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From: <gg...@us...> - 2006-11-24 13:36:30
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Revision: 3
http://svn.sourceforge.net/bugs-r/?rev=3&view=rev
Author: ggorjan
Date: 2006-11-24 05:24:51 -0800 (Fri, 24 Nov 2006)
Log Message:
-----------
populating SVN for R2WinBUGS
Added Paths:
-----------
trunk/R2WinBUGS/Changes
trunk/R2WinBUGS/Changes0
trunk/R2WinBUGS/DESCRIPTION
trunk/R2WinBUGS/NAMESPACE
trunk/R2WinBUGS/R/
trunk/R2WinBUGS/R/as.bugs.array.R
trunk/R2WinBUGS/R/attach.all.R
trunk/R2WinBUGS/R/bugs.R
trunk/R2WinBUGS/R/bugs.data.R
trunk/R2WinBUGS/R/bugs.inits.R
trunk/R2WinBUGS/R/bugs.log.R
trunk/R2WinBUGS/R/bugs.plot.inferences.R
trunk/R2WinBUGS/R/bugs.plot.summary.R
trunk/R2WinBUGS/R/bugs.run.R
trunk/R2WinBUGS/R/bugs.script.R
trunk/R2WinBUGS/R/bugs.sims.R
trunk/R2WinBUGS/R/bugs.update.settings.R
trunk/R2WinBUGS/R/conv.par.R
trunk/R2WinBUGS/R/decode.parameter.name.R
trunk/R2WinBUGS/R/formatdata.R
trunk/R2WinBUGS/R/monitor.R
trunk/R2WinBUGS/R/openbugs.R
trunk/R2WinBUGS/R/plot.bugs.R
trunk/R2WinBUGS/R/print.bugs.R
trunk/R2WinBUGS/R/read.bugs.R
trunk/R2WinBUGS/R/wineutils.R
trunk/R2WinBUGS/R/write.datafile.R
trunk/R2WinBUGS/R/write.model.R
trunk/R2WinBUGS/data/
trunk/R2WinBUGS/data/schools.txt
trunk/R2WinBUGS/inst/
trunk/R2WinBUGS/inst/CITATION
trunk/R2WinBUGS/inst/doc/
trunk/R2WinBUGS/inst/doc/R2WinBUGS.Rnw
trunk/R2WinBUGS/inst/doc/R2WinBUGS.pdf
trunk/R2WinBUGS/inst/doc/RdRW.sty
trunk/R2WinBUGS/inst/doc/Z.cls
trunk/R2WinBUGS/inst/doc/benzolsw.pdf
trunk/R2WinBUGS/inst/doc/bugs.tex
trunk/R2WinBUGS/inst/doc/countssw.pdf
trunk/R2WinBUGS/inst/doc/expectedsw.pdf
trunk/R2WinBUGS/inst/doc/literatur.bib
trunk/R2WinBUGS/inst/doc/literatur.bst
trunk/R2WinBUGS/inst/doc/plot.pdf
trunk/R2WinBUGS/inst/model/
trunk/R2WinBUGS/inst/model/schools.txt
trunk/R2WinBUGS/man/
trunk/R2WinBUGS/man/as.bugs.array.Rd
trunk/R2WinBUGS/man/attach.all.Rd
trunk/R2WinBUGS/man/bugs.Rd
trunk/R2WinBUGS/man/bugs.data.Rd
trunk/R2WinBUGS/man/bugs.inits.Rd
trunk/R2WinBUGS/man/bugs.log.Rd
trunk/R2WinBUGS/man/bugs.plot.Rd
trunk/R2WinBUGS/man/bugs.run.Rd
trunk/R2WinBUGS/man/bugs.script.Rd
trunk/R2WinBUGS/man/bugs.sims.Rd
trunk/R2WinBUGS/man/bugs.update.settings.Rd
trunk/R2WinBUGS/man/decode.parameter.name.Rd
trunk/R2WinBUGS/man/monitor.Rd
trunk/R2WinBUGS/man/openbugs.Rd
trunk/R2WinBUGS/man/plot.bugs.Rd
trunk/R2WinBUGS/man/print.bugs.Rd
trunk/R2WinBUGS/man/read.bugs.Rd
trunk/R2WinBUGS/man/schools.Rd
trunk/R2WinBUGS/man/write.datafile.Rd
trunk/R2WinBUGS/man/write.model.Rd
Added: trunk/R2WinBUGS/Changes
===================================================================
--- trunk/R2WinBUGS/Changes (rev 0)
+++ trunk/R2WinBUGS/Changes 2006-11-24 13:24:51 UTC (rev 3)
@@ -0,0 +1,71 @@
+Changes to R2WinBUGS:
+=====================
+
+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 ...
+
+
+Update 0.2-2 (28 Apr 2004):
+- schools data: original (see references) instead of the rounded data
+
+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 0.2-4 (05 Oct 2004):
+- bugs.script() did not work for large n.iter values in update step
+ (no scientific notation allowed)
+
+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 0.2-6 (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 0.2-8 (30 May 2005):
+- bugs passed DIC to bugs.script in order to be able to disable it
+
+Update 0.2-9 (26 July 2005):
+- bugs has new argument clearWD
+
+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 1.0-1 (14 Nov 2005):
+- make inits=NULL work (again ?)
+
+Update 1.1-0 (14 Dec 2005):
+- Contribution by Ben Bolker and Yun Yan's rbugs package:
+ make R2WinBUGS work under WINE
+
+Update 1.1-1 (17 Feb 2006):
+- WINE tweaks (mainly 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 2.0-1 (26 May 2006):
+- some wine patches for 2.2-0 by Gregor Gorjanc
+
+Update 2.0-2 (26 July 2006):
+- changes for DIC, making use of BUGS internal calculations
+- some doc fixes
+
+Update 2.0-3 (06 October 2006):
+- \\. -> [.] in regular expressions
+
+Update 2.0-4 (01 November 2006):
+- print.bugs / plot.bugs documentation fixes
+- write.model() fix
Added: trunk/R2WinBUGS/Changes0
===================================================================
--- trunk/R2WinBUGS/Changes0 (rev 0)
+++ trunk/R2WinBUGS/Changes0 2006-11-24 13:24:51 UTC (rev 3)
@@ -0,0 +1,142 @@
+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:
+ 1. Fixed "bugs.data.inits" function so you can use data that have the
+ same names as R functions.
+ 2. Changed T and F to TRUE and FALSE everywhere in case the variables
+ T and F are used as data in the main program
+ 3. 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.
+ 4. 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:
+ 1. The "attach.all" function (no longer called "attach2") overwrites
+ so that all components of a list or data frame get attached.
+ 2. Program now looks in the directory /winbug~1/ rather than /winbug~2/
+ 3. Graphics parameters for margins are returned to their original state
+ at the end of the program.
+ 4. Added "digits.summary" option to the numerical display.
+ 5. 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:
+ 1. 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!
+ 2. 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).
+ 3. 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:
+ 1. 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.)
+ 2. 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:
+ 1. Fix display.parallel=T option by adding min.width so that very
+ intervals are still visible.
+ 2. 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:
+ 1. Approximate "effective sample size" n.eff given for each parameter.
+ 2. More explanatory material displayed.
+ 3. Use bringToTop() to automatically bring up the graphics window.
+Update 4 Feb 2003:
+ 1. 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.)
+ 2. 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:
+ 1. Fix of bug that occurred with uppercase and lowercase variable names
+ 2. Set default for n.thin so that no more than about 500 iterations
+ will be saved from each sequence
+ 3. 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:
+ 1. Automatic fixing of adaptive phases. Now you no longer need to run
+ for thousands of iterations when slice or Metropolis sampling is used.
+ 2. Various minor fixes
+Update 10 Dec 2002:
+ 1. Cool graphical display of convergence and inferences!
+ 2. New "attach2" function that overwrites so that all components of
+ the list are attached
+Update 29 Nov 2002:
+ 1. Fix of bug in 24 Nov update.
+ 2. Fix of bug in 16 Nov update.
+ 3. 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:
+ 1. Parameters saved in order of the "parameters.to.save" vector
+ (not alphabetical order).
+ 2. Output saved in both matrix and list form.
+ 3. 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
Added: trunk/R2WinBUGS/DESCRIPTION
===================================================================
--- trunk/R2WinBUGS/DESCRIPTION (rev 0)
+++ trunk/R2WinBUGS/DESCRIPTION 2006-11-24 13:24:51 UTC (rev 3)
@@ -0,0 +1,19 @@
+Package: R2WinBUGS
+Title: Running WinBUGS and OpenBUGS from R
+Date: 2006-11-01
+Version: 2.0-4
+Author: originally written by Andrew Gelman <ge...@st...>;
+ changes and packaged by Sibylle Sturtz <st...@st...>
+ and Uwe Ligges <li...@st...>.
+ With considerable contributions by Gregor Gorjanc <gre...@bf...>
+ and Jouni Kerman <ke...@st...>.
+Description: 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.
+Depends: R (>= 2.2.0)
+Suggests: coda (>= 0.9-0), BRugs (>= 0.3-0)
+SystemRequirements: WinBUGS 1.4 on Windows
+URL: http://www.stat.columbia.edu/~gelman/bugsR/
+Maintainer: Sibylle Sturtz <st...@st...>
+License: GPL version 2
+Packaged: Thu Nov 2 08:53:20 2006; ligges
Added: trunk/R2WinBUGS/NAMESPACE
===================================================================
--- trunk/R2WinBUGS/NAMESPACE (rev 0)
+++ trunk/R2WinBUGS/NAMESPACE 2006-11-24 13:24:51 UTC (rev 3)
@@ -0,0 +1,4 @@
+export(bugs, attach.all, detach.all, attach.bugs, detach.bugs, bugs.data, read.bugs,
+bugs.log, openbugs, as.bugs.array, write.model)
+S3method(print, bugs)
+S3method(plot, bugs)
Added: trunk/R2WinBUGS/R/as.bugs.array.R
===================================================================
--- trunk/R2WinBUGS/R/as.bugs.array.R (rev 0)
+++ trunk/R2WinBUGS/R/as.bugs.array.R 2006-11-24 13:24:51 UTC (rev 3)
@@ -0,0 +1,135 @@
+as.bugs.array <- function(sims.array, model.file=NULL, program=NULL, DIC=FALSE, n.iter=NULL, n.burnin=0, n.thin=1)
+{
+ # Jouni Kerman's function to convert a 3-way array to a Bugs object
+ #
+ # 'sims.array' is supposed to be a 3-way array with
+ # n.sims*n.chains*n.parameters simulations, and
+ # the 3rd component of dimnames(x) should have the parameter names.
+ d <- dim(sims.array)
+ n.keep <- d[1]
+ n.chains <- d[2]
+ n.parameters <- d[3]
+ n.sims <- n.keep*n.chains
+ if (is.null(n.iter)) n.iter <- (n.keep + n.burnin)*n.thin
+ #
+ parameter.names <- dimnames(sims.array)[[3]]
+ if (is.null(parameter.names)) {
+ parameter.names <- paste("P", 1:n.parameters, sep="")
+ dimnames(sims.array)[[3]] <- parameter.names
+ }
+ parameters.to.save <- unique(sapply(strsplit(parameter.names,"\\["),"[",1))
+ #
+ sims <- matrix(NA, n.sims, n.parameters)
+ root.long <- character(n.parameters)
+ indexes.long <- vector(n.parameters, mode = "list")
+ for (i in 1:n.parameters) {
+ temp <- decode.parameter.name(parameter.names[i])
+ root.long[i] <- temp$root
+ indexes.long[[i]] <- temp$indexes
+ }
+ n.roots <- length(parameters.to.save)
+ left.bracket.short <- as.vector(regexpr("[[]", parameters.to.save))
+ right.bracket.short <- as.vector(regexpr("[]]", parameters.to.save))
+ root.short <- ifelse(left.bracket.short == -1, parameters.to.save,
+ substring(parameters.to.save, 1, left.bracket.short - 1))
+ dimension.short <- rep(0, n.roots)
+ indexes.short <- vector(n.roots, mode = "list")
+ n.indexes.short <- vector(n.roots, mode = "list")
+ long.short <- vector(n.roots, mode = "list")
+ length.short <- numeric(n.roots)
+ for (j in 1:n.roots) {
+ long.short[[j]] <- (1:n.parameters)[root.long == root.short[j]]
+ length.short[j] <- length(long.short[[j]])
+ if (length.short[j] == 0){
+ stop(paste("parameter", root.short[[j]], "is not in the model"))
+ }
+ else if (length.short[j] > 1) {
+ dimension.short[j] <- length(indexes.long[[long.short[[j]][1]]])
+ n.indexes.short[[j]] <- numeric(dimension.short[j])
+ for (k in 1:dimension.short[j]){
+ n.indexes.short[[j]][k] <- length(unique(unlist(lapply(indexes.long[long.short[[j]]], .subset, k))))
+ }
+ length.short[j] <- prod(n.indexes.short[[j]])
+ if (length(long.short[[j]]) != length.short[j]){
+ stop(paste("error in parameter", root.short[[j]],
+ "in parameters.to.save"))
+ }
+ indexes.short[[j]] <- as.list(numeric(length.short[j]))
+ for (k in 1:length.short[j]){
+ indexes.short[[j]][[k]] <- indexes.long[[long.short[[j]][k]]]
+ }
+ }
+ }
+ rank.long <- unlist(long.short)
+ # -----
+ # yes, it's inefficient to do this, but for now I'm just letting this be as it is:
+ for (k in 1:n.parameters) {
+ sims[,k] <- as.vector(sims.array[,,k])
+ }
+ # ----
+ dimnames(sims) <- list(NULL, parameter.names)
+ summary <- monitor(sims.array, n.chains, keep.all = TRUE)
+ last.values <- as.list(numeric(n.chains))
+ for (i in 1:n.chains) {
+ n.roots.0 <- if (!is.null(DIC))
+ n.roots - 1
+ else n.roots
+ last.values[[i]] <- as.list(numeric(n.roots.0))
+ names(last.values[[i]]) <- root.short[1:n.roots.0]
+ for (j in 1:n.roots.0) {
+ if (dimension.short[j] <= 1) {
+ last.values[[i]][[j]] <- sims.array[n.keep, i, long.short[[j]]]
+ names(last.values[[i]][[j]]) <- NULL
+ }
+ else{
+ last.values[[i]][[j]] <- aperm(array(sims.array[n.keep, i,
+ long.short[[j]]], rev(n.indexes.short[[j]])), dimension.short[j]:1)
+ }
+ }
+ }
+ sims <- sims[sample(n.sims), ]
+ sims.list <- summary.mean <- summary.sd <- summary.median <- vector(n.roots,
+ mode = "list")
+ names(sims.list) <- names(summary.mean) <- names(summary.sd) <- names(summary.median) <- root.short
+ for (j in 1:n.roots) {
+ if (length.short[j] == 1) {
+ sims.list[[j]] <- sims[, long.short[[j]]]
+ summary.mean[[j]] <- summary[long.short[[j]], "mean"]
+ summary.sd[[j]] <- summary[long.short[[j]], "sd"]
+ summary.median[[j]] <- summary[long.short[[j]], "50%"]
+ }
+ else {
+ temp2 <- dimension.short[j]:1
+ sims.list[[j]] <- aperm(array(sims[, long.short[[j]]],
+ c(n.sims, rev(n.indexes.short[[j]]))), c(1, (dimension.short[j]+1):2))
+ summary.mean[[j]] <- aperm(array(summary[long.short[[j]],
+ "mean"], rev(n.indexes.short[[j]])), temp2)
+ summary.sd[[j]] <- aperm(array(summary[long.short[[j]],
+ "sd"], rev(n.indexes.short[[j]])), temp2)
+ summary.median[[j]] <- aperm(array(summary[long.short[[j]],
+ "50%"], rev(n.indexes.short[[j]])), temp2)
+ }
+ }
+ summary <- summary[rank.long, ]
+ all <- list(n.chains = n.chains, n.iter = n.iter, n.burnin = n.burnin,
+ n.thin = n.thin, n.keep = n.keep, n.sims = n.sims,
+ sims.array = sims.array[,,rank.long,drop = FALSE], sims.list = sims.list,
+ sims.matrix = sims[, rank.long], summary = summary, mean = summary.mean,
+ sd = summary.sd, median = summary.median, root.short = root.short,
+ long.short = long.short, dimension.short = dimension.short,
+ indexes.short = indexes.short, last.values = last.values, program=program,
+ model.file=model.file, is.DIC=!is.null(DIC), DIC=DIC)
+ if(sum(DIC)) {
+ deviance <- all$sims.array[, , dim(sims.array)[3], drop = FALSE]
+ dim(deviance) <- dim(deviance)[1:2]
+ pD <- numeric(n.chains)
+ DIC <- numeric(n.chains)
+ for (i in 1:n.chains) {
+ pD[i] <- var(deviance[, i])/2
+ DIC[i] <- mean(deviance[, i]) + pD[i]
+ }
+ all <- c(all, list(pD = mean(pD), DIC = mean(DIC)))
+ }
+ class(all) <- "bugs"
+ return(all)
+}
Property changes on: trunk/R2WinBUGS/R/as.bugs.array.R
___________________________________________________________________
Name: svn:keywords
+ Id
Added: trunk/R2WinBUGS/R/attach.all.R
===================================================================
--- trunk/R2WinBUGS/R/attach.all.R (rev 0)
+++ trunk/R2WinBUGS/R/attach.all.R 2006-11-24 13:24:51 UTC (rev 3)
@@ -0,0 +1,36 @@
+attach.all <- function(x, overwrite = NA, name = "attach.all"){
+ rem <- names(x) %in% ls(.GlobalEnv)
+ if(!any(rem)) overwrite <- FALSE
+ rem <- names(x)[rem]
+ if(is.na(overwrite)){
+ question <- paste("The following objects in .GlobalEnv will mask\nobjects in the attached database:\n",
+ paste(rem, collapse=", "),
+ "\nRemove these objects from .GlobalEnv?", sep="")
+ if(interactive()){
+ if(.Platform$OS.type == "windows")
+ overwrite <- "YES" == winDialog(type = "yesno", question)
+ else
+ overwrite <- 1 == menu(c("YES", "NO"), graphics = FALSE, title = question)
+ }
+ else overwrite <- FALSE
+ }
+ if(overwrite) remove(list=rem, envir=.GlobalEnv)
+ attach(x, name=name)
+}
+
+attach.bugs <- function (x, overwrite = NA){
+ if(class(x) != "bugs")
+ stop("attach.all() requires a bugs object.")
+ if("bugs.sims" %in% search()){
+ detach("bugs.sims")}
+ x$sims.list$n.sims <- x$n.sims # put n.sims into sims.list for convenience
+ r2 <- attach.all(x$sims.list, overwrite = overwrite, name = "bugs.sims")
+ invisible (bugs.sims = r2)
+}
+
+detach.all <- function(name = "attach.all")
+ do.call("detach", list(name=name))
+
+detach.bugs <- function(){
+ detach.all("bugs.sims")
+}
Property changes on: trunk/R2WinBUGS/R/attach.all.R
___________________________________________________________________
Name: svn:keywords
+ Id
Added: trunk/R2WinBUGS/R/bugs.R
===================================================================
--- trunk/R2WinBUGS/R/bugs.R (rev 0)
+++ trunk/R2WinBUGS/R/bugs.R 2006-11-24 13:24:51 UTC (rev 3)
@@ -0,0 +1,70 @@
+"bugs" <-
+function(data, inits, parameters.to.save, model.file = "model.bug",
+ n.chains = 3, n.iter = 2000, n.burnin = floor(n.iter / 2),
+ n.thin = max(1, floor(n.chains * (n.iter - n.burnin) / 1000)),
+ bin = (n.iter - n.burnin) / n.thin,
+ debug = FALSE, DIC = TRUE, digits = 5, codaPkg = FALSE,
+ bugs.directory = "c:/Program Files/WinBUGS14/",
+ program = c("winbugs", "openbugs", "WinBugs", "OpenBugs"),
+ working.directory = NULL,
+ clearWD = FALSE, useWINE = .Platform$OS.type != "windows", WINE = Sys.getenv("WINE"),
+ newWINE = FALSE, WINEPATH = NULL){
+
+ ## If OpenBUGS, we only call openbugs() and exit...
+ program <- match.arg(program)
+ if (program %in% c("openbugs", "OpenBugs"))
+ return(openbugs(data, inits, parameters.to.save, model.file,
+ n.chains, n.iter, n.burnin, n.thin, DIC, bugs.directory,
+ working.directory, digits))
+
+ ## Checking number of inits, which is NOT save here:
+ if(!missing(inits) && !is.function(inits) && !is.null(inits) && (length(inits) != n.chains))
+ stop("Number of initialized chains (length(inits)) != n.chains")
+ if (useWINE) { # attempt to find wine and winepath
+ if (!nchar(WINE)) {
+ WINE <- system("locate wine | grep bin/wine$", intern = TRUE)
+ WINE <- WINE[length(WINE)]
+ }
+ if (!length(WINE)) stop("couldn't locate WINE binary")
+ if (!nchar(WINEPATH)) {
+ WINEPATH <- system("locate winepath | grep bin/winepath$", intern = TRUE)
+ WINEPATH <- WINEPATH[length(WINEPATH)]
+ }
+ if (!length(WINEPATH)) stop("couldn't locate WINEPATH binary")
+ }
+ if(!is.null(working.directory)){
+ savedWD <- getwd()
+ setwd(working.directory)
+ on.exit(setwd(savedWD))
+ }
+ if(!file.exists(model.file)) stop(paste(model.file, "does not exist."))
+ if(file.info(model.file)$isdir) stop(paste(model.file, "is a directory, but a file is required."))
+ if(!(length(data) == 1 && is.vector(data) && is.character(data) && data == "data.txt")){
+ bugs.data(data, dir = getwd(), digits)
+ } else if(!file.exists(data))
+ stop("File data.txt does not exist.")
