ScienceWeblog:Bayesian data analysis on a Mac

2011-07-22T20:01:01Z

Mvugt:

====specifically: Bayesian Data Analysis on a Mac with R and OpenBUGS via BRugs====

[[Blog:Bayesian_data_analysis_in English|Bayesian data analysis]] is a way of figuring out what you believe given what you just saw, but in math. [http://www.r-project.org/ R] is a free computer language for calculating statistics. [http://www.openbugs.info/w/ OpenBUGS] is a flexible program for doing Bayesian data analysis. [http://www.biostat.umn.edu/~brad/software/BRugs/ BRugs] is a bridge between R and BUGS. Macs are why Steve Jobs wears black turtlenecks.

This post is solving a very narrow problem. R is cross-platform, but OpenBUGS only works on Windows. The same holds either for the cousins of OpenBUGS or for their bridges with R. So it is hard for Mac users to do Bayesian data analysis in R with the flexibility offered by BUGS.

My colleague [http://hri.cogs.indiana.edu/people/jack.php Jack Harris] has a fix that doesn't take any fiddling. Its great. If you know what you are doing, instructions are below. If you wish you knew what you were doing, [http://www.indiana.edu/~kruschke/DoingBayesianDataAnalysis/ read a book].

====Instructions for using BRugs on a Mac====
* Be a Mac user of R (if you are on Windows then you don't have a problem).
* Download [http://hri.cogs.indiana.edu/~jackh/WindowsR.app.tar.bz2 this].
* Extract the tarball or (if you don't know what that means) hope that your computer magically turns the file into one that ends with ''.app'' .
* Open the app, wait a bit. There will be a benign error, just hit OK.
* After R loads, type
install.packages("BRugs")
* Download [http://www.indiana.edu/~jkkteach/BayesTutorial/TutorialBRugsTest.R this test file] and type
setwd("~/whereeverthefilewent")
source("TutorialBRugsTest.R")

You should get pretty graphs. That means it worked. If you want more, the samples from [http://www.indiana.edu/~kruschke/DoingBayesianDataAnalysis Kruschke's book] are [http://www.indiana.edu/~kruschke/DoingBayesianDataAnalysis/Programs/ here]. The samples should all run fine if you download everything to one spot. The book has puppies on the cover to signal its friendliness to the 'fraid-of-math.

====additional notes====
There are other workarounds to get BUGS in R on a Mac. This one is the easiest to get going and I've been told that it has some other advantages (thanks Drew):
*In this wine environment copy/paste/save work (but with the control key instead of the command key on my Mac keyboard).
*Control-R actually runs highlighted text.
*Downside: shift-arrows does not highlight, instead it overwrites text in this version.

ScienceWeblog:Bayesian data analysis on a Mac

2011-07-22T19:33:19Z

Mvugt: /* how can I uninstall Windows R? */ new section

enfascination - User contributions [en]

ScienceWeblog:Bayesian data analysis on a Mac

ScienceWeblog:Bayesian data analysis on a Mac