I finally installed Windows on my Mac (a traumatic experience) and finally got the code working. However, the startup instructions on the website of the book did not work for me. I offer a working example for other souls as clueless as myself. The first problem is that the libraries have to be installed manually, they do not install automatically as adverstised. Second, the library R2WinBUGS has to be called explicitly to run the critical bugs command.
Also, if anyone out there is thinking of installing a dual boot environment in Mac in order to install WinBUGS, there is a bug (no pun intended) in the licence installation of WinBUGS. The decode command for the license does not work as advertised, but the license installs anyway.
The working version is here: http://www.ling.uni-potsdam.de/~vasishth/temp/schools2.R
Thursday, January 25, 2007
Monday, January 22, 2007
Some expensive lessons I recently learnt about R/Sweave
1. If you are going to generate lots of latex tables automatically from an Rnw file, LABEL THEM.
2. weaver does not work with xYplot. If you are using the Hmisc library, just don't use weaver. I will present a solution here sometime soon.
The solution: set caching to off (cache=off) in the chunk that loads the Hmisc library and runs the xYplot command(s). You can turn caching on before and after the chunk, but xYplots need to be computed without caching.
3. xtable is unable to identify the fact that an R output line containing, e.g., log(sigma^2), has to be in math-environment in the tex. In Sweave this has the disastrous consequence that the .tex file does not compile. My kludgy solution is to search and replace the .tex file after Sweaving it.
It's frustrating that such good tools can sometimes be such a pain in the ass. I guess one should be grateful they are there at all.
2. weaver does not work with xYplot. If you are using the Hmisc library, just don't use weaver. I will present a solution here sometime soon.
The solution: set caching to off (cache=off) in the chunk that loads the Hmisc library and runs the xYplot command(s). You can turn caching on before and after the chunk, but xYplots need to be computed without caching.
3. xtable is unable to identify the fact that an R output line containing, e.g., log(sigma^2), has to be in math-environment in the tex. In Sweave this has the disastrous consequence that the .tex file does not compile. My kludgy solution is to search and replace the .tex file after Sweaving it.
It's frustrating that such good tools can sometimes be such a pain in the ass. I guess one should be grateful they are there at all.
Saturday, January 13, 2007
Incomplete Review of Gelman and Hill's Data Analysis using Regression and Multilevel/Hierarchical Models
I'm writing this somewhat cranky review as I read the book. Compared to the Pinheiro and Bates book, the examples in this book are initially irritatingly difficult to get working. A major problem with the book is that code involving BUGS runs only on Windows. This excludes readers like me from the action. So I have to wait until I get a Windows machine--but do I really want to start using Windows now? It would have been more helpful if their webpage prominently mentioned this detail (that the book is Windows specific). Had they done that I would probably not have bought it. But now that I have paid for it I am going to read it.
The website for the book has the data in a pretty disorganized way--why not just make a library? The authors do have a package for arm on the CRAN archive, but it does not install on any OS except Windows (the first R package I have seen with this property in my seven years as an R user). I tried to wget -r the ~gelman/arm/examples directory but ended up with all kinds of other crap in my directory as well, which was annoying. A zip archive could not hurt.
Chapters 1-3
I did not get a huge amount out of these chapters that was deeply interesting, but it is a good intro for newcomers to regression.
The code for the example in chapter 3 doesn't work on non-windows machines. Here is a working version.
Chapter 4
The book becomes more and more exciting from about this point onwards. Only one grouse:
Chapter 4 has some principles doing carrying out regression for prediction (section 4.6) but it is far from clear where they come from and the principles have a cookbookey feel (do this, don't do that, without explaining why). It would have been better if the authors had taught the reader to reason about the problem (surely those are the real principles, and the presented principles the consequences of the thought process generated by those principles).
[to be continued]
The website for the book has the data in a pretty disorganized way--why not just make a library? The authors do have a package for arm on the CRAN archive, but it does not install on any OS except Windows (the first R package I have seen with this property in my seven years as an R user). I tried to wget -r the ~gelman/arm/examples directory but ended up with all kinds of other crap in my directory as well, which was annoying. A zip archive could not hurt.
Chapters 1-3
I did not get a huge amount out of these chapters that was deeply interesting, but it is a good intro for newcomers to regression.
The code for the example in chapter 3 doesn't work on non-windows machines. Here is a working version.
Chapter 4
The book becomes more and more exciting from about this point onwards. Only one grouse:
Chapter 4 has some principles doing carrying out regression for prediction (section 4.6) but it is far from clear where they come from and the principles have a cookbookey feel (do this, don't do that, without explaining why). It would have been better if the authors had taught the reader to reason about the problem (surely those are the real principles, and the presented principles the consequences of the thought process generated by those principles).
[to be continued]
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