Friday, August 17, 2007

Cover Flow!

Yup. Figured it out. One of two ways to browse display plots. There is a more useful mode, using an iPhoto-like Browser that also lets you edit the list of plots. The arrow keys also let you move between plots.

Thursday, August 16, 2007

iWork '08 Spelunking.

Fiddling around with iWork '08 a bit and Numbers support is trivial to add to the R GUI. Basically, it exports a tab delimited version as text, much like Excel, though it uses the more modern pasteboard type (where Excel exports a much less useful string). We can detect that it is numbers from the metadata and "native" pasteboard types and throw up the same dialog as for the Excel pasting. Yay!

I'm thinking, for symmetry, that I should let you right click on a data frame in the workspace and copy as a tab delimited type for pasting into Excel/Numbers as well.

Friday, August 10, 2007

OLPC Musing

So, I've been playing with the OLPC a bit (I got a chance to play with a prototype in person at a party a while back) and I wonder: where's the science/mathematics? Authoring languages and EToys, which seem to be the focus presently (well, that and Tetris of course) are all well and good, but it would be really nice to see some more focus on the physical sciences, which leads naturally into topics like data analysis and statistics (collecting data is just the first step after all).

The minimal implementation would seem to be to start with something like the TILE/StatDocs projects that Duncan Temple Lang (Duncan, I hearby dub you DTL for the remainder of my posts. Sort of like DHH, the Ruby on Rails guy) and Deb Nolan have been doing for a while now (there used to be a website, but it seems to have disappeared). They give you an organizational unit of a "Lab" or an "Experiment," with some data and ways of interacting with the data (plotting and so on). These'd probably be hosted on the school's server and brought across the network dynamically. Another interesting tack would be to let the server also COLLECT data from the kids' experiments to be combined together into larger datasets via surveys or actual data collection. An ad hoc version of this is pretty common in introductory statistics courses for example.

This leads to the question of what to use as the analytical environment. Being biased, I would tend towards using R + GTK + Gecko, with a UI designed for the more modal experience of the OLPC. Alternatively, Python could be used for the implementation, though I'm not convinced that Python would be a particularly good interactive data language (things like R/S's formula DSL are really quite powerful for example). I tend to dislike point-n-click on principal, especially in an environment that stressed authoring languages.

Beyond that, you want kids to be able to collect their own data. I remember having this thing for my Atari 800 when I was a kid that had a number of different probe options for things like temperature and pH and rainfall and such. The software it had was pretty primitive, but it was lots of fun (for me anyway) playing with the temperature probe and such. It seems like the USB ports could be used to build data acquisition systems pretty cheaply these days---you wouldn't need really high performance for the most part and that lets kids collect their own data, which will always be more compelling than some prepackaged dataset since they "own" the data. There's at least one, possibly more, Open Source hardware project for building lots of these sorts of sensors for DIY weather monitoring that can probably be leveraged for that sort of thing.

Saturday, August 4, 2007

RExecServer can load help

It's not the best implementation in the world---I still think that should take place at the R level not in the GUI implementation---but on the plane to Seattle I gave RExecServer the ability to load help via the pager instead of just complaining.

Friday, August 3, 2007

Using RExecServer from ESS

In the long term I hope that most of this can be configured by an Installer of some sort, but for those wanting to use RExecServer with ESS, here's how my setup is currently configured:

When I use Emacs at all (which is very rarely these days, I mostly use TextMate) I use Aquamacs, which ships with ESS installed. Hopefully the instructions won't be all that different for people using Carbon Emacs and what have you (and if they are, perhaps people would be so kind as to post their changes). I'm also not a super-sophisticated ESS user so there might be better ways of doing the ESS side of things.

First, though, we need to get ourselves easy access to RExecServer from the command line. I like to do this via a symbolic link in /usr/local/bin (/usr/bin would also work). You'd think that we could just symlink and be done with it, but the way OS X starts applications is... uh... strange and doing that will cause all sorts of problems because the bundle loader won't be able to find any resources and promptly crash out. It's not pretty. What we need to do is actually set a special environment variable called CFProcessPath to point to the application bundle rather than /usr/local or whatever.

Fortunately, I made this into a little script so you won't have to do it yourself. It lives in the Resources folder of the application bundle. So, from Terminal we would do something like:

$ cd /usr/local/bin
$ sudo ln -s /Applications/ R-exec

if you have put somewhere other than Applications, use that path instead of "/Applications." That's pretty much all there is to it. Of course, "/usr/local/bin" should be in your path

$ R-exec

R version 2.6.0 Under development (unstable) (2007-07-14 r42234)
Copyright (C) 2007 The R Foundation for Statistical Computing
ISBN 3-900051-07-0

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.


You should be able to use R-exec from Terminal just like normal R. For ESS, I have a line in my .emacs file:

(require 'ess-site)
(setq inferior-R-program-name "R-exec")

that starts my RExecServer version of R instead of the normal version. Once upon a time, I think I read that ESS is smart enough to detect multiple installed versions of R with specially named symlinks, but I don't know how to get it to work (if an ESS expert knows how to do this, please chime in).

In any case, that's pretty much all there is to it. Hopefully that helps, but if you have questions please email me or (better yet so others can see) leave a comment.

Thursday, August 2, 2007

Oh, yeah.

I did figure out one thing in an idle moment on vacation last week. How to paste from Excel to the R console. Thought y'all might like something like that. I should probably do another featurecast soon to show some of the things that have been fleshed out a bit. These include...

  • Multi-level hinting. If you have "plot(foo()," the hinting mechanism will show you "plot," rather than nothing

  • Drag-n-drop from the workspace to the console gets a summary() on those objects

  • Excel (or Excel-like things I suppose. Anything that posts VALU or NSTabularPboardType) pasting

  • Device recording, with the option to deactivate as well as clear plot listing

  • Clear the console

  • Copying text from the console optionally does so in a "source()-able" manner. i.e. prompts and output are removed.

  • Keybindings for popular things like Command-= to give you "<-"

  • TextMate-style brace handling. i.e. select some text and type "(" (or ",`,',{,[,Command-[) and it will put the appropriate bracket around the selected text.

  • An editor. :-)

  • Preferences :-)

Any requests?

I'm sure there's other stuff I've forgotten at this point, but I'm still unburying myself otherwise and getting ready to head to BioC'07 in a couple of days.