+ bugs.inits(inits, n.chains, digits)
+ if(DIC) parameters.to.save <- c(parameters.to.save, "deviance")
+ ## Model files with extension ".bug" need to be renamed to ".txt"
+ if(length(grep("[.]bug$", model.file))){
+ new.model.file <- sub("[.]bug$", ".txt", model.file)
+ file.copy(model.file, new.model.file, overwrite = TRUE)
+ on.exit(try(file.remove(new.model.file)), add = TRUE)
+ } else new.model.file <- model.file
+ bugs.script(parameters.to.save, n.chains, n.iter, n.burnin, n.thin,
+ new.model.file, debug=debug, is.inits=!is.null(inits),
+ bin = bin, DIC = DIC, useWINE = useWINE, newWINE = newWINE, WINEPATH = WINEPATH)
+ bugs.run(n.burnin, bugs.directory, WINE = WINE, useWINE = useWINE)
+
+ if(codaPkg)
+ return(file.path(getwd(), paste("coda", 1:n.chains, ".txt", sep="")))
+
+ sims <- c(bugs.sims(parameters.to.save, n.chains, n.iter, n.burnin, n.thin, DIC),
+ model.file = model.file, is.DIC = !is.null(DIC), program = program)
+ if(clearWD)
+ file.remove(c("data.txt", "log.odc", "log.txt", "codaIndex.txt",
+ paste("inits", 1:n.chains, ".txt", sep=""),
+ paste("coda", 1:n.chains, ".txt", sep="")))
+ class(sims) <- "bugs"
+ return(sims)
+}
Property changes on: trunk/R2WinBUGS/R/bugs.R
___________________________________________________________________
Name: svn:keywords
+ Id
Added: trunk/R2WinBUGS/R/bugs.data.R
===================================================================
--- trunk/R2WinBUGS/R/bugs.data.R (rev 0)
+++ trunk/R2WinBUGS/R/bugs.data.R 2006-11-24 13:24:51 UTC (rev 3)
@@ -0,0 +1,12 @@
+"bugs.data" <-
+function(data, dir = getwd(), digits = 5){
+ if(is.numeric(unlist(data)))
+ write.datafile(lapply(data, formatC, digits = digits, format = "E"),
+ file.path(dir, "data.txt"))
+ else {
+ data.list <- lapply(as.list(data), get, pos = parent.frame(2))
+ names(data.list) <- as.list(data)
+ write.datafile(lapply(data.list, formatC, digits = digits, format = "E"),
+ file.path(dir, "data.txt"))
+ }
+}
Property changes on: trunk/R2WinBUGS/R/bugs.data.R
___________________________________________________________________
Name: svn:keywords
+ Id
Added: trunk/R2WinBUGS/R/bugs.inits.R
===================================================================
--- trunk/R2WinBUGS/R/bugs.inits.R (rev 0)
+++ trunk/R2WinBUGS/R/bugs.inits.R 2006-11-24 13:24:51 UTC (rev 3)
@@ -0,0 +1,13 @@
+"bugs.inits" <-
+function (inits, n.chains, digits){
+ if(!is.null(inits)){
+ for (i in 1:n.chains){
+ if (is.function(inits))
+ write.datafile(lapply(inits(), formatC, digits = digits, format = "E"),
+ paste ("inits", i, ".txt", sep=""))
+ else
+ write.datafile(lapply(inits[[i]], formatC, digits = digits, format = "E"),
+ paste ("inits", i, ".txt", sep=""))
+ }
+ }
+}
Property changes on: trunk/R2WinBUGS/R/bugs.inits.R
___________________________________________________________________
Name: svn:keywords
+ Id
Added: trunk/R2WinBUGS/R/bugs.log.R
===================================================================
--- trunk/R2WinBUGS/R/bugs.log.R (rev 0)
+++ trunk/R2WinBUGS/R/bugs.log.R 2006-11-24 13:24:51 UTC (rev 3)
@@ -0,0 +1,46 @@
+bugs.log <- function(file)
+{
+ if(!file.exists(file))
+ stop("Log file", file, "does not exist")
+ logfile <- readLines(file)
+
+ statsStart <- which(logfile == "Node statistics") + 2
+ if(!length(statsStart))
+ stop("Log file", file, "does not contain node statistics.")
+ ## + 2 to remove
+ ## "Node statistics"
+ ## "\t node\t mean\t sd\t MC error\t2.5%\tmedian\t97.5%\tstart\tsample"
+
+ statsEnd <- which(logfile == "dic.stats()") - 1
+ ## + 1 to remove
+ ## "dic.stats()"
+
+ statsTable <- logfile[statsStart:statsEnd]
+ statsTable <- sub("\t", "", statsTable)
+ statsTable <- sapply(strsplit(statsTable, "\t"), "[")
+ colnames(statsTable) <- statsTable[1,]
+ statsTable <- t(apply(statsTable[-1,], 2, as.numeric))
+ colnames(statsTable) <- c("mean", "sd", "MC error", "2.5%", "median", "97.5%", "start", "sample")
+
+ ## DIC
+ DICStart <- which(logfile == "DIC") + 3
+ ## + 3 to remove
+ ## "DIC"
+ ## "Dbar = post.mean of -2logL; Dhat = -2LogL at post.mean of stochastic nodes"
+ ## "\tDbar\tDhat\tpD\tDIC\t"
+
+ DICEnd <- grep("history(", logfile, fixed = TRUE) - 1
+ ## - 1 to remove
+ ## "history(+, ..."
+
+ if(!length(DICEnd) || !length(DICStart) || (DICEnd < DICStart)){
+ DICTable <- NA
+ }else{
+ DICTable <- logfile[DICStart:DICEnd]
+ DICTable <- sapply(strsplit(DICTable, "\t"), "[")
+ colnames(DICTable) <- DICTable[1,]
+ DICTable <- t(apply(DICTable[-1,], 2, as.numeric))
+ colnames(DICTable) <- c("Dbar", "Dhat", "pD", "DIC")
+ }
+ return(list(stats = statsTable, DIC = DICTable))
+}
Property changes on: trunk/R2WinBUGS/R/bugs.log.R
___________________________________________________________________
Name: svn:keywords
+ Id
Added: trunk/R2WinBUGS/R/bugs.plot.inferences.R
===================================================================
--- trunk/R2WinBUGS/R/bugs.plot.inferences.R (rev 0)
+++ trunk/R2WinBUGS/R/bugs.plot.inferences.R 2006-11-24 13:24:51 UTC (rev 3)
@@ -0,0 +1,110 @@
+"bugs.plot.inferences" <-
+function (sims, display.parallel, ...){
+ if (.Device=="windows" ||
+ (.Device=="null device" && options("device")=="windows")){
+ cex.names <- .7
+ cex.axis <- .6
+ cex.tiny <- .4
+ cex.points <- .7
+ standard.width <- 30
+ max.width <- 40
+ min.width <- .02
+ }
+ else {
+ cex.names <- .7
+ cex.axis <- .6
+ cex.tiny <- .4
+ cex.points <- .3
+ standard.width <- 30
+ max.width <- 40
+ min.width <- .01
+ }
+ rootnames <- sims$root.short
+ n.roots <- length(rootnames)
+ sims.array <- sims$sims.array
+ n.chains <- sims$n.chains
+ dimension.short <- sims$dimension.short
+ indexes.short <- sims$indexes.short
+ long.short <- sims$long.short
+ height <- .6
+ par (mar=c(0,0,1,0))
+ plot (c(0,1), c(-n.roots-.5,-.4),
+ ann=FALSE, bty="n", xaxt="n", yaxt="n", type="n")
+ W <- max(strwidth(rootnames, cex=cex.names))
+ B <- (1-W)/3.8
+ A <- 1-3.5*B
+ if (display.parallel)
+ text (A, -.4, "80% interval for each chain", adj=0, cex=cex.names)
+ else
+ text (A, -.4, "medians and 80% intervals", adj=0, cex=cex.names)
+ num.height <- strheight (1:9, cex=cex.tiny)
+ for (k in 1:n.roots){
+ text (0, -k, rootnames[k], adj=0, cex=cex.names)
+ J <- min (length(long.short[[k]]), max.width)
+ if (k==1)
+ index <- 1:J
+ else
+ index <- sum (unlist(lapply(long.short,length))[1:(k-1)]) + 1:J
+ spacing <- 3.5/max(J,standard.width)
+ med <- numeric(J)
+ i80 <- matrix( , J, 2)
+ med.chains <- matrix( , J, sims$n.chains)
+ i80.chains <- array(NA, c(J, sims$n.chains, 2))
+ for (j in 1:J){
+ med[j] <- median(sims.array[,,index[j]])
+ i80[j,] <- quantile(sims.array[,,index[j]], c(.1,.9))
+ for (m in 1:n.chains){
+ med.chains[j,m] <- quantile (sims.array[,m,index[j]], .5)
+ i80.chains[j,m,] <- quantile (sims.array[,m,index[j]], c(.1,.9))
+ }
+ }
+ rng <- range (i80, i80.chains)
+ p.rng <- pretty(rng, n = 2)
+ b <- height/(max(p.rng) - min(p.rng))
+ a <- -(k+height/2) - b*p.rng[1]
+ lines (A+c(0,0), -k+c(-height/2,height/2))
+#
+# plot a line at zero (if zero is in the range of the mini-plot)
+#
+ if (min(p.rng)<0 & max(p.rng)>0)
+ lines (A+B*spacing*c(0,J+1), rep (a,2), lwd=.5, col="gray")
+
+ for (x in p.rng){
+ text (A-B*.2, a+b*x, x, cex=cex.axis)
+ lines (A+B*c(-.05,0), rep(a+b*x,2))
+ }
+ for (j in 1:J){
+ if (display.parallel){
+ for (m in 1:n.chains){
+ interval <- a + b*i80.chains[j,m,]
+ if (interval[2]-interval[1] < min.width)
+ interval <- mean(interval) + c(-1,1)*min.width/2
+ lines (A+B*spacing*rep(j+.6*(m-(n.chains+1)/2)/n.chains,2),
+ interval, lwd=.5, col=m+1)
+ }
+ }
+ else {
+ lines (A+B*spacing*rep(j,2), a + b*i80[j,], lwd=.5)
+ for (m in 1:n.chains)
+# points (A+B*spacing*j, a + b*med[j], pch=20, cex=cex.points)
+ points (A+B*spacing*j, a + b*med.chains[j,m], pch=20, cex=cex.points,
+ col=m+1)
+ }
+ dk <- dimension.short[k]
+ if (dk>0){
+ for (m in 1:dk){
+ index0 <- indexes.short[[k]][[j]][m]
+ if (j==1)
+ text(A+B*spacing*j, -k-height/2-.05-num.height*(m-1), index0,
+ cex=cex.tiny)
+ else if (index0!=indexes.short[[k]][[j-1]][m] &
+ (index0%%(floor(log10(index0)+1))==0))
+ text(A+B*spacing*j, -k-height/2-.05-num.height*(m-1), index0,
+ cex=cex.tiny)
+ }
+ }
+ }
+ if (J<length(long.short[[k]])) text (-.015, -k, "*",
+ cex=cex.names, col="red")
+ }
+}
Property changes on: trunk/R2WinBUGS/R/bugs.plot.inferences.R
___________________________________________________________________
Name: svn:keywords
+ Id
Added: trunk/R2WinBUGS/R/bugs.plot.summary.R
===================================================================
--- trunk/R2WinBUGS/R/bugs.plot.summary.R (rev 0)
+++ trunk/R2WinBUGS/R/bugs.plot.summary.R 2006-11-24 13:24:51 UTC (rev 3)
@@ -0,0 +1,124 @@
+"bugs.plot.summary" <-
+function (sims, ...){
+ DIC <- sims$is.DIC
+ if (.Device=="windows" ||
+ (.Device=="null device" && options("device")=="windows")){
+ cex.names <- .7
+ cex.top <- .7
+ cex.points <- .7
+ max.length <- 50
+ min.width <- .01
+ }
+ else {
+ cex.names <- .7
+ cex.top <- .7
+ cex.points <- .3
+ max.length <- 80
+ min.width <- .005
+ }
+ summ <- sims$summary
+ sims.array <- sims$sims.array
+ n.chains <- sims$n.chains
+ n.parameters <- nrow(summ)
+
+ J0 <- unlist(lapply(sims$long.short, length))
+ if (DIC) J0 <- J0[1:(length(J0)-1)] # don't display deviance summaries
+ J <- J0
+ total <- ceiling(sum(J+.5))
+ while ((total > max.length) && max(J)>1){### vielleicht optimieren ...
+ J[J==max(J)] <- max(J)-1
+ total <- ceiling(sum(J+.5))
+ }
+ pos <- -1
+ ypos <- NULL
+ id <- NULL
+ ystart <- NULL
+ jj <- 1:J[1]
+ n.roots <- length(sims$root.short)
+ if (DIC) n.roots <- n.roots-1 # don't display deviance summaries
+ ystart <- numeric(n.roots)
+ for (k in 1:n.roots){
+ ystart[k] <- pos
+ ypos <- c(ypos, pos - seq(0, J[k]-1))
+ id <- c(id, 1:J[k])
+ pos <- pos - J[k] -.5
+ if (k>1) jj <- c(jj, sum(J0[1:(k-1)]) + (1:J[k]))
+ }
+ bottom <- min(ypos)-1
+
+ med <- numeric(sum(J))
+ i80 <- matrix( , sum(J), 2)
+ i80.chains <- array (NA, c(sum(J), n.chains, 2))
+ for (j in 1:sum(J)){
+ med[j] <- median (sims.array[,,jj[j]])
+ i80[j,] <- quantile (sims.array[,,jj[j]], c(.1,.9))
+ for (m in 1:n.chains)
+ i80.chains[j,m,] <- quantile (sims.array[,m,jj[j]], c(.1,.9))
+ }
+ rng <- range (i80, i80.chains)
+ p.rng <- pretty(rng, n = 2)
+ b <- 2 / (max(p.rng) - min(p.rng))
+ a <- -b * p.rng[1]
+
+ par (mar=c(0,0,1,3))
+ plot (c(0,1), c(min(bottom, -max.length)-3,2.5),
+ ann=FALSE, bty="n", xaxt="n", yaxt="n", type="n")
+ W <- max(strwidth(unlist(dimnames(summ)[[1]]), cex=cex.names))
+ B <- (1-W)/3.6
+ A <- 1-3.5*B
+ B <- (1-A)/3.5
+ b <- B*b
+ a <- A + B*a
+ text (A+B*1, 2.5, "80% interval for each chain", cex=cex.top)
+ lines (A+B*c(0,2), c(0,0))
+ lines (A+B*c(0,2), rep(bottom,2))
+ if(n.chains > 1){
+ text (A+B*3, 2.6, "R-hat", cex=cex.top)
+ lines (A+B*c(2.5,3.5), c(0,0))
+ lines (A+B*c(2.5,3.5), rep(bottom,2))
+ }
+#
+# line at zero
+#
+ if (min(p.rng)<0 & max(p.rng)>0)
+ lines (rep(a,2), c(0,bottom), lwd=.5, col="gray")
+
+ for (x in p.rng){
+ text (a+b*x, 1, x, cex=cex.names)
+ lines (rep(a+b*x,2), c(0,-.2))
+ text (a+b*x, bottom-1, x, cex=cex.names)
+ lines (rep(a+b*x,2), bottom+c(0,.2))
+ }
+ if(n.chains > 1)
+ for (x in seq(1,2,.5)){
+ text (A+B*(1.5+seq(1,2,.5)), rep(1,3), c("1","1.5","2+"), cex=cex.names)
+ lines (A+B*rep(1.5+x,2), c(0,-.2))
+ text (A+B*(1.5+seq(1,2,.5)), rep(bottom-1,3), c("1","1.5","2+"),
+ cex=cex.names)
+ lines (A+B*rep(1.5+x,2), bottom+c(0,.2))
+ }
+ for (j in 1:sum(J)){
+ name <- dimnames(summ)[[1]][jj[j]]
+ if (id[j]==1)
+ text (0, ypos[j], name, adj=0, cex=cex.names)
+ else {
+ pos <- as.vector(regexpr("[[]", name))
+ text (strwidth(substring(name,1,pos-1),cex=cex.names),
+ ypos[j], substring(name, pos, nchar(name)), adj=0, cex=cex.names)
+ }
+ for (m in 1:n.chains){
+ interval <- a + b*i80.chains[j,m,]
+ if (interval[2]-interval[1] < min.width)
+ interval <- mean(interval) + c(-1,1)*min.width/2
+ lines (interval, rep(ypos[j]-.1*(m-(n.chains+1)/2),2), lwd=1, col=m+1)
+ if(n.chains > 1)
+ points (A+B*(1.5 + min(max(summ[jj[j],"Rhat"],1),2)), ypos[j], pch=20, cex=cex.points)
+ }
+ }
+ for (k in 1:n.roots){
+ if (J[k]<J0[k]) text (-.015, ystart[k], "*", cex=cex.names,
+ col="red")
+ }
+ if (sum(J!=J0)>0) text (0, bottom-3,
+ "* array truncated for lack of space", adj=0, cex=cex.names, col="red")
+}
Property changes on: trunk/R2WinBUGS/R/bugs.plot.summary.R
___________________________________________________________________
Name: svn:keywords
+ Id
Added: trunk/R2WinBUGS/R/bugs.run.R
===================================================================
--- trunk/R2WinBUGS/R/bugs.run.R (rev 0)
+++ trunk/R2WinBUGS/R/bugs.run.R 2006-11-24 13:24:51 UTC (rev 3)
@@ -0,0 +1,35 @@
+"bugs.run" <-
+ function(n.burnin, bugs.directory, WINE = "",
+ useWINE = .Platform$OS.type != "windows", newWINE = TRUE){
+
+if(useWINE && !newWINE) bugs.directory <- win2native(bugs.directory)
+
+## Update the lengths of the adaptive phases in the Bugs updaters
+ try(bugs.update.settings(n.burnin, bugs.directory))
+## Return the lengths of the adaptive phases to their original settings
+ on.exit(try(file.copy(file.path(bugs.directory, "System/Rsrc/Registry_Rsave.odc"),
+ file.path(bugs.directory, "System/Rsrc/Registry.odc"),
+ overwrite = TRUE)))
+## Search Win*.exe (WinBUGS executable) within bugs.directory
+ dos.location <- file.path(bugs.directory,
+ grep("^Win[[:alnum:]]*[.]exe$", list.files(bugs.directory), value = TRUE)[1])
+ if(!file.exists(dos.location))
+ stop(paste("WinBUGS executable does not exist in", bugs.directory))
+## Call Bugs and have it run with script.txt
+ bugsCall <- paste("\"", dos.location, "\" /par \"",
+ native2win(file.path(getwd(), "script.txt"), newWINE = newWINE),
+ "\"", sep = "")
+ if (useWINE)
+ bugsCall <- paste(WINE, bugsCall)
+ temp <- system(bugsCall)
+
+ if(temp == -1)
+ stop("Error in bugs.run().\nCheck that WinBUGS is in the specified directory.")
+## Stop and print an error message if Bugs did not run correctly
+ if (length(grep("Bugs did not run correctly",
+ scan("coda1.txt", character(), quiet=TRUE, sep="\n"))) > 0)
+ stop("Look at the log file and\ntry again with debug=TRUE and figure out what went wrong within Bugs.")
+}
+
+
+
Property changes on: trunk/R2WinBUGS/R/bugs.run.R
___________________________________________________________________
Name: svn:keywords
+ Id
Added: trunk/R2WinBUGS/R/bugs.script.R
===================================================================
--- trunk/R2WinBUGS/R/bugs.script.R (rev 0)
+++ trunk/R2WinBUGS/R/bugs.script.R 2006-11-24 13:24:51 UTC (rev 3)
@@ -0,0 +1,48 @@
+"bugs.script" <-
+function (parameters.to.save, n.chains, n.iter, n.burnin,
+ n.thin, model.file, debug=FALSE, is.inits, bin,
+ DIC = FALSE, useWINE = FALSE, newWINE = FALSE, WINEPATH = NULL){
+### Write file script.txt for Bugs to read
+### if (n.chains<2) stop ("n.chains must be at least 2")
+
+ if((ceiling(n.iter/n.thin) - ceiling(n.burnin/n.thin)) < 2)
+ stop ("(n.iter-n.burnin)/n.thin must be at least 2")
+ working.directory <- getwd()
+ script <- "script.txt"
+ model <- if(length(grep("\\\\", model.file)) || length(grep("/", model.file))){
+ model.file
+ } else file.path(working.directory, model.file)
+ data <- file.path(working.directory, "data.txt")
+ history <- file.path(working.directory, "history.odc")
+ coda <- file.path(working.directory, "coda")
+ logfile <- file.path(working.directory, "log.odc")
+ logfileTxt <- file.path(working.directory, "log.txt")
+ inits <- sapply(paste(working.directory, "/inits", 1:n.chains, ".txt", sep=""), native2win)
+ initlist <- paste("inits (", 1:n.chains, ", '", inits, "')\n", sep="")
+ savelist <- paste("set (", parameters.to.save, ")\n", sep="")
+ redo <- ceiling((n.iter-n.burnin)/(n.thin*bin))
+ cat(
+ "display ('log')\n",
+ "check ('", native2win(model), "')\n",
+ "data ('", native2win(data), "')\n",
+ "compile (", n.chains, ")\n",
+ if(is.inits) initlist,
+ "gen.inits()\n",
+ "thin.updater (", n.thin, ")\n",
+ "update (", ceiling(n.burnin/n.thin), ")\n",
+ savelist,
+ if(DIC) "dic.set()\n",
+ rep(
+ c("update (", formatC(ceiling(bin), format = "d"), ")\n",
+ "coda (*, '", native2win(coda), "')\n"),redo),
+ "stats (*)\n",
+ if(DIC) "dic.stats()\n",
+ "history (*, '", native2win(history), "')\n",
+ "save ('", native2win(logfile), "')\n",
+ "save ('", native2win(logfileTxt), "')\n",
+ file=script, sep="", append=FALSE)
+ if (!debug) cat ("quit ()\n", file=script, append=TRUE)
+ sims.files <- paste ("coda", 1:n.chains, ".txt", sep="")
+ for (i in 1:n.chains) cat ("WinBUGS did not run correctly.\n",
+ file=sims.files[i], append=FALSE)
+}
Property changes on: trunk/R2WinBUGS/R/bugs.script.R
___________________________________________________________________
Name: svn:keywords
+ Id
Added: trunk/R2WinBUGS/R/bugs.sims.R
===================================================================
--- trunk/R2WinBUGS/R/bugs.sims.R (rev 0)
+++ trunk/R2WinBUGS/R/bugs.sims.R 2006-11-24 13:24:51 UTC (rev 3)
@@ -0,0 +1,130 @@
+"bugs.sims" <-
+function (parameters.to.save, n.chains, n.iter, n.burnin, n.thin, DIC = TRUE){
+# Read the simulations from Bugs into R, format them, and monitor convergence
+ sims.files <- paste ("coda", 1:n.chains, ".txt", sep="")
+ index <- read.table ("codaIndex.txt", header=FALSE, sep="\t")
+ parameter.names <- as.vector(index[,1])
+ n.keep <- index[1,3] - index[1,2] + 1
+ n.parameters <- length(parameter.names)
+ n.sims <- n.keep*n.chains
+ sims <- matrix( , n.sims, n.parameters)
+ sims.array <- array (NA, c(n.keep, n.chains, n.parameters))
+ root.long <- character(n.parameters)
+ indexes.long <- vector(n.parameters, mode = "list")
+ for (i in 1:n.parameters){
+ temp <- decode.parameter.name(parameter.names[i])
+ root.long[i] <- temp$root
+ indexes.long[[i]] <- temp$indexes
+ }
+ n.roots <- length(parameters.to.save)
+ left.bracket.short <- as.vector (regexpr("[[]", parameters.to.save))
+ right.bracket.short <- as.vector (regexpr("[]]", parameters.to.save))
+ root.short <- ifelse (left.bracket.short==-1, parameters.to.save,
+ substring (parameters.to.save, 1, left.bracket.short-1))
+ dimension.short <- rep(0, n.roots)
+ indexes.short <- vector(n.roots, mode = "list")
+ n.indexes.short <- vector(n.roots, mode = "list")
+ long.short <- vector(n.roots, mode = "list")
+ length.short <- numeric(n.roots)
+ ##SS, UL##: Let's optimize the following loops ...
