Running OpenBUGS from R

Using this package, it is possible to call a BUGS model, summarize inferences and convergence in a table and graph, and save the simulations in arrays for easy access in R.


News

Changes to R2OpenBUGS:

Update 3.2-3.2

  • Change printing of DIC to match the number of digits in the summary
  • Change attach.all for linux compatibility

Update 3.2-3

  • bugs.inits function is now exported.

Update 3.2-2.1

  • Updated reading of CODA file formats for version 3.2.2 of OpenBUGS, which now consistently uses tab delimiters. Problems with reading the log file were corrected as part of the new version of OpenBUGS.

Update 3.2-1.4

  • Corrected printing of pD and DIC, which were reversed
  • Updated documentation to note difference in DIC reporting between Windows and Linux, and the lack of support for the bugs.log function under Linux
  • Fixed problem with references in vignette

Update 3.2-1.3

  • cleanup: removed S-PLUS support completely since that was removed at several other places before
  • fixed the bugs introduced with validInstallOpenBUGS
  • Changed handling of default OpenBUGS program location in a sensible way now
  • import logit from boot nowadays (seems nobody uses that anyway)
  • examples from OpenBUGS copied into the package to allow for tests independent of example data location
  • moved dependencies to imports

Update 3.2-1.2

  • Changed handling of default OpenBUGS program location and other changes required for cran compliance
  • Fixed bug in validInstallOpenBUGS with user-supplied program location

Update 3.2-1

  • Added saveExec and restart options to the bugs function that uses the OpenBUGS internalize/externalize feature to allow a user to store the state of the OpenBUGS execution and continue execution after checking results in R.

Update 3.1-2.1

  • Corrected bug in WINE execution

Update 3.1-2

  • Set default version of OpenBUGS to 3.1.2
  • Fixed upper/lower case error in read.bugs
  • Fixed bug in specification of n.iter with large values in bugs
  • Added test suite
  • Several other less noticeable bugs fixed

Update 3.0-1

  • Converted R2WinBUGS to use OpenBUGS scripts and eliminated BRugs calls.

Update 2.1-17

  • fix as.bugs.array as reported by S. McKay Curtis

Update 2.1-16

  • fix write.model() again by going throught parse tree now

Update 2.1-15

  • added seed argument to openbugs()
  • fix write.model() to work for separatly specified function body
  • fix write.model() to make larger numeric (particularly integer) values in scientific notation work
  • fix bugs.update.settings() for R>=2.10.0 compatibility

Update 2.1-14

  • new argument over.relax=FALSE

Update 2.1-13

  • hack: adding group write permission for a temporary working directory in order to avoid problems with WINE emulator on Mac OS X
  • bugfix: properly using chain parameters in as.mcmc.list.bugs
  • documentation fix

Update 2.1-12

  • new method as.mcmc.list.bugs contributed by Mike Meredith
  • bugfix: plot.bugs() did not reset par(mfrow)
  • bugfix: adaptive phase stuff cannot read from files anymore by openbugs(), feature has been removed
  • openbugs now displays messages before starting the sampling (essentially using flush.console())

Update 2.1-11

  • bugfix: if working.directory was unset and files are assumed to be in R's former wd, these are copied to the tempdir that is set as new working directory now.

Update 2.1-10

  • bugfix: working.directory was not always reset when function terminated.

Update 2.1-9

  • R2WinBUGS now works on OS X and Solaris (with suitable versions of wine)
  • findUnixBinary now fails (with a meaningfull error message) always if the binary file does not exist.
  • If working.directory=NULL (the default setting), then a temporary directory is used as a working directory to prevent overwriting/removing the existing files.
  • File script.txt is also removed when clearWD=TRUE.
  • If model.file does not have a "txt" extension, then it is temporarily copied to a file with "txt" extension in the working directory and removed at the end of WinBUGS run.

Update 2.1-7

  • this file is now available as NEWS file in top folder of installed package

Update 2.1-6 (23 August 2007):

  • reverting back to use thin.updater since it is faster, however CODA files have "wrong" indexes - this needs to be fixed in BUGS program
  • WINE arguments are now set in such a way that defaults work on Windows and Linux
  • minor formatting in the code and help files
  • added R2WinBUGS-package help page

Update 2.1-5 (12 June 2007):

  • proper indexing of CODA files also in R version
  • fixed useWINE documentation in bugs help page
  • note on supported BUGS versions
  • as.bugs.array now returns info on used rule for pD i.e. var(deviance)/2 or Dbar-Dhat
  • some internal fixes related to handling of DIC
  • merging and reversing ChangeLog files

Update 2.1-4 (20 May 2007):

  • Depending on coda now (Namespace issues)
  • some more fixes for codetools checks
  • Vignette has been updated

Update 2.1-3 (13 May 2007):

  • Ported to S-PLUS by Insightful Corp.
  • some fixes for codetools checks

Update 2.0-4 (01 November 2006):

