This manual describes how to use the BRugs software
the name of the program to be used as hypertext browser. It should be in the PATH, or a full path specified.
BRugs is a collection of R functions that allow users to analyze graphical models using MCMC techniques. Most of the R functions in BRugs provide a interface to the BRugs dynamic link library (shared object file). The BRugs dynamic link library is able to make use of many of the WinBUGS components, in particular those components concerned with graphical models and MCMC simulation. BRugs lacks the GUI interface of WinBUGS but is able to use R to create graphical displays of the MCMC simulation. BRugs uses the same model specification language as WinBUGS and the same format for data and initial values. However BRugs always uses plain text files for input inplace of WinBUGS compound documents. The BRugs functions can be split into two groups: those associated with setting up and simulating the graphical model and those associated with making statistical inference. In general the R functions in BRugs correspond to the command buttons and text entry fields in the menus of WinBUGS. Each WinBUGS text entry field splits into two R functions, one to set the quantity and the other to get the value of the quantity.
Andrew Gelman suggests to use the function
bugs in the R2WinBUGS package
program="openbugs" as a wrapper.
BRugs is released under the GNU GENERAL PUBLIC LICENSE.
For details see http://www.openbugs.net/ or type
More informally, potential users are reminded to be extremely careful if using this program for serious statistical analysis. We have tested the program on quite a wide set of examples, but be particularly careful with types of model that are currently not featured. If there is a problem, BRugs might just crash, which is not very good, but it might well carry on and produce answers that are wrong, which is even worse. Please let us know of any successes or failures.
If BRugs does cause R to crash, it is advised to run the model from within the Windows interface to OpenBUGS. This should give a "Trap" window, which indicates an internal problem with OpenBUGS. See
for suggestions for how to interpret these problematic error messages.
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### Step by step example: ### library("BRugs") # loading BRugs ## Prepare the example files in a temporary directory exfiles <- dir(options()$OpenBUGSExamples, pattern="^Rats.*txt$", full.names=TRUE) ok <- file.copy(exfiles, tempdir()) ## Now setting the working directory to the temporary one: oldwd <- setwd(tempdir()) ## some usual steps (like clicking in WinBUGS): modelCheck("Ratsmodel.txt") # check model file modelData("Ratsdata.txt") # read data file modelCompile(numChains=2) # compile model with 2 chains modelInits(rep("Ratsinits.txt", 2)) # read init data file modelUpdate(1000) # burn in samplesSet(c("alpha0", "alpha")) # alpha0 and alpha should be monitored modelUpdate(1000) # 1000 more iterations .... samplesStats("*") # the summarized results ## some plots samplesHistory("*", mfrow = c(4, 2)) # plot the chain, samplesDensity("alpha") # plot the densities, samplesBgr("alpha[1:6]") # plot the bgr statistics, and samplesAutoC("alpha[1:6]", 1) # plot autocorrelations of 1st chain ## switch back to the previous working directory: setwd(oldwd) ## Not run: # Getting more (online-)help: if (is.R()) help.BRugs() ## End(Not run)
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