+ for (j in 1:n.roots){
+ long.short[[j]] <- (1:n.parameters)[root.long==root.short[j]]
+ length.short[j] <- length(long.short[[j]])
+ if (length.short[j]==0)
+ stop (paste ("parameter", root.short[[j]], "is not in the model"))
+ else if (length.short[j]>1){
+ dimension.short[j] <- length(indexes.long[[long.short[[j]][1]]])
+ n.indexes.short[[j]] <- numeric(dimension.short[j])
+ for (k in 1:dimension.short[j]) n.indexes.short[[j]][k] <- length (
+ unique (unlist (lapply (indexes.long[long.short[[j]]], .subset, k))))
+ length.short[j] <- prod(n.indexes.short[[j]])
+ if (length(long.short[[j]])!=length.short[j]) stop (paste
+ ("error in parameter", root.short[[j]], "in parameters.to.save"))
+ indexes.short[[j]] <- as.list(numeric(length.short[j]))
+ for (k in 1:length.short[j])
+ indexes.short[[j]][[k]] <- indexes.long[[long.short[[j]][k]]]
+ }
+ }
+# rank.long <- rank(paste(rep(root.short,length.short),
+# (1:n.parameters)/10^ceiling(log10(n.parameters)),sep="."))
+ rank.long <- unlist(long.short)
+
+ for (i in 1:n.chains){
+ sims.i <- scan (sims.files[i], quiet=TRUE) [2*(1:(n.keep*n.parameters))]
+ sims[(n.keep*(i-1)+1):(n.keep*i), ] <- sims.i
+ sims.array[,i,] <- sims.i
+ }
+ dimnames (sims) <- list (NULL, parameter.names)
+ dimnames (sims.array) <- list (NULL, NULL, parameter.names)
+#
+# Perform convergence checks and compute medians and quantiles.
+#
+ summary <- monitor (sims.array, n.chains, keep.all=TRUE)
+#
+# Create outputs
+#
+ last.values <- as.list (numeric(n.chains))
+ for (i in 1:n.chains){
+ n.roots.0 <- if(DIC) n.roots-1 else n.roots
+ last.values[[i]] <- as.list (numeric(n.roots.0))
+ names(last.values[[i]]) <- root.short[1:n.roots.0]
+ for (j in 1:n.roots.0){
+ if (dimension.short[j]<=1){
+ last.values[[i]][[j]] <- sims.array[n.keep,i,long.short[[j]]]
+ names(last.values[[i]][[j]]) <- NULL
+ }
+ else
+ last.values[[i]][[j]] <- aperm (array(sims.array[n.keep,i,long.short[[j]]],
+ rev(n.indexes.short[[j]])), dimension.short[j]:1)
+ }
+ }
+ sims <- sims [sample(n.sims),] # scramble (for convenience in analysis)
+ sims.list <- summary.mean <- summary.sd <- summary.median <- vector(n.roots, mode = "list")
+ names(sims.list) <- names(summary.mean) <- names(summary.sd) <- names(summary.median) <- root.short
+ for (j in 1:n.roots){
+ if (length.short[j]==1){
+ sims.list[[j]] <- sims[,long.short[[j]]]
+ summary.mean[[j]] <- summary[long.short[[j]],"mean"]
+ summary.sd[[j]] <- summary[long.short[[j]],"sd"]
+ summary.median[[j]] <- summary[long.short[[j]],"50%"]
+ }
+ else{
+ temp2 <- dimension.short[j]:1
+ sims.list[[j]] <- aperm (array (sims[,long.short[[j]]],
+ c(n.sims,rev(n.indexes.short[[j]]))), c(1,(dimension.short[j]+1):2))
+ summary.mean[[j]] <- aperm (array (summary[long.short[[j]],"mean"],
+ rev(n.indexes.short[[j]])), temp2)
+ summary.sd[[j]] <- aperm (array (summary[long.short[[j]],"sd"],
+ rev(n.indexes.short[[j]])), temp2)
+ summary.median[[j]] <- aperm (array (summary[long.short[[j]],"50%"],
+ rev(n.indexes.short[[j]])), temp2)
+ }
+ }
+ summary <- summary[rank.long,]
+ all <- list (n.chains=n.chains, n.iter=n.iter, n.burnin=n.burnin,
+ n.thin=n.thin, n.keep=n.keep, n.sims=n.sims,
+ sims.array=sims.array[,,rank.long,drop=FALSE], sims.list=sims.list,
+ sims.matrix=sims[,rank.long], summary=summary, mean=summary.mean,
+ sd=summary.sd, median=summary.median, root.short=root.short,
+ long.short=long.short, dimension.short=dimension.short,
+ indexes.short=indexes.short, last.values=last.values)
+ if(DIC){
+ LOG <- bugs.log("log.txt")$DIC
+ if(any(is.na(LOG))){
+ deviance <- all$sims.array[, , dim(sims.array)[3], drop = FALSE]
+ dim(deviance) <- dim(deviance)[1:2]
+ pD <- numeric(n.chains)
+ DIC <- numeric(n.chains)
+ for (i in 1:n.chains) {
+ pD[i] <- var(deviance[, i])/2
+ DIC[i] <- mean(deviance[, i]) + pD[i]
+ }
+ all <- c(all, list(pD = mean(pD), DIC = mean(DIC), DICbyR = TRUE))
+ } else {
+ DIC <- LOG[nrow(LOG),4]
+ pD <- LOG[nrow(LOG),3]
+ all <- c(all, list(pD = pD, DIC = DIC, DICbyR = FALSE))
+ }
+ }
+ return(all)
+}
Property changes on: trunk/R2WinBUGS/R/bugs.sims.R
___________________________________________________________________
Name: svn:keywords
+ Id
Added: trunk/R2WinBUGS/R/bugs.update.settings.R
===================================================================
--- trunk/R2WinBUGS/R/bugs.update.settings.R (rev 0)
+++ trunk/R2WinBUGS/R/bugs.update.settings.R 2006-11-24 13:24:51 UTC (rev 3)
@@ -0,0 +1,30 @@
+"bugs.update.settings" <-
+function (n.burnin, bugs.directory){
+ char.burnin <- as.character(n.burnin - 1)
+ file.copy(file.path(bugs.directory, "System/Rsrc/Registry.odc"),
+ file.path(bugs.directory, "System/Rsrc/Registry_Rsave.odc"),
+ overwrite = TRUE)
+ registry <- readBin(file.path(bugs.directory, "System/Rsrc/Registry.odc"),
+ "character", 400, size = 1, endian = "little")
+ locale <- Sys.getlocale("LC_CTYPE")
+ Sys.setlocale("LC_CTYPE", "C")
+ info <- registry[regexpr("Int", registry, fixed = TRUE, useBytes = TRUE) > 0]
+ while(regexpr("\r", info) > 0){
+ newline <- regexpr("\r", info)
+ info <- substring(info, newline + 1)
+ line <- substring(info, 1, regexpr("\r", info) - 1)
+ if(regexpr("AdaptivePhase", line) > 0){
+ numpos <- regexpr("Int", line, fixed = TRUE, useBytes = TRUE) + 4
+ num <- substring(line, numpos)
+ if (as.numeric(num) > n.burnin){
+ blanks <- rep(" ", nchar(num, type = "chars") - nchar(char.burnin, type = "chars"))
+ num.new <- paste(paste(blanks, collapse = ""), char.burnin, sep = "")
+ line.new <- sub(num, num.new, line)
+ registry <- sub(line, line.new, registry)
+ }
+ }
+ }
+ Sys.setlocale("LC_CTYPE", locale)
+ writeBin (registry,
+ file.path(bugs.directory, "System/Rsrc/Registry.odc"), endian = "little")
+}
Property changes on: trunk/R2WinBUGS/R/bugs.update.settings.R
___________________________________________________________________
Name: svn:keywords
+ Id
Added: trunk/R2WinBUGS/R/conv.par.R
===================================================================
--- trunk/R2WinBUGS/R/conv.par.R (rev 0)
+++ trunk/R2WinBUGS/R/conv.par.R 2006-11-24 13:24:51 UTC (rev 3)
@@ -0,0 +1,86 @@
+"conv.par" <-
+function (x, n.chains, Rupper.keep = TRUE) {
+ m <- ncol(x)
+ n <- nrow(x)
+
+# We compute the following statistics:
+#
+# xdot: vector of sequence means
+# s2: vector of sequence sample variances (dividing by n-1)
+# W = mean(s2): within MS
+# B = n*var(xdot): between MS.
+# muhat = mean(xdot): grand mean; unbiased under strong stationarity
+# varW = var(s2)/m: estimated sampling var of W
+# varB = B^2 * 2/(m+1): estimated sampling var of B
+# covWB = (n/m)*(cov(s2,xdot^2) - 2*muhat*cov(s^2,xdot)):
+# estimated sampling cov(W,B)
+# sig2hat = ((n-1)/n))*W + (1/n)*B: estimate of sig2; unbiased under
+# strong stationarity
+# quantiles: emipirical quantiles from last half of simulated sequences
+
+ xdot <- apply(x,2,mean)
+ muhat <- mean(xdot)
+ s2 <- apply(x,2,var)
+ W <- mean(s2)
+ quantiles <- quantile (as.vector(x), probs=c(.025,.25,.5,.75,.975))
+
+ if ((W > 1.e-8) && (n.chains > 1)) { # non-degenerate case
+
+ B <- n*var(xdot)
+ varW <- var(s2)/m
+ varB <- B^2 * 2/(m-1)
+ covWB <- (n/m)*(cov(s2,xdot^2) - 2*muhat*cov(s2,xdot))
+ sig2hat <- ((n-1)*W + B)/n
+
+# Posterior interval post.range combines all uncertainties
+# in a t interval with center muhat, scale sqrt(postvar),
+# and postvar.df degrees of freedom.
+#
+# postvar = sig2hat + B/(mn): variance for the posterior interval
+# The B/(mn) term is there because of the
+# sampling variance of muhat.
+# varpostvar: estimated sampling variance of postvar
+
+ postvar <- sig2hat + B/(m*n)
+ varpostvar <- max(0,
+ (((n-1)^2) * varW + (1 + 1/m)^2 * varB + 2 * (n-1) * (1 + 1/m) * covWB) / n^2)
+ post.df <- min(2*(postvar^2/varpostvar), 1000)
+
+# Estimated potential scale reduction (that would be achieved by
+# continuing simulations forever) has two components: an estimate and
+# an approx. 97.5% upper bound.
+#
+# confshrink = sqrt(postvar/W),
+# multiplied by sqrt(df/(df-2)) as an adjustment for the
+### CHANGED TO sqrt((df+3)/(df+1))
+# width of the t-interval with df degrees of freedom.
+#
+# postvar/W = (n-1)/n + (1+1/m)(1/n)(B/W); we approximate the sampling dist.
+# of (B/W) by an F distribution, with degrees of freedom estimated
+# from the approximate chi-squared sampling dists for B and W. (The
+# F approximation assumes that the sampling dists of B and W are independent;
+# if they are positively correlated, the approximation is conservative.)
+
+ confshrink.range <- postvar/W
+ if(Rupper.keep){
+ varlo.df <- 2*(W^2/varW)
+ confshrink.range <- c(confshrink.range,
+ (n-1)/n + (1+1/m)*(1/n)*(B/W) * qf(.975, m-1, varlo.df))
+ }
+ confshrink.range <- sqrt(confshrink.range * (post.df+3) / (post.df+1))
+
+# Calculate effective sample size: m*n*min(sigma.hat^2/B,1)
+# This is a crude measure of sample size because it relies on the between
+# variance, B, which can only be estimated with m degrees of freedom.
+
+ n.eff <- m*n*min(sig2hat/B,1)
+ list(quantiles=quantiles, confshrink=confshrink.range,
+ n.eff=n.eff)
+
+ }
+ else { # degenerate case: all entries in "data matrix" are identical
+ list (quantiles=quantiles, confshrink = rep(1, Rupper.keep + 1),
+ n.eff=1)
+
+ }
+}
Property changes on: trunk/R2WinBUGS/R/conv.par.R
___________________________________________________________________
Name: svn:keywords
+ Id
Added: trunk/R2WinBUGS/R/decode.parameter.name.R
===================================================================
--- trunk/R2WinBUGS/R/decode.parameter.name.R (rev 0)
+++ trunk/R2WinBUGS/R/decode.parameter.name.R 2006-11-24 13:24:51 UTC (rev 3)
@@ -0,0 +1,22 @@
+"decode.parameter.name" <-
+function (a){
+#
+# Decodes Bugs parameter names
+# (e.g., "beta[3,14]" becomes "beta" with 2 indexes: 3 and 14)
+# for use by the bugs.sim() function
+#
+ left.bracket <- regexpr ("[[]", a)
+ if (left.bracket==-1){
+ root <- a
+ dimension <- 0
+ indexes <- NA
+ }
+ else {
+ root <- substring (a, 1, left.bracket-1)
+ right.bracket <- regexpr ("[]]", a)
+ a <- substring (a, left.bracket+1, right.bracket-1)
+ indexes <- as.numeric(unlist(strsplit(a, ",")))
+ dimension <- length(indexes)
+ }
+ return (list (root=root, dimension=dimension, indexes=indexes))
+}
Property changes on: trunk/R2WinBUGS/R/decode.parameter.name.R
___________________________________________________________________
Name: svn:keywords
+ Id
Added: trunk/R2WinBUGS/R/formatdata.R
===================================================================
--- trunk/R2WinBUGS/R/formatdata.R (rev 0)
+++ trunk/R2WinBUGS/R/formatdata.R 2006-11-24 13:24:51 UTC (rev 3)
@@ -0,0 +1,24 @@
+"formatdata" <-
+function (datalist){
+ if (!is.list(datalist) || is.data.frame(datalist))
+ stop("Argument to formatdata() must be a list.")
+ n <- length(datalist)
+ datalist.string <- vector(n, mode = "list")
+ for (i in 1:n) {
+ if (length(datalist[[i]]) == 1)
+ datalist.string[[i]] <- paste(names(datalist)[i],
+ "=", as.character(datalist[[i]]), sep = "")
+ if (is.vector(datalist[[i]]) && length(datalist[[i]]) > 1)
+ datalist.string[[i]] <- paste(names(datalist)[i],
+ "=c(", paste(as.character(datalist[[i]]), collapse = ", "),
+ ")", sep = "")
+ if (is.array(datalist[[i]]))
+ datalist.string[[i]] <- paste(names(datalist)[i],
+ "= structure(.Data= c(", paste(as.character(as.vector(aperm(datalist[[i]]))),
+ collapse = ", "), "), .Dim=c(", paste(as.character(dim(datalist[[i]])),
+ collapse = ", "), "))", sep = "")
+ }
+ datalist.tofile <- paste("list(", paste(unlist(datalist.string),
+ collapse = ", "), ")", sep = "")
+ return(datalist.tofile)
+}
Property changes on: trunk/R2WinBUGS/R/formatdata.R
___________________________________________________________________
Name: svn:keywords
+ Id
Added: trunk/R2WinBUGS/R/monitor.R
===================================================================
--- trunk/R2WinBUGS/R/monitor.R (rev 0)
+++ trunk/R2WinBUGS/R/monitor.R 2006-11-24 13:24:51 UTC (rev 3)
@@ -0,0 +1,51 @@
+"monitor" <-
+function (a, n.chains, trans=NULL, keep.all=FALSE, Rupper.keep=FALSE) {
+
+# If keep.all=T: a is a n x m x k array:
+# m sequences of length n, k variables measured
+# If keep.all=F: a is a 2n x m x k array (first half will be discarded)
+#
+# trans is a vector of length k: "" if no transformation, or "log" or "logit"
+# (If trans is not defined, it will be set to "log" for parameters that
+# are all-positive and 0 otherwise.)
+#
+# If Rupper.keep=T: keep Rupper. (Otherwise don't display it.)
+ invlogit <- function (x) {1 / (1 + exp(-x))}
+ nparams <- if(length(dim(a)) < 3) 1 else dim(a)[length(dim(a))]
+ # Calculation and initialization of the required matrix "output"
+ output <- matrix( , ncol = if(n.chains > 1){if(Rupper.keep) 10 else 9} else 7, nrow = nparams)
+ if (length(dim(a))==2) a <- array (a, c(dim(a),1))
+ if (!keep.all){
+ n <- floor(dim(a)[1]/2)
+ a <- a[(n+1):(2*n), , , drop = FALSE]
+ }
+ if (is.null(trans))
+ trans <- ifelse ((apply (a<=0, 3, sum))==0, "log", "")
+ for (i in 1:nparams){
+ # Rupper.keep: discard Rupper (nobody ever uses it)
+ ai <- a[ , , i, drop = FALSE]
+ if (trans[i]=="log"){
+ conv.p <- conv.par(log(ai), n.chains, Rupper.keep=Rupper.keep) # reason????
+ conv.p <- list(quantiles = exp(conv.p$quantiles),
+ confshrink = conv.p$confshrink, n.eff = conv.p$n.eff)
+ }
+ else if (trans[i]=="logit"){
+ conv.p <- conv.par(logit(ai), n.chains, Rupper.keep=Rupper.keep)
+ conv.p <- list(quantiles = invlogit(conv.p$quantiles),
+ confshrink = conv.p$confshrink, n.eff = conv.p$n.eff)
+ }
+ else conv.p <- conv.par(ai, n.chains, Rupper.keep=Rupper.keep)
+ output[i, ] <- c(mean(ai), sd(as.vector(ai)),
+ conv.p$quantiles,
+ if(n.chains > 1) conv.p$confshrink,
+ if(n.chains > 1) round(conv.p$n.eff, min(0, 1 - floor(log10(conv.p$n.eff))))
+ )
+ }
+ if(n.chains > 1)
+ dimnames(output) <- list(dimnames(a)[[3]], c("mean","sd",
+ "2.5%","25%","50%","75%","97.5%", "Rhat", if(Rupper.keep) "Rupper","n.eff"))
+ else
+ dimnames(output) <- list(dimnames(a)[[3]], c("mean","sd",
+ "2.5%","25%","50%","75%","97.5%"))
+ return (output)
+}
Property changes on: trunk/R2WinBUGS/R/monitor.R
___________________________________________________________________
Name: svn:keywords
+ Id
Added: trunk/R2WinBUGS/R/openbugs.R
===================================================================
--- trunk/R2WinBUGS/R/openbugs.R (rev 0)
+++ trunk/R2WinBUGS/R/openbugs.R 2006-11-24 13:24:51 UTC (rev 3)
@@ -0,0 +1,85 @@
+openbugs <- function(d...
[truncated message content] |
|
From: <li...@us...> - 2007-04-07 18:04:19
|
Revision: 9
http://svn.sourceforge.net/bugs-r/?rev=9&view=rev
Author: ligges
Date: 2007-04-07 11:04:11 -0700 (Sat, 07 Apr 2007)
Log Message:
-----------
R2WinBUGS has been ported to S-PLUS by Insightful Corp.
Special thanks to Dawn Woodard!
Modified Paths:
--------------
trunk/R2WinBUGS/Changes
trunk/R2WinBUGS/DESCRIPTION
trunk/R2WinBUGS/R/as.bugs.array.R
trunk/R2WinBUGS/R/attach.all.R
trunk/R2WinBUGS/R/bugs.R
trunk/R2WinBUGS/R/bugs.data.R
trunk/R2WinBUGS/R/bugs.inits.R
trunk/R2WinBUGS/R/bugs.plot.inferences.R
trunk/R2WinBUGS/R/bugs.plot.summary.R
trunk/R2WinBUGS/R/bugs.run.R
trunk/R2WinBUGS/R/bugs.sims.R
trunk/R2WinBUGS/R/bugs.update.settings.R
trunk/R2WinBUGS/R/conv.par.R
trunk/R2WinBUGS/R/monitor.R
trunk/R2WinBUGS/R/openbugs.R
trunk/R2WinBUGS/R/plot.bugs.R
trunk/R2WinBUGS/R/wineutils.R
trunk/R2WinBUGS/R/write.model.R
trunk/R2WinBUGS/man/bugs.Rd
trunk/R2WinBUGS/man/bugs.log.Rd
trunk/R2WinBUGS/man/bugs.run.Rd
trunk/R2WinBUGS/man/bugs.script.Rd
trunk/R2WinBUGS/man/bugs.sims.Rd
trunk/R2WinBUGS/man/openbugs.Rd
trunk/R2WinBUGS/man/write.model.Rd
Modified: trunk/R2WinBUGS/Changes
===================================================================
--- trunk/R2WinBUGS/Changes 2006-12-29 16:10:15 UTC (rev 8)
+++ trunk/R2WinBUGS/Changes 2007-04-07 18:04:11 UTC (rev 9)
@@ -69,3 +69,6 @@
Update 2.0-4 (01 November 2006):
- print.bugs / plot.bugs documentation fixes
- write.model() fix
+
+Update 2.1-1 (07 April 2007):
+- Ported to S-PLUS by Insightful Corp.
