsteen

If anyone can step up and help get a working windows build up and running that would be great! I have little expertise with windows and I am just about stuck as what to do next. The task involved linking to some precompiled dlls and such since ming depends on libpng, zlib, libungig and freetype. If you would like to help, send me an email (cameron.bracken [at] gmail.com).

Todo before initial CRAN release:

• Working windows build that does not crash when any operation is performed
• option to wrap swf output in HTML

Todo in the future (possibly before initial release but probably not):

Device features

• xCharOffset yCharOffset
• yLineBias
• ipr: pixels per inch
• cra: default character size in pixels
• canClip: will be much harder than tikzDevice
• canChangeGamma
• canHAdj: not supported
• startps: ditto
• hasTextUTF8: should be possible with ming
• wantSymbolUTF8: ditto

Implement remaining graphics parameters

• gamma
• lend
• ljoin
• lmitre
• lineheight

Graphics primitives

• metricInfo (is currently returning the same metrics for all characters, this is bad but does not severely affect the text placement)
• textUTF8
• strWidthUTF8

I really like to use Github but R-Forge has alot of nice features for package development, so why not get the best of both worlds.

Say you have a git repo (with an R package or something else) but want to create a local brach which tracks an svn repo (from R-Forge) such that you can merge changes from your git repo in and then commit them to svn. First use the following command to grab the current svn:

This will create a new git repository that is a mirror of whatever svn repo you pointed at. This may take a while if you have a big existing svn repo.

If you want to add a svn bound branch to an existing git repo:

Edit .git/config and add the following:

Once you’ve done this, you have created an entry for a new git remote server- fetch the status and history of it’s branches using the following:

If this command is successful, git branch -a should show:

In the list of available branches. This branch is a remote branch- to make a local copy, do the following:

Now you have a local branch which is bound to the svn server- once again straight up adding/removing/moving files in this branch should work fine. It’s merging that gets you into trouble.

How to merge between a git branch and a git-svn branch

The point is that you don’t want git infecting your subversion repository with any of its awesomeness. Exposure to the kind of concentrated badass possessed by git causes poor SVN’s head to pop. So, the merge must be done as follows:

The --squash option tells git to leave out any info about what happened during the merge and act like it just mashed a bunch of files into your svn branch using copy commands.

Once you’ve added/copied/moved/squashmerged new files into your local svn branch- do the following to push the changes to the svn repo:

To pull changes from the svn repo run the following:

Here are some samples:

http://swfdevice.r-forge.r-project.org/swfDevice_test29.swf

http://swfdevice.r-forge.r-project.org/swfDevice_test28.swf

There are still a few things left to be done such as clipping and a working windows build.

So the three plugins that I rely on in Safari are finally up and running on Snow Leopard. Those being:

• Glims
  • Adds Numerous sweet features to Safari such as improved search suggestions, many tab options, like “always open in new tab”, favicons on tabs and keyword searches!
• SafariStand
  • The other essential plugin, add toolbar button for viewing individual site scripts and downloading flash movies (among other things).
• GlimmerBlocker
  • THE ad blocker. I might also mention that I also use Fanboy’s element hider for good measure.

Other programs I rely on that now are working great on SL are:

• SIMBL
  • Allows programs like SafariStand to work.
• Growl
  • You use Mac OS X and you don’t know what Growl is?
• iStat Menus
  • Various type of monitors for your system, in the menu bar! Keeps you very in touch with your system. I used to use MenuMeters for the same purpose, but iStat Menus basically took that project and totally tricked it out, making it way better.

(1) Log on to the server. (2) Create the script ~/.mailthis

(3) Then edit your crontab with crontab -e and put the following in there

You must put the absolute path here. This will send a mail to your pop3 account every minute.

(4) Finally create a filter in Gmail that says any message with the word x123456789x in it, delete it. That way you don’t spam yourself.

Thats it, now gmail will check your mail every minute since you are getting messages every minute.

The beta version of tikzDevice is now available here.

An additional location for downloading source tarballs and windows binaries is here.

There are many significant improvements compared to the alpha version:

Features:

• Rd documentation
• A vignette
• Proper string placement (because of string width and character metric calculations via latex)
• Custom LaTeX headers, footers and typesetting engines
• R-Level Annotation of graphics with TikZ commands (see TeXample for great examples of using TikZ commands)

Limitations:

• ASCII character support only
• No recognition of the R symbol font (i.e. no plotmath symbols)
• A bevy of other quirks and “personality traits” that will make themselves known in time

The device requires a working installation of LaTeX and the TIkZ package in order to function. This is because font metrics are currently calculated through direct calls to the LaTeX compiler. Unfortunately, this results in some significant computational overhead- it may take several seconds to create a plot that contains a lot of text. In an attempt to offset this behavior, the tikzDevice uses the filehash package to store font metrics that it has already computed. Hopefully the more the device is used, the faster it will be. We suggest reviewing the package vignette, especially the section “R Options That Affect Package Behavior ” for more information on how the caching process works.

We think the package is quite usable as it is, but there are surely many bugs that we don’t know about. We welcome bug reports at our R-Forge tracker

Enjoy!

The tikzDevice Team