  • print.bugs / plot.bugs documentation fixes
  • write.model() fix

Update 2.0-3 (06 October 2006):

  • \. -> [.] in regular expressions

Update 2.0-2 (26 July 2006):

  • changes for DIC, making use of BUGS internal calculations
  • some doc fixes

Update 2.0-1 (26 May 2006):

  • some wine patches for 2.2-0 by Gregor Gorjanc

Update 2.0-0 (08 May 2006):

  • bugs() doc fix/updates on scrambling
  • bugs.run() has new arg useWINE (by Gregor Gorjanc)
  • bugs() and bugs.script() patched for WINEPATH issue
  • bugs.script() changed to save log file in ASCII
  • new function bugs.log() by Gregor Gorjanc
  • new functions as.bugs.array, openbugs and sort.name by Jouni Kerman and Andrew Gelman
  • new function write.model() based on ideas from Jouni Kerman

Update 1.1-1 (17 Feb 2006):

  • WINE tweaks (mainly by Gregor Gorjanc)

Update 1.1-0 (14 Dec 2005):

  • Contribution by Ben Bolker and Yun Yan's rbugs package: make R2WinBUGS work under WINE

Update 1.0-1 (14 Nov 2005):

  • make inits=NULL work (again ?)

Update 1.0-0 (05 Aug 2005):

  • attach.all(), detach.all(), attach.bugs() and detach.bugs() added/changed more or less according to Andrew Gelman's current bugs.R

Update 0.2-9 (26 July 2005):

  • bugs has new argument clearWD

Update 0.2-8 (30 May 2005):

  • bugs passed DIC to bugs.script in order to be able to disable it

Update 0.2-6 (18 May 2005):

  • bugs() changes in order to return a file names of coda output files
  • new read.bugs() returns a coda mcmc.list object, if codaPkg=TRUE.

Update 0.2-5 (20 Oct 2004):

  • bugs() and bugs.script() have a new argument bin that allows to specify a number of iterations. After each "bin" iterations the coda files are saved.

Update 0.2-4 (05 Oct 2004):

  • bugs.script() did not work for large n.iter values in update step (no scientific notation allowed)

Update 0.2-3 (10 Sept 2004):

  • bugs.data.inits split to bugs.inits and bugs.data, the latter exported from the Namespace. Now we can use already written data files in bugs().

Update 0.2-2 (28 Apr 2004):

  • schools data: original (see references) instead of the rounded data

During the process of packaging R2WinBUGS_0.1 - R2WinBUGS_0.2-1, quite a lot of changes had been made. Those changes are not documented anywhere ...

During the process of packaging R2WinBUGS_0.1, quite a lot of changes had been made. Those changes are not documented anywhere ...

Changes prior to R2WinBUGS_0.1:

Update 30 Oct 2003:

  1. Minor change to a return() statement to be compatible with R 1.8

  2. Just a warning (from Ben Goodrich): if you are running Bugs.R inside a loop, you have to be careful with the data() and the inits() functions since they will not necessarily recognize locally-defined variables. One workaround is to define the variables used in data() and inits() using global assignments (<<-), but this can sometimes make the program run slower. Update 29 Aug 2003:

  3. Fixed "bugs.data.inits" function so you can use data that have the same names as R functions.

  4. Changed T and F to TRUE and FALSE everywhere in case the variables T and F are used as data in the main program

  5. Caution: if you are entering the data as a list of variable names (see 10 Apr 2003 update, item 1), the data to be input into must be global variables. This can be relevant if you are running bugs() inside an R function.

  6. Caution: bugs() has difficulty processing ragged arrays. It is better to save a whole matrix (e.g., "theta") rather than parts (e.g., "theta[1:10,1]", "theta[1:5,2]"). If you want to save part of a vector, you should do it as "theta[1:2]", not "theta[1]", "theta[2]". Update 30 Apr 2003: added time monitoring Update 29 Apr 2003:

  7. The "attach.all" function (no longer called "attach2") overwrites so that all components of a list or data frame get attached.

  8. Program now looks in the directory /winbug~1/ rather than /winbug~2/

  9. Graphics parameters for margins are returned to their original state at the end of the program.

  10. Added "digits.summary" option to the numerical display.

  11. Added "last.values" output: a list that can be input as "inits" if you want to run the simulations longer. Update 13 Apr 2003: fixed new bug in round.bugs(). Now all numbers are saved in scientific notation. Update 10 Apr 2003:

  12. It is now possible to enter the data as a list of variable names. For example, before you had to enter data as, data <- list (n=8, y=c(28,8,-3,7,-1,1,18,12)) or n <- 8 y <- c(28,8,-3,7,-1,1,18,12) data <- list (n=n, y=y) Now you can enter the data as, n <- 8 y <- c(28,8,-3,7,-1,1,18,12) data <- list ("n", "y") The bugs() function will figure out which method you are using (based on whether "data" is a list of numbers or a vector of character strings). This doesn't look like much, but it's convenient when you're entering lots of data!