Modified: trunk/R2WinBUGS/DESCRIPTION
===================================================================
--- trunk/R2WinBUGS/DESCRIPTION 2006-12-29 16:10:15 UTC (rev 8)
+++ trunk/R2WinBUGS/DESCRIPTION 2007-04-07 18:04:11 UTC (rev 9)
@@ -1,18 +1,22 @@
Package: R2WinBUGS
-Title: Running WinBUGS and OpenBUGS from R
-Date: 2006-11-01
-Version: 2.0-4
+Title: Running WinBUGS and OpenBUGS from R / S-PLUS
+Date: 2007-04-07
+Version: 2.1-1
Author: originally written by Andrew Gelman <ge...@st...>;
changes and packaged by Sibylle Sturtz <st...@st...>
and Uwe Ligges <li...@st...>.
With considerable contributions by Gregor Gorjanc <gre...@bf...>
and Jouni Kerman <ke...@st...>.
+ Ported to S-PLUS by Insightful Corp.
Description: 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.
-Depends: R (>= 2.2.0)
+ convergence in a table and graph, and save the simulations in arrays for easy access
+ in R / S-PLUS. In S-PLUS, the openbugs functionality and the windows emulation
+ functionality is not yet available.
+Depends: R (>= 2.4.0)
Suggests: coda (>= 0.9-0), BRugs (>= 0.3-0)
SystemRequirements: WinBUGS 1.4 on Windows
URL: http://www.stat.columbia.edu/~gelman/bugsR/
Maintainer: Sibylle Sturtz <st...@st...>
License: GPL version 2
+Dialect: R, S-PLUS
Modified: trunk/R2WinBUGS/R/as.bugs.array.R
===================================================================
--- trunk/R2WinBUGS/R/as.bugs.array.R 2006-12-29 16:10:15 UTC (rev 8)
+++ trunk/R2WinBUGS/R/as.bugs.array.R 2007-04-07 18:04:11 UTC (rev 9)
@@ -71,9 +71,11 @@
summary <- monitor(sims.array, n.chains, keep.all = TRUE)
last.values <- as.list(numeric(n.chains))
for (i in 1:n.chains) {
- n.roots.0 <- if (!is.null(DIC))
- n.roots - 1
- else n.roots
+ if (is.R()) {
+ n.roots.0 <- if(!is.null(DIC)) n.roots - 1 else n.roots
+ } else {
+ n.roots.0 <- if(DIC) n.roots - 1 else n.roots
+ }
last.values[[i]] <- as.list(numeric(n.roots.0))
names(last.values[[i]]) <- root.short[1:n.roots.0]
for (j in 1:n.roots.0) {
@@ -111,6 +113,11 @@
}
}
summary <- summary[rank.long, ]
+ if (is.R())
+ is.DIC = !is.null(DIC)
+ else
+ is.DIC = DIC
+
all <- list(n.chains = n.chains, n.iter = n.iter, n.burnin = n.burnin,
n.thin = n.thin, n.keep = n.keep, n.sims = n.sims,
sims.array = sims.array[,,rank.long,drop = FALSE], sims.list = sims.list,
@@ -118,7 +125,7 @@
sd = summary.sd, median = summary.median, root.short = root.short,
long.short = long.short, dimension.short = dimension.short,
indexes.short = indexes.short, last.values = last.values, program=program,
- model.file=model.file, is.DIC=!is.null(DIC), DIC=DIC)
+ model.file=model.file, is.DIC=is.DIC, DIC=DIC)
if(sum(DIC)) {
deviance <- all$sims.array[, , dim(sims.array)[3], drop = FALSE]
dim(deviance) <- dim(deviance)[1:2]
Modified: trunk/R2WinBUGS/R/attach.all.R
===================================================================
--- trunk/R2WinBUGS/R/attach.all.R 2006-12-29 16:10:15 UTC (rev 8)
+++ trunk/R2WinBUGS/R/attach.all.R 2007-04-07 18:04:11 UTC (rev 9)
@@ -1,11 +1,12 @@
attach.all <- function(x, overwrite = NA, name = "attach.all"){
+ if(is.R()){
rem <- names(x) %in% ls(.GlobalEnv)
if(!any(rem)) overwrite <- FALSE
rem <- names(x)[rem]
if(is.na(overwrite)){
question <- paste("The following objects in .GlobalEnv will mask\nobjects in the attached database:\n",
- paste(rem, collapse=", "),
- "\nRemove these objects from .GlobalEnv?", sep="")
+ paste(rem, collapse=", "),
+ "\nRemove these objects from .GlobalEnv?", sep="")
if(interactive()){
if(.Platform$OS.type == "windows")
overwrite <- "YES" == winDialog(type = "yesno", question)
@@ -16,6 +17,9 @@
}
if(overwrite) remove(list=rem, envir=.GlobalEnv)
attach(x, name=name)
+ } else {
+ attach.default(x, name = name)
+ }
}
attach.bugs <- function (x, overwrite = NA){
@@ -25,12 +29,24 @@
detach("bugs.sims")}
x$sims.list$n.sims <- x$n.sims # put n.sims into sims.list for convenience
r2 <- attach.all(x$sims.list, overwrite = overwrite, name = "bugs.sims")
- invisible (bugs.sims = r2)
+ if (is.R())
+ invisible (bugs.sims = r2)
+ else
+ invisible (r2)
}
-detach.all <- function(name = "attach.all")
+detach.all <- function(name = "attach.all"){
+ if (is.R()){
do.call("detach", list(name=name))
+ } else {
+ do.call("detach", list(what=name))
+ }
+}
detach.bugs <- function(){
+ if (is.R()){
detach.all("bugs.sims")
+ } else {
+ invisible(detach.all("bugs.sims"))
+ }
}
Modified: trunk/R2WinBUGS/R/bugs.R
===================================================================
--- trunk/R2WinBUGS/R/bugs.R 2006-12-29 16:10:15 UTC (rev 8)
+++ trunk/R2WinBUGS/R/bugs.R 2007-04-07 18:04:11 UTC (rev 9)
@@ -10,17 +10,23 @@
clearWD = FALSE, useWINE = .Platform$OS.type != "windows", WINE = Sys.getenv("WINE"),
newWINE = FALSE, WINEPATH = NULL){
- ## If OpenBUGS, we only call openbugs() and exit...
program <- match.arg(program)
if (program %in% c("openbugs", "OpenBugs"))
- return(openbugs(data, inits, parameters.to.save, model.file,
- n.chains, n.iter, n.burnin, n.thin, DIC, bugs.directory,
- working.directory, digits))
-
+ if (is.R()){
+ ## If OpenBUGS, we only call openbugs() and exit...
+ return(openbugs(data, inits, parameters.to.save, model.file,
+ n.chains, n.iter, n.burnin, n.thin, DIC, bugs.directory,
+ working.directory, digits))
+ } else {
+ stop ("OpenBUGS is not yet available in S-PLUS")
+ }
## Checking number of inits, which is NOT save here:
if(!missing(inits) && !is.function(inits) && !is.null(inits) && (length(inits) != n.chains))
stop("Number of initialized chains (length(inits)) != n.chains")
- if (useWINE) { # attempt to find wine and winepath
+ if(useWINE) {
+ if (!is.R())
+ stop ("Non-Windows platforms not yet supported in R2WinBUGS for S-PLUS")
+ ## attempt to find wine and winepath
if (!nchar(WINE)) {
WINE <- system("locate wine | grep bin/wine$", intern = TRUE)
WINE <- WINE[length(WINE)]
@@ -31,7 +37,7 @@
WINEPATH <- WINEPATH[length(WINEPATH)]
}
if (!length(WINEPATH)) stop("couldn't locate WINEPATH binary")
- }
+ }
if(!is.null(working.directory)){
savedWD <- getwd()
setwd(working.directory)
@@ -59,8 +65,13 @@
if(codaPkg)
return(file.path(getwd(), paste("coda", 1:n.chains, ".txt", sep="")))
- sims <- c(bugs.sims(parameters.to.save, n.chains, n.iter, n.burnin, n.thin, DIC),
- model.file = model.file, is.DIC = !is.null(DIC), program = program)
+ if (is.R()){
+ sims <- c(bugs.sims(parameters.to.save, n.chains, n.iter, n.burnin, n.thin, DIC),
+ model.file = model.file, is.DIC = !is.null(DIC), program = program)
+ } else {
+ sims <- c(bugs.sims(parameters.to.save, n.chains, n.iter, n.burnin, n.thin, DIC),
+ model.file = model.file, is.DIC = DIC, program = program)
+ }
if(clearWD)
file.remove(c("data.txt", "log.odc", "log.txt", "codaIndex.txt",
paste("inits", 1:n.chains, ".txt", sep=""),
Modified: trunk/R2WinBUGS/R/bugs.data.R
===================================================================
--- trunk/R2WinBUGS/R/bugs.data.R 2006-12-29 16:10:15 UTC (rev 8)
+++ trunk/R2WinBUGS/R/bugs.data.R 2007-04-07 18:04:11 UTC (rev 9)
@@ -1,12 +1,222 @@
-"bugs.data" <-
+"bugs.data" <-
function(data, dir = getwd(), digits = 5){
if(is.numeric(unlist(data)))
- write.datafile(lapply(data, formatC, digits = digits, format = "E"),
- file.path(dir, "data.txt"))
+ if(is.R()) {
+ write.datafile(lapply(data, formatC, digits = digits, format = "E"),
+ file.path(dir, "data.txt"))
+ }
+ else {
+ writeDatafileS4(data, towhere = "data.txt")
+ }
else {
- data.list <- lapply(as.list(data), get, pos = parent.frame(2))
- names(data.list) <- as.list(data)
- write.datafile(lapply(data.list, formatC, digits = digits, format = "E"),
- file.path(dir, "data.txt"))
- }
+ if(is.R()) {
+ data.list <- lapply(as.list(data), get, pos = parent.frame(2))
+ names(data.list) <- as.list(data)
+ write.datafile(lapply(data.list, formatC, digits = digits, format = "E"),
+ file.path(dir, "data.txt"))
+ }
+ else {
+ data.list <- lapply(as.list(data), get, where = parent.frame(2))
+ names(data.list) <- unlist(data)
+ writeDatafileS4(data.list, towhere = "data.txt")
+ }
+ }
}
+
+if (!is.R()) {
+
+"writeDatafileS4" <-
+#
+# Writes to file "towhere" text defining a list containing "DATA" in a form compatable with WinBUGS.
+# Required arguments:
+# DATA - either a data frame or else a list consisting of any combination of scalars, vectors, arrays or data frames (but not lists).
+# If a list, all list elements that are not data.frames must be named. Names of data.frames in DATA are ignored.
+# Optional arguments:
+# towhere - file to receive output. Is clipboard by default, which is convenient for pasting into a WinBUTS ODC file.
+# fill - If numeric, number of columns for output. If FALSE, output will be on one line. If TRUE (default), number of
+# columns is given by .Options$width.
+# Value:
+# Text defining a list is output to file "towhere".
+# Details:
+# The function performs considerable checking of DATA argument. Since WinBUGS requires numeric input, no factors or character vectors
+# are allowed. All data must be named, either as named elements of DATA (if it is a list) or else using the names given in data frames.
+# Data frames may contain matrices.
+# Arrays of any dimension are rearranged to be in row-major order, as required by WinBUGS. Scientific notation is also handled properly.
+# In particular, the number will consist of a mantissa _containing a decimal point_ followed by "E", then either "+" or "-", and finally
+# a _two-digit_ number. S-Plus does not always provide a decimal point in the mantissa, uses "e" instead of "E", followed by
+# either a "+" or "-" and then _three_ digits.
+# Written by Terry Elrod. Disclaimer: This function is used at the user's own risk.
+# Please send comments to Ter...@UA....
+# Revision history: 2002-11-19. Fixed to handle missing values properly.
+function(DATA, towhere = "clipboard", fill = TRUE)
+{
+ formatDataS4 =
+ #
+ # Prepared DATA for input to WinBUGS.
+ function(DATA)
+ {
+ toSingleS4 =
+ #
+ # Takes numeric vector and removes digit of exponent in scientific notation (if any)
+ function(x)
+ {
+ xdim <- dim(x)
+ x <- as.character(as.single(x))
+ # First to look for positives:
+ pplus <- regMatchPos(x, "e\\+0")
+ pplusind <- apply(pplus, 1, function(y)
+ (!any(is.na(y))))
+ if(any(pplusind)) {
+ # Making sure that periods are in mantissa...
+ init <- substring(x[pplusind], 1, pplus[
+ pplusind, 1] - 1)
+ #...preceeding exponent
+ pper <- regMatchPos(init, "\\.")
+ pperind <- apply(pper, 1, function(y)
+ (all(is.na(y))))
+ if(any(pperind))
+ init[pperind] <- paste(init[pperind],
+ ".0", sep = "")
+ # Changing the format of the exponent...
+ x[pplusind] <- paste(init, "E+", substring(
+ x[pplusind], pplus[pplusind, 2] + 1),
+ sep = "")
+ }
+ # Then to look for negatives:
+ pminus <- regMatchPos(x, "e\\-0")
+ pminusind <- apply(pminus, 1, function(y)
+ (!any(is.na(y))))
+ if(any(pminusind)) {
+ # Making sure that periods are in mantissa...
+ init <- substring(x[pminusind], 1, pminus[
+ pminusind, 1] - 1)
+ #...preceeding exponent
+ pper <- regMatchPos(init, "\\.")
+ pperind <- apply(pper, 1, function(y)
+ (all(is.na(y))))
+ if(any(pperind))
+ init[pperind] <- paste(init[pperind],
+ ".0", sep = "")
+ # Changing the format of the exponent...
+ x[pminusind] <- paste(init, "E-", substring(
+ x[pminusind], pminus[pminusind, 2] +
+ 1), sep = "")
+ }
+ x
+ }
+ if(!is.list(DATA))
+ stop("DATA must be a named list or data frame.")
+ dlnames <- names(DATA)
+ if(is.data.frame(DATA))
+ DATA <- as.list(DATA)
+ #
+ # Checking for lists in DATA....
+ lind <- sapply(DATA, is.list)
+ # Checking for data frames in DATA....
+ dfind <- sapply(DATA, is.data.frame)
+ # Any lists that are not data frames?...
+ if(any(lind & !dfind)) stop("DATA may not contain lists.")
+ # Checking for unnamed elements of list that are not data frames....
+ if(any(dlnames[!dfind] == "")) stop(
+ "When DATA is a list, all its elements that are not data frames must be named."
+ )
+ # Checking for duplicate names....
+ dupnames <- unique(dlnames[duplicated(dlnames)])
+ if(length(dupnames) > 0)
+ stop(paste(
+ "The following names are used more than once in DATA:",
+ paste(dupnames, collapse = ", ")))
+ if(any(dfind)) {
+ dataold <- DATA
+ DATA <- vector("list", 0)
+ for(i in seq(along = dataold)) {
+ if(dfind[i])
+ DATA <- c(DATA, as.list(dataold[[i]]))
+ else DATA <- c(DATA, dataold[i])
+ }
+ dataold <- NULL
+ }
+ dlnames <- names(DATA)
+ dupnames <- unique(dlnames[duplicated(dlnames)])
+ # Checking for duplicated names again (now that columns of data frames are included)....
+ if(length(dupnames) > 0) stop(paste(
+ "The following names are used more than once in DATA (at least once within a data frame):",
+ paste(dupnames, collapse = ", ")))
+ # Checking for factors....
+ factorind <- sapply(DATA, is.factor)
+ if(any(factorind))
+ stop(paste(
+ "DATA may not include factors. One or more factor variables were detected:",
+ paste(dlnames[factorind], collapse = ", ")))
+ # Checking for character vectors....
+ charind <- sapply(DATA, is.character)
+ if(any(charind))
+ stop(paste(
+ "WinBUGS does not handle character data. One or more character variables were detected:",
+ paste(dlnames[charind], collapse = ", ")))
+ # Checking for complex vectors....
+ complexind <- sapply(DATA, is.complex)
+ if(any(complexind))
+ stop(paste(
+ "WinBUGS does not handle complex data. One or more complex variables were detected:",
+ paste(dlnames[complexind], collapse = ", ")))
+ # Checking for values farther from zero than 1E+38 (which is limit of single precision)....
+ toobigind <- sapply(DATA, function(x)
+ {
+ y <- abs(x[!is.na(x)])
+ any(y[y > 0] > 9.9999999999999998e+37)
+ }
+ )
+ if(any(toobigind))
+ stop(paste(
+ "WinBUGS works in single precision. The following variables contain data outside the range +/-1.0E+38: ",
+ paste(dlnames[toobigind], collapse = ", "),
+ ".\n", sep = ""))
+ # Checking for values in range +/-1.0E-38 (which is limit of single precision)....
+ toosmallind <- sapply(DATA, function(x)
+ {
+ y <- abs(x[!is.na(x)])
+ any(y[y > 0] < 9.9999999999999996e-39)
+ }
+ )
+ n <- length(dlnames)
+ data.string <- as.list(rep(NA, n))
+ for(i in 1:n) {
+ if(length(DATA[[i]]) == 1) {
+ ac <- toSingleS4(DATA[[i]])
+ data.string[[i]] <- paste(names(DATA)[i], "=",
+ ac, sep = "")
+ next
+ }
+ if(is.vector(DATA[[i]]) & length(DATA[[i]]) > 1) {
+ ac <- toSingleS4(DATA[[i]])
+ data.string[[i]] <- paste(names(DATA)[i], "=c(",
+ paste(ac, collapse = ", "), ")", sep =
+ "")
+ next
+ }
+ if(is.array(DATA[[i]])) {
+ ac <- toSingleS4(aperm(DATA[[i]]))
+ data.string[[i]] <- paste(names(DATA)[i],
+ "= structure(.Data= c(", paste(ac,
+ collapse = ", "), "), \n .Dim=c(",
+ paste(as.character(dim(DATA[[i]])),
+ collapse = ", "), "))", sep = "")
+ }
+ }
+ data.tofile <- paste("list(", paste(unlist(data.string),
+ collapse = ", "), ")", sep = "")
+ if(any(toosmallind))
+ warning(paste(
+ "WinBUGS works in single precision. The following variables contained nonzero data",
+ "\ninside the range +/-1.0E-38 that were set to zero: ",
+ paste(dlnames[toosmallind], collapse = ", "),
+ ".\n", sep = ""))
+ return(data.tofile)
+ }
+ rslt <- formatDataS4(DATA)
+ cat(rslt, file = towhere, fill = fill)
+ invisible(0)
+}
+
+} # ends if (!is.R())
Modified: trunk/R2WinBUGS/R/bugs.inits.R
===================================================================
--- trunk/R2WinBUGS/R/bugs.inits.R 2006-12-29 16:10:15 UTC (rev 8)
+++ trunk/R2WinBUGS/R/bugs.inits.R 2007-04-07 18:04:11 UTC (rev 9)
@@ -1,13 +1,22 @@
-"bugs.inits" <-
+"bugs.inits" <-
function (inits, n.chains, digits){
- if(!is.null(inits)){
- for (i in 1:n.chains){
- if (is.function(inits))
- write.datafile(lapply(inits(), formatC, digits = digits, format = "E"),
- paste ("inits", i, ".txt", sep=""))
- else
- write.datafile(lapply(inits[[i]], formatC, digits = digits, format = "E"),
- paste ("inits", i, ".txt", sep=""))
- }
- }
+ if(!is.null(inits)) {
+ for(i in 1:n.chains) {
+ if(is.function(inits))
+ if(is.R()) {
+ write.datafile(lapply(inits(), formatC, digits = digits, format = "E"),
+ paste("inits", i, ".txt", sep = ""))
+ } else {
+ writeDatafileS4(inits(), towhere =
+ paste("inits", i, ".txt", sep = ""))
+ }
+ else if(is.R()) {
+ write.datafile(lapply(inits[[i]], formatC, digits = digits, format = "E"),
+ paste("inits", i, ".txt", sep = ""))
+ } else {
+ writeDatafileS4(inits[[i]], towhere = paste(
+ "inits", i, ".txt", sep = ""))
+ }
+ }
+ }
}
Modified: trunk/R2WinBUGS/R/bugs.plot.inferences.R
===================================================================
--- trunk/R2WinBUGS/R/bugs.plot.inferences.R 2006-12-29 16:10:15 UTC (rev 8)
+++ trunk/R2WinBUGS/R/bugs.plot.inferences.R 2007-04-07 18:04:11 UTC (rev 9)
@@ -28,8 +28,18 @@
long.short <- sims$long.short
height <- .6
par (mar=c(0,0,1,0))
+
+ ## if in Splus, suppress printing of warnings during the plotting.
+ ## otherwise a warning is generated
+ if (!is.R()){
+ warn.settings <- options("warn")[[1]]
+ options (warn = -1)
+ }
plot (c(0,1), c(-n.roots-.5,-.4),
ann=FALSE, bty="n", xaxt="n", yaxt="n", type="n")
+ if (!is.R())
+ options(warn = warn.settings)
+
W <- max(strwidth(rootnames, cex=cex.names))
B <- (1-W)/3.8
A <- 1-3.5*B
Modified: trunk/R2WinBUGS/R/bugs.plot.summary.R
===================================================================
--- trunk/R2WinBUGS/R/bugs.plot.summary.R 2006-12-29 16:10:15 UTC (rev 8)
+++ trunk/R2WinBUGS/R/bugs.plot.summary.R 2007-04-07 18:04:11 UTC (rev 9)
@@ -1,6 +1,7 @@
"bugs.plot.summary" <-
function (sims, ...){
DIC <- sims$is.DIC
+
if (.Device=="windows" ||
(.Device=="null device" && options("device")=="windows")){
cex.names <- .7
@@ -29,7 +30,11 @@
J[J==max(J)] <- max(J)-1
total <- ceiling(sum(J+.5))
}
- pos <- -1
+ if (is.R()){
+ pos <- -1
+ } else {
+ pos <- -1.5
+ }
ypos <- NULL
id <- NULL
ystart <- NULL
@@ -39,13 +44,25 @@
ystart <- numeric(n.roots)
for (k in 1:n.roots){
ystart[k] <- pos
- ypos <- c(ypos, pos - seq(0, J[k]-1))
+ if (is.R()) {
+ ypos <- c(ypos, pos - seq(0, J[k]-1))
+ } else {
+ # In S-PLUS, increase the vertical spacing
+ ypos <- c(ypos, pos - 1.5*seq(0, J[k]-1))
+ }
id <- c(id, 1:J[k])
- pos <- pos - J[k] -.5
+ if (is.R()) {
+ pos <- pos - J[k] -.5
+ } else {
+ pos <- pos - 1.5*J[k] -0.75
+ }
if (k>1) jj <- c(jj, sum(J0[1:(k-1)]) + (1:J[k]))
}
- bottom <- min(ypos)-1
-
+ if (is.R()){
+ bottom <- min(ypos)-1
+ } else {
+ bottom <- min(ypos)-1.5
+ }
med <- numeric(sum(J))
i80 <- matrix( , sum(J), 2)
i80.chains <- array (NA, c(sum(J), n.chains, 2))
@@ -61,8 +78,17 @@
a <- -b * p.rng[1]
par (mar=c(0,0,1,3))
+ # if in Splus, suppress printing of warnings during the plotting.
+ # otherwise a warning is generated
+ if (!is.R()){
+ warn.settings <- options("warn")[[1]]
+ options (warn = -1)
+ }
plot (c(0,1), c(min(bottom, -max.length)-3,2.5),
ann=FALSE, bty="n", xaxt="n", yaxt="n", type="n")
+ if (!is.R())
+ options(warn = warn.settings)
+
W <- max(strwidth(unlist(dimnames(summ)[[1]]), cex=cex.names))
B <- (1-W)/3.6
A <- 1-3.5*B
@@ -100,7 +126,16 @@
for (j in 1:sum(J)){
name <- dimnames(summ)[[1]][jj[j]]
if (id[j]==1)
- text (0, ypos[j], name, adj=0, cex=cex.names)
+ if (is.R()) {
+ text (0, ypos[j], name, adj=0, cex=cex.names)
+ } else {
+ # in S-PLUS, strwidth is an upper bound on the length of the string,
+ # so we must align the brackets differently than in R
+ pos <- as.vector(regexpr("[[]", name))
+ text (0, ypos[j], substring(name, 1, pos-1), adj=0, cex=cex.names)
+ text (strwidth(substring(name,1,pos-1),cex=cex.names),
+ ypos[j], substring(name, pos, nchar(name)), adj=0, cex=cex.names)
+ }
else {
pos <- as.vector(regexpr("[[]", name))
text (strwidth(substring(name,1,pos-1),cex=cex.names),
Modified: trunk/R2WinBUGS/R/bugs.run.R
===================================================================
--- trunk/R2WinBUGS/R/bugs.run.R 2006-12-29 16:10:15 UTC (rev 8)
+++ trunk/R2WinBUGS/R/bugs.run.R 2007-04-07 18:04:11 UTC (rev 9)
@@ -1,15 +1,24 @@
"bugs.run" <-
function(n.burnin, bugs.directory, WINE = "",
useWINE = .Platform$OS.type != "windows", newWINE = TRUE){
-
+
+if(useWINE && !is.R())
+ stop ("Non-Windows platforms not yet supported in R2WinBUGS for S-PLUS")
if(useWINE && !newWINE) bugs.directory <- win2native(bugs.directory)
## Update the lengths of the adaptive phases in the Bugs updaters
try(bugs.update.settings(n.burnin, bugs.directory))
## Return the lengths of the adaptive phases to their original settings
- on.exit(try(file.copy(file.path(bugs.directory, "System/Rsrc/Registry_Rsave.odc"),
- file.path(bugs.directory, "System/Rsrc/Registry.odc"),
- overwrite = TRUE)))
+ if (is.R()){
+ on.exit(try(file.copy(file.path(bugs.directory, "System/Rsrc/Registry_Rsave.odc"),
+ file.path(bugs.directory, "System/Rsrc/Registry.odc"),
+ overwrite = TRUE)))
+ } else {
+ on.exit(try(splus.file.copy(file.path(bugs.directory, "System/Rsrc/Registry_Rsave.odc"),
+ file.path(bugs.directory, "System/Rsrc/Registry.odc"),
+ overwrite = TRUE)))
+ }
+
## Search Win*.exe (WinBUGS executable) within bugs.directory
dos.location <- file.path(bugs.directory,
grep("^Win[[:alnum:]]*[.]exe$", list.files(bugs.directory), value = TRUE)[1])
@@ -26,9 +35,15 @@
if(temp == -1)
stop("Error in bugs.run().\nCheck that WinBUGS is in the specified directory.")
## Stop and print an error message if Bugs did not run correctly
- if (length(grep("Bugs did not run correctly",
- scan("coda1.txt", character(), quiet=TRUE, sep="\n"))) > 0)
- stop("Look at the log file and\ntry again with debug=TRUE and figure out what went wrong within Bugs.")
+ if(is.R()) {
+ if(length(grep("Bugs did not run correctly",
+ scan("coda1.txt", character(), quiet=TRUE, sep="\n"))) > 0)
+ stop("Look at the log file and\ntry again with debug=TRUE and figure out what went wrong within Bugs.")
+ } else {
+ if (length(grep("Bugs did not run correctly",
+ scan("coda1.txt", character(), sep="\n"))) > 0)
+ stop("Look at the log file and\ntry again with debug=TRUE and figure out what went wrong within Bugs.")
+ }
}
Modified: trunk/R2WinBUGS/R/bugs.sims.R
===================================================================
--- trunk/R2WinBUGS/R/bugs.sims.R 2006-12-29 16:10:15 UTC (rev 8)
+++ trunk/R2WinBUGS/R/bugs.sims.R 2007-04-07 18:04:11 UTC (rev 9)
@@ -1,10 +1,18 @@
"bugs.sims" <-
function (parameters.to.save, n.chains, n.iter, n.burnin, n.thin, DIC = TRUE){
-# Read the simulations from Bugs into R, format them, and monitor convergence
+## Read the simulations from Bugs into R, format them, and monitor convergence
sims.files <- paste ("coda", 1:n.chains, ".txt", sep="")
- index <- read.table ("codaIndex.txt", header=FALSE, sep="\t")
- parameter.names <- as.vector(index[,1])
- n.keep <- index[1,3] - index[1,2] + 1
+ index <- read.table("codaIndex.txt", header = FALSE, sep = "\t") # read in the names of the parameters and the indices of their samples
+ ## in Splus, read.table interprets the first row of the file as row names,
+ ## while in R it does not
+ if(is.R()) {
+ parameter.names <- as.vector(index[, 1])
+ n.keep <- index[1, 3] - index[1, 2] + 1
+ }
+ else {
+ parameter.names <- row.names(index)
+ n.keep <- index[1, 2] - index[1, 1] + 1
+ }
n.parameters <- length(parameter.names)
n.sims <- n.keep*n.chains
sims <- matrix( , n.sims, n.parameters)
@@ -50,7 +58,9 @@
rank.long <- unlist(long.short)
for (i in 1:n.chains){
- sims.i <- scan (sims.files[i], quiet=TRUE) [2*(1:(n.keep*n.parameters))]
+ if(is.R())
+ sims.i <- scan(sims.files[i], quiet = TRUE)[2 * (1:(n.keep * n.parameters))]
+ else sims.i <- scan(sims.files[i])[2 * (1:(n.keep * n.parameters))]
sims[(n.keep*(i-1)+1):(n.keep*i), ] <- sims.i
sims.array[,i,] <- sims.i
}
@@ -112,6 +122,8 @@
LOG <- bugs.log("log.txt")$DIC
if(any(is.na(LOG))){
deviance <- all$sims.array[, , dim(sims.array)[3], drop = FALSE]
+ if(!is.R())
+ dimnames(deviance) <- NULL
dim(deviance) <- dim(deviance)[1:2]
pD <- numeric(n.chains)
DIC <- numeric(n.chains)
@@ -128,3 +140,9 @@
}
return(all)
}
+
+if (!is.R()){
+ .subset <- function(x, index){
+ return (x[index])
+ }
+}
Modified: trunk/R2WinBUGS/R/bugs.update.settings.R
===================================================================
--- trunk/R2WinBUGS/R/bugs.update.settings.R 2006-12-29 16:10:15 UTC (rev 8)
+++ trunk/R2WinBUGS/R/bugs.update.settings.R 2007-04-07 18:04:11 UTC (rev 9)
@@ -1,20 +1,36 @@
"bugs.update.settings" <-
function (n.burnin, bugs.directory){
+ if (!is.R())
+ if (!require(rwBin)) stop ("The rwBin package is required")
+
char.burnin <- as.character(n.burnin - 1)
- file.copy(file.path(bugs.directory, "System/Rsrc/Registry.odc"),
+ if (is.R()){
+ file.copy(file.path(bugs.directory, "System/Rsrc/Registry.odc"),
file.path(bugs.directory, "System/Rsrc/Registry_Rsave.odc"),
- overwrite = TRUE)
+ overwrite = TRUE)
+ } else {
+ splus.file.copy(file.path(bugs.directory, "System/Rsrc/Registry.odc"),
+ file.path(bugs.directory, "System/Rsrc/Registry_Rsave.odc"),
+ overwrite = TRUE)
+ }
registry <- readBin(file.path(bugs.directory, "System/Rsrc/Registry.odc"),
"character", 400, size = 1, endian = "little")
locale <- Sys.getlocale("LC_CTYPE")
Sys.setlocale("LC_CTYPE", "C")
- info <- registry[regexpr("Int", registry, fixed = TRUE, useBytes = TRUE) > 0]
+ if (is.R())
+ info <- registry[regexpr("Int", registry, fixed = TRUE, useBytes = TRUE) > 0]
+ else
+ info <- registry[regexpr("Int", registry, fixed = TRUE) > 0]
while(regexpr("\r", info) > 0){
newline <- regexpr("\r", info)
info <- substring(info, newline + 1)
line <- substring(info, 1, regexpr("\r", info) - 1)
if(regexpr("AdaptivePhase", line) > 0){
- numpos <- regexpr("Int", line, fixed = TRUE, useBytes = TRUE) + 4
+ if (is.R())
+ numpos <- regexpr("Int", line, fixed = TRUE, useBytes = TRUE) + 4
+ else
+ numpos <- regexpr("Int", line, fixed = TRUE) + 4
+
num <- substring(line, numpos)
if (as.numeric(num) > n.burnin){
blanks <- rep(" ", nchar(num, type = "chars") - nchar(char.burnin, type = "chars"))
@@ -28,3 +44,21 @@
writeBin (registry,
file.path(bugs.directory, "System/Rsrc/Registry.odc"), endian = "little")
}
+
+if (!is.R()){
+
+"splus.file.copy"<-
+function(from, to, overwrite = FALSE)
+{
+ require(rwBin)
+ if(!file.exists(from))
+ stop("File: ", from, " does not exist")
+ if(!overwrite && file.exists(to))
+ stop("File: ", to, " already exists and overwrite is FALSE")
+ n <- file.info(from)$size
+ z <- writeBin(readBin(from, what = "integer", size = 1, n = n), to,
+ size = 1)
+ invisible(z)
+}
+
+} #ends if (!is.R())
Modified: trunk/R2WinBUGS/R/conv.par.R
===================================================================
--- trunk/R2WinBUGS/R/conv.par.R 2006-12-29 16:10:15 UTC (rev 8)
+++ trunk/R2WinBUGS/R/conv.par.R 2007-04-07 18:04:11 UTC (rev 9)
@@ -29,7 +29,7 @@
B <- n*var(xdot)
varW <- var(s2)/m
varB <- B^2 * 2/(m-1)
- covWB <- (n/m)*(cov(s2,xdot^2) - 2*muhat*cov(s2,xdot))
+ covWB <- (n/m)*(var(s2, xdot^2) - 2*muhat*var(s2, xdot))
sig2hat <- ((n-1)*W + B)/n
# Posterior interval post.range combines all uncertainties
Modified: trunk/R2WinBUGS/R/monitor.R
===================================================================
--- trunk/R2WinBUGS/R/monitor.R 2006-12-29 16:10:15 UTC (rev 8)
+++ trunk/R2WinBUGS/R/monitor.R 2007-04-07 18:04:11 UTC (rev 9)
@@ -30,6 +30,9 @@
confshrink = conv.p$confshrink, n.eff = conv.p$n.eff)
}
else if (trans[i]=="logit"){
+ if (!is.R()){
+ logit <- function (x) { log(x /(1- x)) }
+ }
conv.p <- conv.par(logit(ai), n.chains, Rupper.keep=Rupper.keep)
conv.p <- list(quantiles = invlogit(conv.p$quantiles),
confshrink = conv.p$confshrink, n.eff = conv.p$n.eff)
Modified: trunk/R2WinBUGS/R/openbugs.R
===================================================================
--- trunk/R2WinBUGS/R/openbugs.R 2006-12-29 16:10:15 UTC (rev 8)
+++ trunk/R2WinBUGS/R/openbugs.R 2007-04-07 18:04:11 UTC (rev 9)
@@ -1,3 +1,5 @@
+if (is.R()){
+
openbugs <- function(data, inits, parameters.to.save, model.file="model.txt",
n.chains = 3, n.iter = 2000, n.burnin = floor(n.iter/2),
n.thin = max(1, floor(n.chains *(n.iter - n.burnin)/1000)),
@@ -83,3 +85,5 @@
a.stem <- substr(a, 1, ifelse(bracket.pos>0, bracket.pos-1, nchar(a)))
return(a[order(match(a.stem, b))])
}
+
+}
Modified: trunk/R2WinBUGS/R/plot.bugs.R
===================================================================
--- trunk/R2WinBUGS/R/plot.bugs.R 2006-12-29 16:10:15 UTC (rev 8)
+++ trunk/R2WinBUGS/R/plot.bugs.R 2007-04-07 18:04:11 UTC (rev 9)
@@ -1,7 +1,11 @@
plot.bugs <- function (x, display.parallel = FALSE, ...){
mar.old <- par("mar")
pty.old <- par(pty = "m")
- layout(matrix(c(1,2),1,2))
+ if (is.R())
+ layout(matrix(c(1,2),1,2))
+ else
+ par(mfrow = c(1,2))
+
bugs.plot.summary (x, ...)
bugs.plot.inferences (x, display.parallel, ...)
header <- ""
@@ -12,5 +16,42 @@
header <- paste(header, x$n.chains, " chains, each with ",
x$n.iter, " iterations (first ", x$n.burnin, " discarded)", sep = "")
mtext(header, outer = TRUE, line = -1, cex = 0.7)
- par(pty = pty.old[[1]], mar = mar.old)
+ if (is.R()) par(pty = pty.old[[1]], mar = mar.old)
+ else invisible(par(pty = pty.old[[1]], mar = mar.old))
}
+
+if (!is.R()) {
+
+strwidth <-function(s, units = c("user", "inches", "figure"), cex = NULL) {
+ s<-as.character(s)
+ if (!missing(cex)) {
+ oldcex <- par(cex=cex)
+ on.exit(par(oldcex))
+ }
+ units <- match.arg(units)
+ if (units == "user") {
+ nchar(s) * par("cxy")[1]
+ } else if (units == "inches") {
+ nchar(s) * par("cin")[1]
+ } else if (units == "figure") {
+ nchar(s) * par("cin")[1] / par("fin")[1]
+ }
+}
+
+strheight <- function(s, units = "user", cex = NULL) {
+ s<-as.character(s)
+ if (!missing(cex)) {
+ oldcex <- par(cex=cex)
+ on.exit(par(oldcex))
+ }
+ units <- match.arg(units)
+ if (units == "user") {
+ par("cxy")[2]
+ } else if (units == "inches") {
+ par("cin")[2]
+ } else if (units == "figure") {
+ par("cin")[2] / par("fin")[2]
+ }
+}
+
+} #ends if (!is.R())
Modified: trunk/R2WinBUGS/R/wineutils.R
===================================================================
--- trunk/R2WinBUGS/R/wineutils.R 2006-12-29 16:10:15 UTC (rev 8)
+++ trunk/R2WinBUGS/R/wineutils.R 2007-04-07 18:04:11 UTC (rev 9)
@@ -1,5 +1,7 @@
## from Jun Yan's rbugs package, extended
+if (is.R()){
+
## get drive mapping table from ~/.wine/config
winedriveMap <- function(config="~/.wine/config") {
if (!file.exists(config)) return (NULL);
@@ -48,10 +50,16 @@
else x
}
+} # end if (is.R())
+
native2win <- function(x, useWINE=.Platform$OS.type != "windows", newWINE=TRUE) { # native -> win
- if (useWINE && !newWINE) return(winedriveRTr(x))
- if (useWINE && newWINE) {
- x <- system(paste(WINEPATH, "-w", x), intern = TRUE)
- return(gsub("\\\\", "/", x)) ## under wine BUGS cannot use \ or \\
- } else x
+ if(is.R()){
+ if (useWINE && !newWINE) return(winedriveRTr(x))
+ if (useWINE && newWINE) {
+ x <- system(paste(WINEPATH, "-w", x), intern = TRUE)
+ return(gsub("\\\\", "/", x)) ## under wine BUGS cannot use \ or \\
+ } else x
+ } else { #S-PLUS
+ gsub("\\\\", "/", x)
+ }
}
Modified: trunk/R2WinBUGS/R/write.model.R
===================================================================
--- trunk/R2WinBUGS/R/write.model.R 2006-12-29 16:10:15 UTC (rev 8)
+++ trunk/R2WinBUGS/R/write.model.R 2007-04-07 18:04:11 UTC (rev 9)
@@ -1,7 +1,14 @@
write.model <- function(model, con = "model.bug")
{
- model.text <- attr(model, "source")
- model.text <- sub("^\\s*function\\s*\\(\\s*\\)", "model", model.text)
+ if (is.R()){
+ model.text <- attr(model, "source")
+ model.text <- sub("^\\s*function\\s*\\(\\s*\\)", "model", model.text)
+ } else {
+ ## In S-PLUS the source code of a function can be obtained with
+ ## as.character(function_name). This omits the "function_name <- function()" piece
+ model.text <- as.character(model)
+ model.text <- paste("model", model.text)
+ }
model.text <- gsub("%_%", "", model.text)
writeLines(model.text, con = con)
}
Modified: trunk/R2WinBUGS/man/bugs.Rd
===================================================================
--- trunk/R2WinBUGS/man/bugs.Rd 2006-12-29 16:10:15 UTC (rev 8)
+++ trunk/R2WinBUGS/man/bugs.Rd 2007-04-07 18:04:11 UTC (rev 9)
@@ -1,9 +1,9 @@
\name{bugs}
\alias{bugs}
-\title{Run WinBUGS and OpenBUGS from R}
+\title{Run WinBUGS and OpenBUGS from R or S-PLUS}
\description{The \code{bugs} function takes data and starting values as input.
It automatically writes a WinBUGS script, calls the model,
-and saves the simulations for easy access in R.}
+and saves the simulations for easy access in R or S-PLUS.}
\usage{
bugs(data, inits, parameters.to.save, model.file = "model.bug",
n.chains = 3, n.iter = 2000, n.burnin = floor(n.iter/2),
@@ -57,7 +57,8 @@
through function \code{\link{read.bugs}}. (not used if \code{program = "openbugs"})}
\item{bugs.directory}{directory that contains the WinBUGS executable}
\item{program}{the program to use, either \code{winbugs}/\code{WinBugs} or \code{openbugs}/\code{OpenBugs},
- the latter makes use of function \code{\link{openbugs}} and requires the CRAN package \pkg{BRugs}.}
+ the latter makes use of function \code{\link{openbugs}} and requires the CRAN package \pkg{BRugs}.
+ The \code{openbugs}/\code{OpenBugs} choice is not available in S-PLUS.}
\item{working.directory}{sets working directory during execution of this function;
WinBUGS' in- and output will be stored in this directory;
if \code{NULL}, the current working directory is chosen.}
@@ -69,7 +70,8 @@
\item{useWINE}{logical; attempt to use the WINE emulator to run WinBUGS,
defaults to \code{TRUE} on Windows, and \code{FALSE} otherwise.
If WINE is used, the arguments \code{bugs.directory} and \code{working.directory} must be given in form of Linux paths
- rather than Windows paths (if not \code{NULL}).}
+ rather than Windows paths (if not \code{NULL}).
+ The \code{useWINE = TRUE} option is not available in S-PLUS.}
\item{WINE}{character; name of WINE binary file}
\item{newWINE}{Set this one to \code{TRUE} for new versions of WINE.}
\item{WINEPATH}{Path the WINE, it is tried hard to get the information automatically if not given.}
@@ -78,12 +80,12 @@
To run:
\enumerate{
\item Write a WinBUGS model in a ASCII file.
-\item Go into R.
+\item Go into R / S-PLUS.
\item Prepare the inputs to the \code{bugs} function and run it (see Example).
-\item A WinBUGS window will pop up amd R will freeze up. The model
+\item A WinBUGS window will pop up and R / S-PLUS will freeze up. The model
will now run in WinBUGS. It might take awhile. You will see
things happening in the Log window within WinBUGS. When WinBugs
- is done, its window will close and R will work again.
+ is done, its window will close and R / S-PLUS will work again.