  13. It is now possible to enter the initial values as a function, so as to automatically a random list of inits for each of the chains. For example, in the 8-schools example below, we can do: inits <- function() list (theta=rnorm(J,0,1), mu.theta=rnorm(1,0,100), sigma.theta=runif(1,0,100))

    to set up the inits as a function (rather than setting up n.chains sets of specific initial values). Then, the function call, schools.sim <- bugs (data, inits, parameters, "schools.txt", n.chains=3, n.iter=1000) automatically sets up 3 sets of initial values (each a list of theta, mu.theta, sigma.theta).

  14. Bug in the initial rounding (the function round.bugs()) has been fixed. Thanks for Mark Clements for finding the bug and fixing it! Also, we have set the default rounding to 5 digits instead of 2. Update 01 Apr 2003: use layout() rather than split.screen() for graphical display Update 18 Mar 2003:

  15. Get the Bugs configuration information from the original file (Registry_default.odc) rather than overwriting each time. (Fixes a bug that occurred when R was interrupted in the middle of a Bugs run.)

  16. Display different colored dots in the right panel of the graphical display, to show the medians from each chain. Update 13 Mar 2003: fix minor bug in monitor() Update 10 Mar 2003: fix bug in pD and DIC calculations Update 7 Mar 2003:

  17. Fix display.parallel=T option by adding min.width so that very intervals are still visible.

  18. Compute pD separately for each sequence (which gives much more reasonable estimates before convergence). Update 8 Feb 2003: minor fixes in graphical display Update 6 Feb 2003:

  19. Approximate "effective sample size" n.eff given for each parameter.

  20. More explanatory material displayed.

  21. Use bringToTop() to automatically bring up the graphics window. Update 4 Feb 2003:

  22. Automatically compute the deviance, DIC, and pD. Bugs will not always compute DIC and pD, so we do so using the definition, DIC = E(deviance) + pD, using var(deviance)/2 as an estimate of pD. (This is derived from the chi^2 distribution. We can't use the Spiegelhalter et al. definition of DIC because we don't have access to the deviance function.)

  23. Set default for n.thin so that, after thinning, the total number saved iterations, n.sims, is approximately 1000. Update 14 Jan 2003 to run with the new WinBugs1.4. You may see an error message and need to fix the dos.location assignment in bugs(). Update 6 Jan 2003:

  24. Fix of bug that occurred with uppercase and lowercase variable names

  25. Set default for n.thin so that no more than about 500 iterations will be saved from each sequence

  26. New option "display.parallel" added to show 80% inferences from parallel sequences on the right panel of the graphical display. This can be useful to understand what is going on when there are convergence problems. Update 26 Dec 2002: fix of minwidth in bugs.plot.summary Update 11 Dec 2002:

  27. Automatic fixing of adaptive phases. Now you no longer need to run for thousands of iterations when slice or Metropolis sampling is used.

  28. Various minor fixes Update 10 Dec 2002:

  29. Cool graphical display of convergence and inferences!

  30. New "attach2" function that overwrites so that all components of the list are attached Update 29 Nov 2002:

  31. Fix of bug in 24 Nov update.

  32. Fix of bug in 16 Nov update.

  33. Length of chains is now pecified in terms of "n.iter" rather than "n.keep". Update 24 Nov 2002: improved treatment of "parameters.to.save". For example, you can now use "alpha" to indicate an entire array of parameters, whereas before you had to save "alpha[]" or "alpha[,]" or whatever. Update 16 Nov 2002: mean, sd, median added to outputs Update 4 Nov 2002: more error-flagging added Update 26 Oct 2002:

  34. Parameters saved in order of the "parameters.to.save" vector (not alphabetical order).

  35. Output saved in both matrix and list form.

  36. With the attach.sims=T setting (which is the default), the simulations for all the saved parameters are saved as R objects. This is convenient for later use of the simulations. Updates to 16 Oct 2002: more error-flagging added, mean/sd added to summary, fixing scientific notation so Bugs can always read data and inits Update 21 Sept 2002: "quit=F" option changed to "debug=T" First version written 18 Sept 2002 by Andrew Gelman, adapted from the EmBedBugs package by Kenneth Rice

Reference manual

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install.packages("R2OpenBUGS")

3.2-3.2 by Neal Thomas, 3 years ago


Browse source code at https://github.com/cran/R2OpenBUGS


Authors: originally written as R2WinBUGS by Andrew Gelman <[email protected]>; changes and packaged by Sibylle Sturtz <[email protected]> and Uwe Ligges <[email protected]>. With considerable contributions by Gregor Gorjanc <[email protected]> and Jouni Kerman <[email protected]>. Adapted to R2OpenBUGS from R2WinBUGS by Neal Thomas.


Documentation:   PDF Manual  


Task views: gRaphical Models in R


GPL-2 license


Imports coda, boot

System requirements: OpenBUGS (>= 3.2.2)


Imported by BTSPAS.

Suggested by AICcmodavg, BCEA, dclone.


See at CRAN