\item If an error message appears, re-run with \code{debug = TRUE}.
}}
\value{
Modified: trunk/R2WinBUGS/man/bugs.log.Rd
===================================================================
--- trunk/R2WinBUGS/man/bugs.log.Rd 2006-12-29 16:10:15 UTC (rev 8)
+++ trunk/R2WinBUGS/man/bugs.log.Rd 2007-04-07 18:04:11 UTC (rev 9)
@@ -17,7 +17,7 @@
}
\details{
In later releases of R2WiNBUGS, this function is considered to read the relevant data from the log file rather than
-analysing and calculating the relevant data in R again.
+analysing and calculating the relevant data in R / S-PLUS again.
}
\seealso{The main function that generates the log file is \code{\link{bugs}}.}
\keyword{IO}
Modified: trunk/R2WinBUGS/man/bugs.run.Rd
===================================================================
--- trunk/R2WinBUGS/man/bugs.run.Rd 2006-12-29 16:10:15 UTC (rev 8)
+++ trunk/R2WinBUGS/man/bugs.run.Rd 2007-04-07 18:04:11 UTC (rev 9)
@@ -13,7 +13,8 @@
\item{bugs.directory}{directory that contains the WinBUGS executable}
\item{WINE}{name of WINE binary, for Windows emulation}
\item{useWINE}{logical; attempt to use the WINE emulator to run WinBUGS,
- defaults to \code{TRUE} on Windows, and \code{FALSE} otherwise.}
+ defaults to \code{TRUE} on Windows, and \code{FALSE} otherwise.
+ The \code{useWINE = TRUE} option is not available in S-PLUS.}
\item{newWINE}{set this one to \code{TRUE} for new versions of WINE.}
}
\value{
Modified: trunk/R2WinBUGS/man/bugs.script.Rd
===================================================================
--- trunk/R2WinBUGS/man/bugs.script.Rd 2006-12-29 16:10:15 UTC (rev 8)
+++ trunk/R2WinBUGS/man/bugs.script.Rd 2007-04-07 18:04:11 UTC (rev 9)
@@ -20,7 +20,8 @@
or have to be generated by WinBUGS}
\item{bin}{number of iterations between saving of results}
\item{DIC}{logical; if \code{TRUE}, compute deviance, pD, and DIC automatically in WinBUGS}
- \item{useWINE}{logical; use WINE to run WinBUGS under Linux}
+ \item{useWINE}{logical; use WINE to run WinBUGS under Linux.
+ The \code{useWINE = TRUE} option is not available in S-PLUS.}
\item{newWINE}{set this one to \code{TRUE} for new versions of WINE.}
\item{WINEPATH}{Path the WINE, \code{bugs} tries hard to get the information automatically and
pass it to this function, if not given.}
Modified: trunk/R2WinBUGS/man/bugs.sims.Rd
===================================================================
--- trunk/R2WinBUGS/man/bugs.sims.Rd 2006-12-29 16:10:15 UTC (rev 8)
+++ trunk/R2WinBUGS/man/bugs.sims.Rd 2007-04-07 18:04:11 UTC (rev 9)
@@ -2,7 +2,7 @@
\alias{bugs.sims}
\title{WinBUGS output reader - intended for internal use only}
\description{
-Reads simulations from WinBUGS into R, formats them, monitors convergence,
+Reads simulations from WinBUGS into R/ S-PLUS, formats them, monitors convergence,
performs convergence checks, and computes medians and quantiles. Intended for internal use only.}
\usage{
bugs.sims(parameters.to.save, n.chains, n.iter, n.burnin, n.thin,
Modified: trunk/R2WinBUGS/man/openbugs.Rd
===================================================================
--- trunk/R2WinBUGS/man/openbugs.Rd 2006-12-29 16:10:15 UTC (rev 8)
+++ trunk/R2WinBUGS/man/openbugs.Rd 2007-04-07 18:04:11 UTC (rev 9)
@@ -2,7 +2,8 @@
\alias{openbugs}
\title{Wrapper to run OpenBUGS}
\description{The \code{openbugs} function takes data and starting values as input.
-It automatically calls the package \pkg{BRugs} and runs something similar to \code{\link[BRugs]{BRugsFit}}.}
+It automatically calls the package \pkg{BRugs} and runs something similar to \code{\link[BRugs]{BRugsFit}}.
+Not available in S-PLUS.}
\usage{
openbugs(data, inits, parameters.to.save,
model.file = "model.txt", n.chains = 3, n.iter = 2000,
Modified: trunk/R2WinBUGS/man/write.model.Rd
===================================================================
--- trunk/R2WinBUGS/man/write.model.Rd 2006-12-29 16:10:15 UTC (rev 8)
+++ trunk/R2WinBUGS/man/write.model.Rd 2007-04-07 18:04:11 UTC (rev 9)
@@ -1,12 +1,12 @@
\name{write.model}
\alias{write.model}
\title{Creating a WinBUGS model file}
-\description{Convert R function to a WinBUGS model file}
+\description{Convert R / S-PLUS function to a WinBUGS model file}
\usage{
write.model(model, con = "model.bug")
}
\arguments{
- \item{model}{R function containg the BUGS model in the BUGS model language, for minor differences see Section Details.}
+ \item{model}{R / S-PLUS function containing the BUGS model in the BUGS model language, for minor differences see Section Details.}
\item{con}{passed to \code{link{writeLines}} which actually writes the model file}
}
\value{
@@ -18,7 +18,7 @@
As a difference, BUGS syntax allows truncation specification like this:
\code{dnorm(...) I(...)}
-but this is illegal in R. To overcome this incompatibility, use \code{\%_\%} before \code{I(...)}:
+but this is illegal in R / S-PLUS. To overcome this incompatibility, use \code{\%_\%} before \code{I(...)}:
\code{dnorm(...) \%_\% I(...)}.
The dummy operator \code{\%_\%} will be removed before the BUGS code is saved.
}
@@ -36,8 +36,14 @@
sigma.theta ~ dunif (0, 1000)
}
-## some temporary filename:
-filename <- file.path(tempdir(), "schoolsmodel.bug")
+if (is.R()){ # for R
+ ## some temporary filename:
+ filename <- file.path(tempdir(), "schoolsmodel.bug")
+} else{ # for S-PLUS
+ ## put the file in the working directory:
+ filename <- "schoolsmodel.bug"
+}
+
## write model file:
write.model(schoolsmodel, filename)
## and let's take a look:
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: Gregor G. <gre...@bf...> - 2007-04-08 15:02:31
|
li...@us... wrote: > Revision: 9 > http://svn.sourceforge.net/bugs-r/?rev=9&view=rev > Author: ligges > Date: 2007-04-07 11:04:11 -0700 (Sat, 07 Apr 2007) > > Log Message: > ----------- > R2WinBUGS has been ported to S-PLUS by Insightful Corp. > Special thanks to Dawn Woodard! Great. It is nice to see some development going on. Unfortunately, I did not have any time since setting up SF project to work on R2BUGS stuff. I hope this will change in near future. -- Lep pozdrav / With regards, Gregor Gorjanc ---------------------------------------------------------------------- University of Ljubljana PhD student Biotechnical Faculty www: http://www.bfro.uni-lj.si/MR/ggorjan Zootechnical Department blog: http://ggorjan.blogspot.com Groblje 3 mail: gregor.gorjanc <at> bfro.uni-lj.si SI-1230 Domzale fax: +386 (0)1 72 17 888 Slovenia, Europe tel: +386 (0)1 72 17 861 ---------------------------------------------------------------------- |
|
From: <li...@us...> - 2007-05-20 15:45:37
|
Revision: 20
http://svn.sourceforge.net/bugs-r/?rev=20&view=rev
Author: ligges
Date: 2007-05-20 08:45:39 -0700 (Sun, 20 May 2007)
Log Message:
-----------
Reverted some former changes:
- Added some tricks (defining no-op-functions) to make codetools calm.
- we do depend on coda now and we are importing parts of its Namespace now, in order to make codetools calm (S-PLUS does not like the "::" operator).
Modified Paths:
--------------
trunk/R2WinBUGS/Changes
trunk/R2WinBUGS/DESCRIPTION
trunk/R2WinBUGS/NAMESPACE
trunk/R2WinBUGS/R/attach.all.R
trunk/R2WinBUGS/R/bugs.data.R
trunk/R2WinBUGS/R/read.bugs.R
Modified: trunk/R2WinBUGS/Changes
===================================================================
--- trunk/R2WinBUGS/Changes 2007-05-20 15:42:40 UTC (rev 19)
+++ trunk/R2WinBUGS/Changes 2007-05-20 15:45:39 UTC (rev 20)
@@ -74,3 +74,7 @@
- Ported to S-PLUS by Insightful Corp.
- some fixes for codetools checks
+Update 2.1-4 (20 May 2007):
+- Depending on coda now (Namespace issues)
+- some more fixes for codetools checks
+- Vignette has been updated
Modified: trunk/R2WinBUGS/DESCRIPTION
===================================================================
--- trunk/R2WinBUGS/DESCRIPTION 2007-05-20 15:42:40 UTC (rev 19)
+++ trunk/R2WinBUGS/DESCRIPTION 2007-05-20 15:45:39 UTC (rev 20)
@@ -1,7 +1,7 @@
Package: R2WinBUGS
Title: Running WinBUGS and OpenBUGS from R / S-PLUS
-Date: 2007-05-13
-Version: 2.1-3
+Date: 2007-05-20
+Version: 2.1-4
Author: originally written by Andrew Gelman <ge...@st...>;
changes and packaged by Sibylle Sturtz <st...@st...>
and Uwe Ligges <li...@st...>.
@@ -13,8 +13,8 @@
convergence in a table and graph, and save the simulations in arrays for easy access
in R / S-PLUS. In S-PLUS, the openbugs functionality and the windows emulation
functionality is not yet available.
-Depends: R (>= 2.4.0)
-Suggests: coda (>= 0.9-0), BRugs (>= 0.3-0)
+Depends: R (>= 2.4.0), coda (>= 0.9-0)
+Suggests: BRugs (>= 0.3-0)
SystemRequirements: WinBUGS 1.4
URL: http://www.stat.columbia.edu/~gelman/bugsR/
Maintainer: Sibylle Sturtz <st...@st...>
Modified: trunk/R2WinBUGS/NAMESPACE
===================================================================
--- trunk/R2WinBUGS/NAMESPACE 2007-05-20 15:42:40 UTC (rev 19)
+++ trunk/R2WinBUGS/NAMESPACE 2007-05-20 15:45:39 UTC (rev 20)
@@ -1,3 +1,5 @@
+importFrom(coda, mcmc.list, read.coda)
+
export(bugs,
attach.all,
detach.all,
@@ -12,3 +14,4 @@
S3method(print, bugs)
S3method(plot, bugs)
+
Modified: trunk/R2WinBUGS/R/attach.all.R
===================================================================
--- trunk/R2WinBUGS/R/attach.all.R 2007-05-20 15:42:40 UTC (rev 19)
+++ trunk/R2WinBUGS/R/attach.all.R 2007-05-20 15:45:39 UTC (rev 20)
@@ -18,6 +18,9 @@
if(overwrite) remove(list=rem, envir=.GlobalEnv)
attach(x, name=name)
} else {
+ ## next line is a dirty trick for R'd codetools check in R-2.5.0
+ ## (should be removed after codetoold have been improved):
+ attach.default <- get("attach.default")
attach.default(x, name = name)
}
}
Modified: trunk/R2WinBUGS/R/bugs.data.R
===================================================================
--- trunk/R2WinBUGS/R/bugs.data.R 2007-05-20 15:42:40 UTC (rev 19)
+++ trunk/R2WinBUGS/R/bugs.data.R 2007-05-20 15:45:39 UTC (rev 20)
@@ -24,6 +24,15 @@
}
+if(is.R()){
+ ## need some fake functions for codetools
+ "writeDatafileS4" <- toSingleS4 <- function(...)
+ stop("This function is not intended to be called in R!")
+} else {
+
+### The rest of this file is for S-PLUS only...
+
+
"writeDatafileS4" <-
#
# Writes to file "towhere" text defining a list containing "DATA" in a form compatable with WinBUGS.
@@ -224,3 +233,5 @@
}
x
}
+
+}
Modified: trunk/R2WinBUGS/R/read.bugs.R
===================================================================
--- trunk/R2WinBUGS/R/read.bugs.R 2007-05-20 15:42:40 UTC (rev 19)
+++ trunk/R2WinBUGS/R/read.bugs.R 2007-05-20 15:45:39 UTC (rev 20)
@@ -1,13 +1,7 @@
read.bugs <- function(codafiles, ...){
- if(!require(coda))
+ if(!is.R() && !require("coda"))
stop("package 'coda' is required to use this function")
- if (is.R()){
- coda::mcmc.list(lapply(codafiles, coda::read.coda,
- index.file = file.path(dirname(codafiles[1]), "codaIndex.txt"),
- ...))
- }else{
- mcmc.list(lapply(codafiles, read.coda,
- index.file = file.path(dirname(codafiles[1]), "codaIndex.txt"),
- ...))
- }
+ mcmc.list(lapply(codafiles, read.coda,
+ index.file = file.path(dirname(codafiles[1]), "codaIndex.txt"),
+ ...))
}
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <gg...@us...> - 2007-06-13 00:59:07
|
Revision: 30
http://svn.sourceforge.net/bugs-r/?rev=30&view=rev
Author: ggorjan
Date: 2007-06-12 17:59:08 -0700 (Tue, 12 Jun 2007)
Log Message:
-----------
There was a bug related to use of OpenBUGS and as.bugs.array due to using
DIC as a placholder for DIC stats and not a TRUE/FALSE - now using isDIC
more consistently as well as DICbyR to distinguish between BUGS and R
calculation of pD. I have also made some cosmetic changes in help as well
as code files.
Modified Paths:
--------------
trunk/R2WinBUGS/Changes
trunk/R2WinBUGS/R/as.bugs.array.R
trunk/R2WinBUGS/R/bugs.R
trunk/R2WinBUGS/R/bugs.plot.summary.R
trunk/R2WinBUGS/R/bugs.sims.R
trunk/R2WinBUGS/R/openbugs.R
trunk/R2WinBUGS/R/print.bugs.R
trunk/R2WinBUGS/man/as.bugs.array.Rd
trunk/R2WinBUGS/man/attach.all.Rd
trunk/R2WinBUGS/man/bugs.Rd
trunk/R2WinBUGS/man/bugs.data.Rd
trunk/R2WinBUGS/man/bugs.inits.Rd
trunk/R2WinBUGS/man/bugs.log.Rd
trunk/R2WinBUGS/man/bugs.plot.Rd
trunk/R2WinBUGS/man/bugs.run.Rd
trunk/R2WinBUGS/man/bugs.script.Rd
trunk/R2WinBUGS/man/bugs.sims.Rd
trunk/R2WinBUGS/man/bugs.update.settings.Rd
trunk/R2WinBUGS/man/decode.parameter.name.Rd
trunk/R2WinBUGS/man/monitor.Rd
trunk/R2WinBUGS/man/openbugs.Rd
trunk/R2WinBUGS/man/plot.bugs.Rd
trunk/R2WinBUGS/man/print.bugs.Rd
trunk/R2WinBUGS/man/read.bugs.Rd
trunk/R2WinBUGS/man/write.datafile.Rd
trunk/R2WinBUGS/man/write.model.Rd
Modified: trunk/R2WinBUGS/Changes
===================================================================
--- trunk/R2WinBUGS/Changes 2007-06-12 10:10:26 UTC (rev 29)
+++ trunk/R2WinBUGS/Changes 2007-06-13 00:59:08 UTC (rev 30)
@@ -1,229 +1,230 @@
-Changes to R2WinBUGS:
-=====================
-
-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
-- some internal fixes related to is.null(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:
- 1. Fixed "bugs.data.inits" function so you can use data that have the
- same names as R functions.
- 2. Changed T and F to TRUE and FALSE everywhere in case the variables
- T and F are used as data in the main program
- 3. 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.
- 4. 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:
- 1. The "attach.all" function (no longer called "attach2") overwrites
- so that all components of a list or data frame get attached.
- 2. Program now looks in the directory /winbug~1/ rather than /winbug~2/
- 3. Graphics parameters for margins are returned to their original state
- at the end of the program.
- 4. Added "digits.summary" option to the numerical display.
- 5. 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:
- 1. 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!
- 2. 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).
- 3. 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:
- 1. 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.)
- 2. 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:
- 1. Fix display.parallel=T option by adding min.width so that very
- intervals are still visible.
- 2. 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:
- 1. Approximate "effective sample size" n.eff given for each parameter.
- 2. More explanatory material displayed.
- 3. Use bringToTop() to automatically bring up the graphics window.
-Update 4 Feb 2003:
- 1. 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.)
- 2. 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:
- 1. Fix of bug that occurred with uppercase and lowercase variable names
- 2. Set default for n.thin so that no more than about 500 iterations
- will be saved from each sequence
- 3. 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:
- 1. Automatic fixing of adaptive phases. Now you no longer need to run
- for thousands of iterations when slice or Metropolis sampling is used.
- 2. Various minor fixes
-Update 10 Dec 2002:
- 1. Cool graphical display of convergence and inferences!
- 2. New "attach2" function that overwrites so that all components of
- the list are attached
-Update 29 Nov 2002:
- 1. Fix of bug in 24 Nov update.
- 2. Fix of bug in 16 Nov update.
- 3. 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:
- 1. Parameters saved in order of the "parameters.to.save" vector
- (not alphabetical order).
- 2. Output saved in both matrix and list form.
- 3. 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
+Changes to R2WinBUGS:
+=====================
+
+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:
+ 1. Fixed "bugs.data.inits" function so you can use data that have the
+ same names as R functions.
+ 2. Changed T and F to TRUE and FALSE everywhere in case the variables
+ T and F are used as data in the main program
+ 3. 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.
+ 4. 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:
+ 1. The "attach.all" function (no longer called "attach2") overwrites
+ so that all components of a list or data frame get attached.
+ 2. Program now looks in the directory /winbug~1/ rather than /winbug~2/
+ 3. Graphics parameters for margins are returned to their original state
+ at the end of the program.
+ 4. Added "digits.summary" option to the numerical display.
+ 5. 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:
+ 1. 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!
+ 2. 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).
+ 3. 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:
+ 1. 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.)
+ 2. 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:
+ 1. Fix display.parallel=T option by adding min.width so that very
+ intervals are still visible.
+ 2. 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:
+ 1. Approximate "effective sample size" n.eff given for each parameter.
+ 2. More explanatory material displayed.
+ 3. Use bringToTop() to automatically bring up the graphics window.
+Update 4 Feb 2003:
+ 1. 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.)
+ 2. 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:
+ 1. Fix of bug that occurred with uppercase and lowercase variable names
+ 2. Set default for n.thin so that no more than about 500 iterations
+ will be saved from each sequence
+ 3. 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:
+ 1. Automatic fixing of adaptive phases. Now you no longer need to run
+ for thousands of iterations when slice or Metropolis sampling is used.
+ 2. Various minor fixes
+Update 10 Dec 2002:
+ 1. Cool graphical display of convergence and inferences!
+ 2. New "attach2" function that overwrites so that all components of
+ the list are attached
+Update 29 Nov 2002:
+ 1. Fix of bug in 24 Nov update.
+ 2. Fix of bug in 16 Nov update.
+ 3. 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:
+ 1. Parameters saved in order of the "parameters.to.save" vector
+ (not alphabetical order).
+ 2. Output saved in both matrix and list form.
+ 3. 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
Modified: trunk/R2WinBUGS/R/as.bugs.array.R
===================================================================
--- trunk/R2WinBUGS/R/as.bugs.array.R 2007-06-12 10:10:26 UTC (rev 29)
+++ trunk/R2WinBUGS/R/as.bugs.array.R 2007-06-13 00:59:08 UTC (rev 30)
@@ -1,10 +1,12 @@
-as.bugs.array <- function(sims.array, model.file=NULL, program=NULL, DIC=FALSE, n.iter=NULL, n.burnin=0, n.thin=1)
+as.bugs.array <- function(sims.array, model.file=NULL, program=NULL,
+ DIC=FALSE, DICOutput=NULL,
+ n.iter=NULL, n.burnin=0, n.thin=1)
{
- # Jouni Kerman's function to convert a 3-way array to a Bugs object
- #
- # 'sims.array' is supposed to be a 3-way array with
- # n.sims*n.chains*n.parameters simulations, and
- # the 3rd component of dimnames(x) should have the parameter names.
+ ## Jouni Kerman's function to convert a 3-way array to a Bugs object
+ ##
+ ## 'sims.array' is supposed to be a 3-way array with
+ ## n.sims*n.chains*n.parameters simulations, and
+ ## the 3rd component of dimnames(x) should have the parameter names.
d <- dim(sims.array)
n.keep <- d[1]
n.chains <- d[2]
@@ -30,7 +32,7 @@
n.roots <- length(parameters.to.save)
left.bracket.short <- as.vector(regexpr("[[]", parameters.to.save))
right.bracket.short <- as.vector(regexpr("[]]", parameters.to.save))
- root.short <- ifelse(left.bracket.short == -1, parameters.to.save,
+ root.short <- ifelse(left.bracket.short == -1, parameters.to.save,
substring(parameters.to.save, 1, left.bracket.short - 1))
dimension.short <- rep(0, n.roots)
indexes.short <- vector(n.roots, mode = "list")
@@ -51,7 +53,7 @@
}
length.short[j] <- prod(n.indexes.short[[j]])
if (length(long.short[[j]]) != length.short[j]){
- stop(paste("error in parameter", root.short[[j]],
+ stop(paste("error in parameter", root.short[[j]],
"in parameters.to.save"))
}
indexes.short[[j]] <- as.list(numeric(length.short[j]))
@@ -71,11 +73,7 @@
summary <- monitor(sims.array, n.chains, keep.all = TRUE)
last.values <- as.list(numeric(n.chains))
for (i in 1:n.chains) {
- if (is.R()) {
- n.roots.0 <- if(!is.null(DIC)) n.roots - 1 else n.roots
- } else {
- n.roots.0 <- if(DIC) n.roots - 1 else n.roots
- }
+ n.roots.0 <- if(DIC) n.roots - 1 else n.roots
last.values[[i]] <- as.list(numeric(n.roots.0))
names(last.values[[i]]) <- root.short[1:n.roots.0]
for (j in 1:n.roots.0) {
@@ -90,7 +88,7 @@
}
}
sims <- sims[sample(n.sims), ]
- sims.list <- summary.mean <- summary.sd <- summary.median <- vector(n.roots,
+ sims.list <- summary.mean <- summary.sd <- summary.median <- vector(n.roots,
mode = "list")
names(sims.list) <- names(summary.mean) <- names(summary.sd) <- names(summary.median) <- root.short
for (j in 1:n.roots) {
@@ -102,31 +100,28 @@
}
else {
temp2 <- dimension.short[j]:1
- sims.list[[j]] <- aperm(array(sims[, long.short[[j]]],
+ sims.list[[j]] <- aperm(array(sims[, long.short[[j]]],
c(n.sims, rev(n.indexes.short[[j]]))), c(1, (dimension.short[j]+1):2))
- summary.mean[[j]] <- aperm(array(summary[long.short[[j]],
+ summary.mean[[j]] <- aperm(array(summary[long.short[[j]],
"mean"], rev(n.indexes.short[[j]])), temp2)
- summary.sd[[j]] <- aperm(array(summary[long.short[[j]],
+ summary.sd[[j]] <- aperm(array(summary[long.short[[j]],
"sd"], rev(n.indexes.short[[j]])), temp2)
- summary.median[[j]] <- aperm(array(summary[long.short[[j]],
+ summary.median[[j]] <- aperm(array(summary[long.short[[j]],
"50%"], rev(n.indexes.short[[j]])), temp2)
}
}
summary <- summary[rank.long, ]
- if (is.R())
- is.DIC = !is.null(DIC)
- else
- is.DIC = DIC
-
- all <- list(n.chains = n.chains, n.iter = n.iter, n.burnin = n.burnin,
+
+ all <- list(n.chains = n.chains, n.iter = n.iter, n.burnin = n.burnin,
n.thin = n.thin, n.keep = n.keep, n.sims = n.sims,
- sims.array = sims.array[,,rank.long,drop = FALSE], sims.list = sims.list,
- sims.matrix = sims[, rank.long], summary = summary, mean = summary.mean,
- sd = summary.sd, median = summary.median, root.short = root.short,
- long.short = long.short, dimension.short = dimension.short,
+ sims.array = sims.array[,,rank.long,drop = FALSE], sims.list = sims.list,
+ sims.matrix = sims[, rank.long], summary = summary, mean = summary.mean,
+ sd = summary.sd, median = summary.median, root.short = root.short,
+ long.short = long.short, dimension.short = dimension.short,
indexes.short = indexes.short, last.values = last.values, program=program,
- model.file=model.file, is.DIC=is.DIC, DIC=DIC)
- if(sum(DIC)) {
+ model.file=model.file)
+
+ if(DIC && is.null(DICOutput)) { ## calculate DIC from deviance
deviance <- all$sims.array[, , dim(sims.array)[3], drop = FALSE]
dim(deviance) <- dim(deviance)[1:2]
pD <- numeric(n.chains)
@@ -135,8 +130,15 @@
pD[i] <- var(deviance[, i])/2
DIC[i] <- mean(deviance[, i]) + pD[i]
}
- all <- c(all, list(pD = mean(pD), DIC = mean(DIC)))
+ all <- c(all, list(isDIC=TRUE, DICbyR=TRUE,
+ pD=mean(pD), DIC=mean(DIC)))
+ } else if(DIC && !is.null(DICOutput)) { ## use DIC from BUGS
+ all <- c(all, list(isDIC=TRUE, DICbyR=FALSE,
+ pD=DICOutput[nrow(DICOutput),4],
+ DIC=DICOutput[nrow(DICOutput),3]))
+ } else {
+ all <- c(all, isDIC=FALSE)
}
class(all) <- "bugs"
- return(all)
+ all
}
Modified: trunk/R2WinBUGS/R/bugs.R
===================================================================
--- trunk/R2WinBUGS/R/bugs.R 2007-06-12 10:10:26 UTC (rev 29)
+++ trunk/R2WinBUGS/R/bugs.R 2007-06-13 00:59:08 UTC (rev 30)
@@ -5,18 +5,18 @@
bin=(n.iter - n.burnin) / n.thin,
debug=FALSE, DIC=TRUE, digits=5, codaPkg=FALSE,
bugs.directory="c:/Program Files/WinBUGS14/",
- program=c("winbugs", "openbugs", "WinBugs", "OpenBugs"),
+ program=c("WinBUGS", "OpenBUGS", "winbugs", "openbugs"),
working.directory=NULL,
clearWD=FALSE, useWINE=.Platform$OS.type != "windows", WINE=Sys.getenv("WINE"),
newWINE=FALSE, WINEPATH=NULL)
{
program <- match.arg(program)
- if(program %in% c("openbugs", "OpenBugs")) {
+ if(program %in% c("openbugs", "OpenBUGS", "OpenBugs")) {
if(is.R()) {
## If OpenBUGS, we only call openbugs() and exit...
return(openbugs(data, inits, parameters.to.save, model.file,
- n.chains, n.iter, n.burnin, n.thin, DIC, bugs.directory,
- working.directory, digits))
+ n.chains, n.iter, n.burnin, n.thin, DIC=DIC,
+ bugs.directory, working.directory, digits))
} else {
stop ("OpenBUGS is not yet available in S-PLUS")
}
@@ -72,7 +72,7 @@
return(file.path(getwd(), paste("coda", 1:n.chains, ".txt", sep="")))
sims <- c(bugs.sims(parameters.to.save, n.chains, n.iter, n.burnin,
n.thin, DIC),
- model.file=model.file, is.DIC=DIC, program=program)
+ model.file=model.file, program=program)
if(clearWD) {
file.remove(c("data.txt", "log.odc", "log.txt", "codaIndex.txt",
paste("inits", 1:n.chains, ".txt", sep=""),
Modified: trunk/R2WinBUGS/R/bugs.plot.summary.R
===================================================================
--- trunk/R2WinBUGS/R/bugs.plot.summary.R 2007-06-12 10:10:26 UTC (rev 29)
+++ trunk/R2WinBUGS/R/bugs.plot.summary.R 2007-06-13 00:59:08 UTC (rev 30)
@@ -1,6 +1,6 @@
"bugs.plot.summary" <-
function (sims, ...){
- DIC <- sims$is.DIC
+ isDIC <- sims$isDIC
if (.Device=="windows" ||
(.Device=="null device" && options("device")=="windows")){
@@ -23,7 +23,7 @@
n.parameters <- nrow(summ)
J0 <- unlist(lapply(sims$long.short, length))
- if (DIC) J0 <- J0[1:(length(J0)-1)] # don't display deviance summaries
+ if (isDIC) J0 <- J0[1:(length(J0)-1)] # don't display deviance summaries
J <- J0
total <- ceiling(sum(J+.5))
while ((total > max.length) && max(J)>1){### vielleicht optimieren ...
@@ -40,7 +40,7 @@
ystart <- NULL
jj <- 1:J[1]
n.roots <- length(sims$root.short)
- if (DIC) n.roots <- n.roots-1 # don't display deviance summaries
+ if (isDIC) n.roots <- n.roots-1 # don't display deviance summaries
ystart <- numeric(n.roots)
for (k in 1:n.roots){
ystart[k] <- pos
Modified: trunk/R2WinBUGS/R/bugs.sims.R
===================================================================
--- trunk/R2WinBUGS/R/bugs.sims.R 2007-06-12 10:10:26 UTC (rev 29)
+++ trunk/R2WinBUGS/R/bugs.sims.R 2007-06-13 00:59:08 UTC (rev 30)
@@ -123,8 +123,9 @@
long.short=long.short, dimension.short=dimension.short,
indexes.short=indexes.short, last.values=last.values)
if(DIC) {
+ ## Read DIC from BUGS log
LOG <- bugs.log("log.txt")$DIC
- if(any(is.na(LOG))) {
+ if(any(is.na(LOG))) { ## Something went wrong --> Use Gelmans tweak
deviance <- all$sims.array[, , dim(sims.array)[3], drop = FALSE]
if(!is.R()) dimnames(deviance) <- NULL
dim(deviance) <- dim(deviance)[1:2]
@@ -134,12 +135,14 @@
pD[i] <- var(deviance[, i])/2
DIC[i] <- mean(deviance[, i]) + pD[i]
}
- all <- c(all, list(pD = mean(pD), DIC = mean(DIC), DICbyR = TRUE))
- } else {
- DIC <- LOG[nrow(LOG),4]
- pD <- LOG[nrow(LOG),3]
- all <- c(all, list(pD = pD, DIC = DIC, DICbyR = FALSE))
+ all <- c(all, list(isDIC=TRUE, DICbyR=TRUE,
+ pD=mean(pD), DIC=mean(DIC)))
+ } else { ## Use BUGS calculation of DIC
+ all <- c(all, list(isDIC=TRUE, DICbyR=FALSE,
+ pD=LOG[nrow(LOG),3], DIC=LOG[nrow(LOG),4]))
}
+ } else {
+ all <- c(all, isDIC=FALSE)
}
all
}
Modified: trunk/R2WinBUGS/R/openbugs.R
===================================================================
--- trunk/R2WinBUGS/R/openbugs.R 2007-06-12 10:10:26 UTC (rev 29)
+++ trunk/R2WinBUGS/R/openbugs.R 2007-06-13 00:59:08 UTC (rev 30)
@@ -1,20 +1,21 @@
-if (is.R()){
-openbugs <- function(data, inits, parameters.to.save, model.file="model.txt",
- n.chains = 3, n.iter = 2000, n.burnin = floor(n.iter/2),
- n.thin = max(1, floor(n.chains *(n.iter - n.burnin)/1000)),
+if (is.R()) {
+
+openbugs <- function(data, inits, parameters.to.save, model.file="model.txt",
+ n.chains = 3, n.iter = 2000, n.burnin = floor(n.iter/2),
+ n.thin = max(1, floor(n.chains *(n.iter - n.burnin)/1000)),
DIC = TRUE, bugs.directory = "c:/Program Files/OpenBUGS/",
- working.directory=NULL, digits = 5) {
-
-# switching from bugs() to BRugsFit() notation
- if(!require(BRugs))
+ working.directory=NULL, digits = 5)
+{
+ if(!require(BRugs))
stop("BRugs is required")
+ ## switching from bugs() to BRugsFit() notation
modelFile <- model.file
numChains <- n.chains
nBurnin <- n.burnin
nIter <- n.iter - n.burnin
nThin <- n.thin
- if(!is.null(DIC)) parameters.to.save <- c(parameters.to.save, "deviance")
+ if(DIC) parameters.to.save <- c(parameters.to.save, "deviance")
parametersToSave <- parameters.to.save
if(!is.null(working.directory)) {
savedWD <- getwd()
@@ -27,7 +28,7 @@
if(file.info(modelFile)$isdir) {
stop(modelFile, " is a directory, but a file is required")
}
-# kludge to add carriage-returns (line-feeds?) to the model file
+ ## kludge to add carriage-returns (line-feeds?) to the model file
if(!length(grep("\r\n", readChar(modelFile, 10^3)))) {
message("Carriage returns added to model file ", modelFile)
model <- readLines(modelFile)
@@ -41,24 +42,27 @@
BRugs::modelCompile(numChains)
if(missing(inits) || is.null(inits)) {
BRugs::modelGenInits()
- }
- else {
- if(is.list(inits) || is.function(inits) || (is.character(inits) &&
- !any(file.exists(inits)))){
- inits <- BRugs::bugsInits(inits = inits, numChains = numChains, digits = digits)
+ } else {
+ if(is.list(inits) || is.function(inits) || (is.character(inits) &&
+ !any(file.exists(inits)))) {
+ inits <- BRugs::bugsInits(inits = inits, numChains = numChains,
+ digits = digits)
}
BRugs::modelInits(inits)
BRugs::modelGenInits()
}
- BRugs::samplesSetThin(nThin)
-# set the adaptive phases
- adaptivelines <- scan(system.file("OpenBUGS", "Bugs", "Rsrc", "Registry.txt", package="BRugs"), what="character")
+ ## BRugs::samplesSetThin(nThin)
+ ## set the adaptive phases
+ adaptivelines <- scan(system.file("OpenBUGS", "Bugs", "Rsrc",
+ "Registry.txt", package="BRugs"),
+ what="character")
factories <- sub(".adaptivePhase", "",
- adaptivelines[grep("adaptivePhase",adaptivelines)])
- sapply(factories, BRugs::modelSetAP, max(0, nBurnin-1))
-
+ adaptivelines[grep("adaptivePhase",adaptivelines)])
+ sapply(factories, BRugs::modelSetAP, max(0, nBurnin-1))
+
BRugs::modelUpdate(nBurnin)
- if(!is.null(DIC)) {
+ BRugs::samplesSetThin(nThin)
+ if(DIC) {
BRugs::dicSet()
on.exit(BRugs::dicClear(), add = TRUE)
}
@@ -69,21 +73,25 @@
n.saved.per.chain <- nrow(samples)/numChains
samples.array <- array(samples, c(n.saved.per.chain, numChains, ncol(samples)))
dimnames(samples.array)[[3]] <- dimnames(samples)[[2]]
- if(!is.null(DIC)) DIC <- BRugs::dicStats()
- bugs.output <- as.bugs.array(samples.array, modelFile, program="OpenBUGS",
- n.iter=n.iter, n.burnin=n.burnin, n.thin=n.thin, DIC=DIC)
- return(bugs.output)
+ if(DIC) {
+ DICOutput <- BRugs::dicStats()
+ } else {
+ DICOutput <- NULL
+ }
+ bugs.output <- as.bugs.array(sims.array=samples.array,
+ model.file=modelFile, program="OpenBUGS",
+ DIC=DIC, DICOutput=DICOutput,
+ n.iter=n.iter, n.burnin=n.burnin, n.thin=n.thin)
+ bugs.output
}
-
-
-# sorter called by openbugs() to save the parameters in the specified order
+## sorter called by openbugs() to save the parameters in the specified order
sort.name <- function(a, b){
-# sort the scalar parameter names in the vector "a" according to the ordering
-# of their stems in the shorter vector "b"
+ ## sort the scalar parameter names in the vector "a" according to the
+ ## ordering of their stems in the shorter vector "b"
bracket.pos <- regexpr("\\[", a)
a.stem <- substr(a, 1, ifelse(bracket.pos>0, bracket.pos-1, nchar(a)))
- return(a[order(match(a.stem, b))])
+ a[order(match(a.stem, b))]
}
}
Modified: trunk/R2WinBUGS/R/print.bugs.R
===================================================================
--- trunk/R2WinBUGS/R/print.bugs.R 2007-06-12 10:10:26 UTC (rev 29)
+++ trunk/R2WinBUGS/R/print.bugs.R 2007-06-13 00:59:08 UTC (rev 30)
@@ -12,22 +12,23 @@
if(x$n.thin > 1) cat(", n.thin =", x$n.thin)
cat("\n n.sims =", x$n.sims, "iterations saved\n")
print(round(x$summary, digits.summary), ...)
+
if(x$n.chains > 1) {
cat("\nFor each parameter, n.eff is a crude measure of effective sample size,")
cat("\nand Rhat is the potential scale reduction factor (at convergence, Rhat=1).\n")
}
- msgDICrule <- ifelse(x$DICbyR,
- "(using the rule, pD = var(deviance)/2)\n",
- "(using the rule, pD = Dbar-Dhat)\n")
- msgDIC <- "DIC is an estimate of expected predictive error (lower deviance is better).\n"
- if(length(x$DIC) == 1 && x$DIC) {
- cat("\npD =", fround(x$pD, 1), "and DIC =", fround(x$DIC, 1), msgDICrule)
- cat(msgDIC)
+
+ if(x$isDIC) {
+ msgDICRule <- ifelse(x$DICbyR,
+ "(using the rule, pD = var(deviance)/2)", ## Gelman tweak
+ "(using the rule, pD = Dbar-Dhat)") ## BUGS
+ cat(paste("\nDIC info ", msgDICRule, "\n", sep=""))
+ if(length(x$DIC) == 1) {
+ cat("pD =", fround(x$pD, 1), "and DIC =", fround(x$DIC, 1))
+ } else if(length(x$DIC)>1) {
+ print(round(x$DIC, 1))
+ }
+ cat("\nDIC is an estimate of expected predictive error (lower deviance is better).\n")
}
- else if(length(x$DIC)>1) {
- cat("\n")
- print(round(x$DIC, 1))
- cat(msgDIC)
- }
invisible(x)
}
Modified: trunk/R2WinBUGS/man/as.bugs.array.Rd
===================================================================
--- trunk/R2WinBUGS/man/as.bugs.array.Rd 2007-06-12 10:10:26 UTC (rev 29)
+++ trunk/R2WinBUGS/man/as.bugs.array.Rd 2007-06-13 00:59:08 UTC (rev 30)
@@ -1,38 +1,58 @@
\name{as.bugs.array}
\alias{as.bugs.array}
\title{Convert to bugs object}
-\description{Function converting results from Markov chain simulations that are not from BUGS
- to be displayed using \code{\link{plot.bugs}}.
+
+\description{Function converting results from Markov chain simulations,
+ that might not be from BUGS, to bugs object. Used mainly to display
+ results with \code{\link{plot.bugs}}.
}
+
\usage{
-as.bugs.array(sims.array, model.file=NULL, program=NULL,
- DIC=FALSE, n.iter=NULL, n.burnin=0, n.thin=1)
+as.bugs.array(sims.array, model.file=NULL, program=NULL,
+ DIC=FALSE, DICOutput=NULL, n.iter=NULL, n.burnin=0, n.thin=1)
}
+
\arguments{
\item{sims.array}{3-way array of simulation output, with dimensions
n.keep, n.chains, and length of combined parameter vector.}
\item{model.file}{file containing the model written in WinBUGS code}
\item{program}{the program used}
- \item{DIC}{logical; whether DIC is given}
- \item{n.iter}{number of total iterations per chain used for generating \code{sims.array}}
- \item{n.burnin}{length of burn in, i.e. number of iterations to discarded
- at the beginning for generating \code{sims.array}}
- \item{n.thin}{thinning rate, a positive integer, used for generating \code{sims.array}}
+ \item{DIC}{logical; whether DIC should be calculated, see also
+ argument \code{DICOutput} and details}
+ \item{DICOutput}{DIC value}
+ \item{n.iter}{number of total iterations per chain used for generating
+ \code{sims.array}}
+ \item{n.burnin}{length of burn in, i.e. number of iterations to
+ discarded at the beginning for generating \code{sims.array}}
+ \item{n.thin}{thinning rate, a positive integer, used for generating
+ \code{sims.array}}
}
+
\details{
-This function takes a 3-way array of simulations and makes it into a \code{\link{bugs}}
-object that can be conveniently displayed using \code{print} and
-\code{plot} and accessed using \code{attach.bugs}. If the third
-dimension of sims() has names, the resulting bugs object will respect
-that naming convention. For example, if the parameter names are
-\dQuote{alpha[1]}, \dQuote{alpha[2]}, ..., \dQuote{alpha[8]}, \dQuote{mu}, \dQuote{tau}, then
-\code{as.bugs.array} will know that alpha is a vector of length 8, and mu and
-tau are scalar parameters. These will all be plotted appropriately by
-\code{plot} and attached appropriately by \code{attach.bugs}.}
-\value{
- A \code{\link{bugs}} object is returned.
+
+This function takes a 3-way array of simulations and makes it into a
+\code{\link{bugs}} object that can be conveniently displayed using
+\code{print} and \code{plot} and accessed using \code{attach.bugs}. If
+the third dimension of sims() has names, the resulting bugs object will
+respect that naming convention. For example, if the parameter names are
+\dQuote{alpha[1]}, \dQuote{alpha[2]}, ..., \dQuote{alpha[8]},
+\dQuote{mu}, \dQuote{tau}, then \code{as.bugs.array} will know that
+alpha is a vector of length 8, and mu and tau are scalar parameters.
+These will all be plotted appropriately by \code{plot} and attached
+appropriately by \code{attach.bugs}.
+
+If \code{DIC=TRUE} then DIC can be either already passed to argument
+\code{DICOutput} as it is done in \code{\link{openbugs}} or calculated
+from deviance values in \code{sims.array}.
+
}
-\author{Jouni Kerman, \email{ke...@st...} with modification by Andrew Gelman, \email{ge...@st...},
- packaged by Uwe Ligges, \email{li...@st...}.}
+
+\value{A \code{\link{bugs}} object is returned}
+
+\author{Jouni Kerman, \email{ke...@st...} with modification
+ by Andrew Gelman, \email{ge...@st...}, packaged by Uwe
+ Ligges, \email{li...@st...}.}
+
\seealso{\code{\link{bugs}}}
\keyword{interface}
+\keyword{manip}
Modified: trunk/R2WinBUGS/man/attach.all.Rd
===================================================================
--- trunk/R2WinBUGS/man/attach.all.Rd 2007-06-12 10:10:26 UTC (rev 29)
+++ trunk/R2WinBUGS/man/attach.all.Rd 2007-06-13 00:59:08 UTC (rev 30)
@@ -4,78 +4,95 @@
\alias{attach.bugs}
\alias{detach.bugs}
\title{Attach / detach elements of (bugs) objects to search path}
-\description{The database is attached/detached to the search path. See \code{\link{attach}} for details.}
+
+\description{The database is attached/detached to the search path. See
+ \code{\link{attach}} for details.}
+
\usage{
attach.all(x, overwrite = NA, name = "attach.all")
attach.bugs(x, overwrite = NA)
detach.all(name = "attach.all")
detach.bugs()
}
+
\arguments{
- \item{x}{An object, which must be of class \code{bugs} for \code{attach.bugs}.}
- \item{overwrite}{If \code{TRUE}, objects with identical names in the Workspace (.GlobalEnv)
- that are masking objects in the database to be attached will be deleted.
+ \item{x}{An object, which must be of class \code{bugs} for
+ \code{attach.bugs}.}
+ \item{overwrite}{If \code{TRUE}, objects with identical names in the
+ Workspace (.GlobalEnv) that are masking objects in the database to
+ be attached will be deleted. If \code{NA} (the default) and an
+ interactive session is running, a dialog box asks the user whether
+ masking objects should be deleted. In non-interactive mode,
+ behaviour is identical to \code{overwrite=FALSE}, i.e. nothing will
+ be deleted.}
+ \item{name}{The name of the environment where \code{x} will be
+ attached / which will be detached.}
+}
- If \code{NA} (the default) and an interactive session is running, a dialog box asks the user
- whether masking objects should be deleted.
- In non-interactive mode, behaviour is identical to \code{overwrite=FALSE}, i.e. nothing will be deleted.}
- \item{name}{The name of the environment where \code{x} will be attached / which will be detached.}
-}
\details{
- While \code{attach.all} attaches all elements of an object \code{x} to a database called \code{name},
- \code{attach.bugs} attaches all elements of \code{x$sims.list} to the database \code{bugs.sims}
- itself making use of \code{attach.all}.\cr
- \code{detach.all} and \code{detach.bugs} are removing the databases
- mentioned above.\cr
- \code{attach.all} also attaches \code{n.sims} (the number of
- simulations saved from the MCMC runs) to the database.\cr\cr
+ While \code{attach.all} attaches all elements of an object \code{x} to
+ a database called \code{name}, \code{attach.bugs} attaches all
+ elements of \code{x$sims.list} to the database \code{bugs.sims} itself
+ making use of \code{attach.all}.\cr
- Each scalar parameter in the model is attached as vectors of length
- \code{n.sims}, each vector is attached as a 2-way array (with first
- dimension equal to \code{n.sims}, each matrix is attached as a 3-way
- array, and so forth.}
+ \code{detach.all} and \code{detach.bugs} are removing the databases
+ mentioned above.\cr \code{attach.all} also attaches \code{n.sims} (the
+ number of simulations saved from the MCMC runs) to the database.\cr\cr
+
+ Each scalar parameter in the model is attached as vectors of length
+ \code{n.sims}, each vector is attached as a 2-way array (with first
+ dimension equal to \code{n.sims}), each matrix is attached as a 3-way
+ array, and so forth.
+}
+
\note{
- Without detaching, do not use \code{attach.all} or \code{attach.bugs} on another (\code{bugs}) object,
- because instead of the given name, an object called \code{name} is attached.
- Therefore strange things may happen...
+ Without detaching, do not use \code{attach.all} or \code{attach.bugs}
+ on another (\code{bugs}) object, because instead of the given name, an
+ object called \code{name} is attached. Therefore strange things may
+ happen \ldots
}
+
\value{
- \code{attach.all} and \code{attach.bugs} invisibly return the \code{\link{environment}}(s).\cr
- \code{detach.all} and \code{detach.bugs} detach the \code{environment}(s) named \code{name}
- created by \code{attach.all}.
+ \code{attach.all} and \code{attach.bugs} invisibly return the
+ \code{\link{environment}}(s).\cr
+
+ \code{detach.all} and \code{detach.bugs} detach the
+ \code{environment}(s) named \code{name} created by \code{attach.all}.
}
+
\seealso{\code{\link{bugs}}, \code{\link{attach}}, \code{\link{detach}}}
+
\examples{
# An example model file is given in:
model.file <- file.path(.path.package("R2WinBUGS"), "model", "schools.txt")
# Some example data (see ?schools for details):
-data(schools)
+data(schools)
J <- nrow(schools)
y <- schools$estimate
sigma.y <- schools$sd
data <- list ("J", "y", "sigma.y")
inits <- function(){
- list(theta = rnorm(J, 0, 100), mu.theta = rnorm(1, 0, 100),
+ list(theta = rnorm(J, 0, 100), mu.theta = rnorm(1, 0, 100),
sigma.theta = runif(1, 0, 100))
}
-parameters <- c("theta", "mu.theta", "sigma.theta")
+parameters <- c("theta", "mu.theta", "sigma.theta")
\dontrun{
## You may need to edit "bugs.directory",
## also you need write access in the working directory:
-schools.sim <- bugs(data, inits, parameters, model.file,
- n.chains = 3, n.iter = 1000,
+schools.sim <- bugs(data, inits, parameters, model.file,
+ n.chains = 3, n.iter = 1000,
bugs.directory = "c:/Program Files/WinBUGS14/",
working.directory = NULL)
# Do some inferential summaries
attach.bugs(schools.sim)
-# posterior probability that the coaching program in school A
+# posterior probability that the coaching program in school A
# is better than in school C:
print(mean(theta[,1] > theta[,3]))
-# 50% posterior interval for the difference between school A's
+# 50% posterior interval for the difference between school A's
# and school C's program:
-print(quantile(theta[,1] - theta[,3], c(.25, .75)))
-plot(theta[,1], theta[,3])
+print(quantile(theta[,1] - theta[,3], c(.25, .75)))
+plot(theta[,1], theta[,3])
detach.bugs()
}
}
Modified: trunk/R2WinBUGS/man/bugs.Rd
===================================================================
--- trunk/R2WinBUGS/man/bugs.Rd 2007-06-12 10:10:26 UTC (rev 29)
+++ trunk/R2WinBUGS/man/bugs.Rd 2007-06-13 00:59:08 UTC (rev 30)
@@ -1,9 +1,11 @@
\name{bugs}
\alias{bugs}
\title{Run WinBUGS and OpenBUGS from R or S-PLUS}
-\description{The \code{bugs} function takes data and starting values as input.
-It automatically writes a WinBUGS script, calls the model,
-and saves the simulations for easy access in R or S-PLUS.}
+
+\description{The \code{bugs} function takes data and starting values as
+ input. It automatically writes a WinBUGS script, calls the model, and
+ saves the simulations for easy access in R or S-PLUS.}
+
\usage{
bugs(data, inits, parameters.to.save, model.file="model.bug",
n.chains=3, n.iter=2000, n.burnin=floor(n.iter/2),
@@ -11,11 +13,12 @@
bin=(n.iter - n.burnin) / n.thin,
debug=FALSE, DIC=TRUE, digits=5, codaPkg=FALSE,
bugs.directory="c:/Program Files/WinBUGS14/",
- program=c("winbugs", "openbugs", "WinBugs", "OpenBugs"),
+ program=c("WinBUGS", "OpenBUGS", "winbugs", "openbugs"),
working.directory=NULL, clearWD=FALSE,
useWINE=.Platform$OS.type != "windows", WINE=Sys.getenv("WINE"),
newWINE=FALSE, WINEPATH=NULL)
}
+
\arguments{
\item{data}{either a named list (names corresponding to variable names
in the \code{model.file}) of the data for the WinBUGS model,
@@ -32,7 +35,7 @@
parameters to save which should be monitored}
\item{model.file}{file containing the model written in WinBUGS code.
The extension can be either \file{.bug} or \file{.txt}.
- If the extension is \file{.bug} and \code{program=="winbugs"},
+ If the extension is \file{.bug} and \code{program=="WinBUGS"},
a copy of the file with extension \file{.txt} will be created
in the \code{bugs()} call and removed afterwards. Note that
similarly named \file{.txt} files will be overwritten.}
@@ -62,12 +65,12 @@
\item{codaPkg}{logical; if \code{FALSE} (default) a \code{bugs} object
is returned, if \code{TRUE} file names of WinBUGS output are
returned for easy access by the \pkg{coda} package through function
- \code{\link{read.bugs}} (not used if \code{program="openbugs"}).}
+ \code{\link{read.bugs}} (not used if \code{program="OpenBUGS"}).}
\item{bugs.directory}{directory that contains the WinBUGS executable}
\item{program}{the program to use, either
- \code{winbugs}/\code{WinBugs} or \code{openbugs}/\code{OpenBugs},
+ \code{winbugs}/\code{WinBUGS} or \code{openbugs}/\code{OpenBUGS},
the latter makes use of function \code{\link{openbugs}} and requires
- the CRAN package \pkg{BRugs}. The \code{openbugs}/\code{OpenBugs}
+ the CRAN package \pkg{BRugs}. The \code{openbugs}/\code{OpenBUGS}
choice is not available in S-PLUS.}
\item{working.directory}{sets working directory during execution of
this function; WinBUGS' in- and output will be stored in this
@@ -98,7 +101,7 @@
\item A WinBUGS window will pop up and R / S-PLUS will freeze
up. The model will now run in WinBUGS. It might take awhile. You
will see things happening in the Log window within WinBUGS. When
- WinBugs is done, its window will close and R / S-PLUS will work
+ WinBUGS is done, its window will close and R / S-PLUS will work
again.
\item If an error message appears, re-run with \code{debug=TRUE}.
}
@@ -171,8 +174,8 @@
packaged by Sibylle Sturtz, \email{st...@st...},
and Uwe Ligges.}
-\seealso{\code{\link{print.bugs}}, \code{\link{plot.bugs}}, and the
- \pkg{coda} package}
+\seealso{\code{\link{print.bugs}}, \code{\link{plot.bugs}}, as well as
+ \pkg{coda} and \pkg{BRugs} packages}
\examples{
# An example model file is given in:
@@ -214,5 +217,6 @@
plot(schools.sim)
}
}
+
\keyword{interface}
\keyword{models}
Modified: trunk/R2WinBUGS/man/bugs.data.Rd
===================================================================
--- trunk/R2WinBUGS/man/bugs.data.Rd 2007-06-12 10:10:26 UTC (rev 29)
+++ trunk/R2WinBUGS/man/bugs.data.Rd 2007-06-13 00:59:08 UTC (rev 30)
@@ -1,19 +1,27 @@
\name{bugs.data}
\alias{bugs.data}
\title{Writing input for WinBUGS}
-\description{Write file \file{data.txt} for WinBUGS to read.}
+
+\description{Write file \file{data.txt} for WinBUGS to read - for
+ internal use.}
+
\usage{
bugs.data(data, dir = getwd(), digits = 5)
}
\arguments{
- \item{data}{either a named list (names corresponding to variable names in the \code{model.file})
- of the data for the WinBUGS model, \emph{or}
- a vector or list of the names of the data objects used by the model}
+ \item{data}{either a named list (names corresponding to variable names
+ in the \code{model.file}) of the data for the WinBUGS model,
+ \emph{or} a vector or list of the names of the data objects used by
+ the model}
\item{dir}{the directory to write the file \file{data.txt} to}
- \item{digits}{number of significant digits used for WinBUGS input, see \code{\link{formatC}}}
+ \item{digits}{number of significant digits used for WinBUGS input, see
+ \code{\link{formatC}}}
}
-\value{
- Does not return anything.
-}
-\seealso{\code{\link{bugs}}}
+
+\value{Nothing, but as a side effect, the data file \file{data.txt} is
+ written}
+
+\seealso{The main function to be called by the user is \code{\link{bugs}}.}
+\keyword{internal}
\keyword{file}
+\keyword{IO}
\ No newline at end of file
Modified: trunk/R2WinBUGS/man/bugs.inits.Rd
===================================================================
--- trunk/R2WinBUGS/man/bugs.inits.Rd 2007-06-12 10:10:26 UTC (rev 29)
+++ trunk/R2WinBUGS/man/bugs.inits.Rd 2007-06-13 00:59:08 UTC (rev 30)
@@ -1,20 +1,26 @@
\name{bugs.inits}
\alias{bugs.inits}
\title{Writing input for WinBUGS - intended for internal use only}
-\description{Write files \file{inits1.txt}, \file{inits2.txt}, etc., in the working directory
-for WinBUGS to read. For internal use only.}
+
+\description{Write files \file{inits1.txt}, \file{inits2.txt}, etc., in
+ the working directory for WinBUGS to read - for internal use.}
+
\usage{
bugs.inits(inits, n.chains, digits)
}
\arguments{
- \item{inits}{a list with \code{n.chains} elements; each element of the list is
- itself a list of starting values for the WinBUGS model, \emph{or}
- a function creating (possibly random) initial values}
+ \item{inits}{a list with \code{n.chains} elements; each element of the
+ list is itself a list of starting values for the WinBUGS model,
+ \emph{or} a function creating (possibly random) initial values}
\item{n.chains}{number of Markov chains}
- \item{digits}{number of significant digits used for WinBUGS input, see \code{\link{formatC}}}
+ \item{digits}{number of significant digits used for WinBUGS input, see
+ \code{\link{formatC}}}
}
-\value{
- Does not return anything.
-}
+
+\value{Nothing, but as a side effect, the inits files \file{inits*.txt}
+ are written}
+
\seealso{The main function to be called by the user is \code{\link{bugs}}.}
\keyword{internal}
+\keyword{IO}
+\keyword{file}
Modified: trunk/R2WinBUGS/man/bugs.log.Rd
===================================================================
--- trunk/R2WinBUGS/man/bugs.log.Rd 2007-06-12 10:10:26 UTC (rev 29)
+++ trunk/R2WinBUGS/man/bugs.log.Rd 2007-06-13 00:59:08 UTC (rev 30)
@@ -10,7 +10,7 @@
\item{file}{Location of the WinBUGS logfile}
}
\value{
- A list with components
+ A list with components:
\item{stats}{A matrix containing summary statistics for each saved
parameter. Comparable to the information in the element
\code{summary} of a bugs object as returned by \code{\link{bugs}}.}
@@ -24,3 +24,4 @@
}
\seealso{The main function that generates the log file is \code{\link{bugs}}.}
\keyword{IO}
+\keyword{file}
Modified: trunk/R2WinBUGS/man/bugs.plot.Rd
===================================================================
--- trunk/R2WinBUGS/man/bugs.plot.Rd 2007-06-12 10:10:26 UTC (rev 29)
+++ trunk/R2WinBUGS/man/bugs.plot.Rd 2007-06-13 00:59:08 UTC (rev 30)
@@ -2,23 +2,29 @@
\alias{bugs.plot.summary}
\alias{bugs.plot.inferences}
\title{Plotting summary information - intended for internal use only}
-\description{Plotting summary information - intended for internal use only}
+\description{Plotting summary information - intended for internal use}
\usage{
bugs.plot.summary(sims, ...)
bugs.plot.inferences(sims, display.parallel, ...)
}
\arguments{
- \item{sims}{an object of class `bugs', see \code{\link{bugs}} for details}
- \item{display.parallel}{display parallel intervals in both halves of the summary plots;
- this is a convergence-monitoring tool and is not necessary once you have approximate convergence
- (default is \code{FALSE})}
+ \item{sims}{an object of class `bugs', see \code{\link{bugs}} for
+ details}
+ \item{display.parallel}{display parallel intervals in both halves of
+ the summary plots; this is a convergence-monitoring tool and is not
+ necessary once you have approximate convergence (default is
+ \code{FALSE})}
\item{...}{further arguments to be passed to low-level plot functions}
}
+
\details{
-\code{bugs.plot.summary} (left hand side of plot) and \code{bugs.plot.inferences} (right hand side of plot).
+ \code{bugs.plot.summary} (left hand side of plot) and
+ \code{bugs.plot.inferences} (right hand side of plot).
}
-\value{
-Does not return anything, but prints and plots as side-effects.
-}
-\seealso{The main function to be called by the user is \code{plot}, see \code{\link{plot.bugs}} for details.}
+
+\value{Does not return anything, but prints and plots as side-effects.}
+
+\seealso{The main function to be called by the user is \code{plot}, see
+ \code{\link{plot.bugs}} for details.}
+
\keyword{internal}
Modified: trunk/R2WinBUGS/man/bugs.run.Rd
===================================================================
--- trunk/R2WinBUGS/man/bugs.run.Rd 2007-06-12 10:10:26 UTC (rev 29)
+++ trunk/R2WinBUGS/man/bugs.run.Rd 2007-06-13 00:59:08 UTC (rev 30)
@@ -1,27 +1,31 @@
\name{bugs.run}
\alias{bugs.run}
-\title{Calling WinBUGS - intended for internal use only}
-\description{
-Updates the lengths of the adaptive phases in the WinBUGS registry (using \code{\link{bugs.update.settings}}),
-calls WinBUGS and runs it with \file{script.txt}. Intended for internal use only}
+\title{Calling WinBUGS}
+
+\description{Updates the lengths of the adaptive phases in the WinBUGS
+ registry (using \code{\link{bugs.update.settings}}), calls WinBUGS and
+ runs it with \file{script.txt} - intended for internal use}
+
\usage{
-bugs.run(n.burnin, bugs.directory, WINE = "",
- useWINE = .Platform$OS.type != "windows",
+bugs.run(n.burnin, bugs.directory, WINE = "",
+ useWINE = .Platform$OS.type != "windows",
newWINE = TRUE, WINEPATH = NULL)
}
\arguments{
\item{n.burnin}{length of bu...
[truncated message content] |
|
From: <gg...@us...> - 2007-09-18 13:21:31
|
Revision: 67
http://bugs-r.svn.sourceforge.net/bugs-r/?rev=67&view=rev
Author: ggorjan
Date: 2007-09-18 06:21:09 -0700 (Tue, 18 Sep 2007)
Log Message:
-----------
move so that NEWS file will be also in installed package
Added Paths:
-----------
trunk/R2WinBUGS/inst/NEWS
Removed Paths:
-------------
trunk/R2WinBUGS/Changes
Deleted: trunk/R2WinBUGS/Changes
===================================================================
--- trunk/R2WinBUGS/Changes 2007-09-18 13:17:39 UTC (rev 66)
+++ trunk/R2WinBUGS/Changes 2007-09-18 13:21:09 UTC (rev 67)
@@ -1,237 +0,0 @@
-Changes to R2WinBUGS:
-=====================
-
-Update 2.1-6 (23 August 2007):
-- reverting back to use thin.updater since it is faster, however CODA files
- have "wrong" indexes
-- WINE arguments are now set in such a way that defaults work on Windows
- and Linux
-- minor formatting in the code and help files
-
-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:
- 1. Fixed "bugs.data.inits" function so you can use data that have the
- same names as R functions.
- 2. Changed T and F to TRUE and FALSE everywhere in case the variables
- T and F are used as data in the main program
- 3. 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.
- 4. 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:
- 1. The "attach.all" function (no longer called "attach2") overwrites
- so that all components of a list or data frame get attached.
- 2. Program now looks in the directory /winbug~1/ rather than /winbug~2/
- 3. Graphics parameters for margins are returned to their original state
- at the end of the program.
- 4. Added "digits.summary" option to the numerical display.
- 5. 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:
- 1. 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!
- 2. 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).
- 3. 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:
- 1. 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.)
- 2. 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:
- 1. Fix display.parallel=T option by adding min.width so that very
- intervals are still visible.
- 2. 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:
- 1. Approximate "effective sample size" n.eff given for each parameter.
- 2. More explanatory material displayed.
- 3. Use bringToTop() to automatically bring up the graphics window.
-Update 4 Feb 2003:
- 1. 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.)
- 2. 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:
- 1. Fix of bug that occurred with uppercase and lowercase variable names
- 2. Set default for n.thin so that no more than about 500 iterations
- will be saved from each sequence
- 3. 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:
- 1. Automatic fixing of adaptive phases. Now you no longer need to run
- for thousands of iterations when slice or Metropolis sampling is used.
- 2. Various minor fixes
-Update 10 Dec 2002:
- 1. Cool graphical display of convergence and inferences!
- 2. New "attach2" function that overwrites so that all components of
- the list are attached
-Update 29 Nov 2002:
- 1. Fix of bug in 24 Nov update.
- 2. Fix of bug in 16 Nov update.
- 3. 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:
- 1. Parameters saved in order of the "parameters.to.save" vector
- (not alphabetical order).
- 2. Output saved in both matrix and list form.
- 3. 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
Copied: trunk/R2WinBUGS/inst/NEWS (from rev 65, trunk/R2WinBUGS/Changes)
===================================================================
--- trunk/R2WinBUGS/inst/NEWS (rev 0)
+++ trunk/R2WinBUGS/inst/NEWS 2007-09-18 13:21:09 UTC (rev 67)
@@ -0,0 +1,237 @@
+Changes to R2WinBUGS:
+=====================
+
+Update 2.1-6 (23 August 2007):
+- reverting back to use thin.updater since it is faster, however CODA files
+ have "wrong" indexes
+- WINE arguments are now set in such a way that defaults work on Windows
+ and Linux
+- minor formatting in the code and help files
+
+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:
+ 1. Fixed "bugs.data.inits" function so you can use data that have the
+ same names as R functions.
+ 2. Changed T and F to TRUE and FALSE everywhere in case the variables
+ T and F are used as data in the main program
+ 3. 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.
+ 4. 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:
+ 1. The "attach.all" function (no longer called "attach2") overwrites
+ so that all components of a list or data frame get attached.
+ 2. Program now looks in the directory /winbug~1/ rather than /winbug~2/
+ 3. Graphics parameters for margins are returned to their original state
+ at the end of the program.
+ 4. Added "digits.summary" option to the numerical display.
+ 5. 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:
+ 1. 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!
+ 2. 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).
+ 3. 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:
+ 1. 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.)
+ 2. 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:
+ 1. Fix display.parallel=T option by adding min.width so that very
+ intervals are still visible.
+ 2. 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:
+ 1. Approximate "effective sample size" n.eff given for each parameter.
+ 2. More explanatory material displayed.
+ 3. Use bringToTop() to automatically bring up the graphics window.
+Update 4 Feb 2003:
+ 1. 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.)
+ 2. 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:
+ 1. Fix of bug that occurred with uppercase and lowercase variable names
+ 2. Set default for n.thin so that no more than about 500 iterations
+ will be saved from each sequence
+ 3. 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:
+ 1. Automatic fixing of adaptive phases. Now you no longer need to run
+ for thousands of iterations when slice or Metropolis sampling is used.
+ 2. Various minor fixes
+Update 10 Dec 2002:
+ 1. Cool graphical display of convergence and inferences!
+ 2. New "attach2" function that overwrites so that all components of
+ the list are attached
+Update 29 Nov 2002:
+ 1. Fix of bug in 24 Nov update.
+ 2. Fix of bug in 16 Nov update.
+ 3. 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:
+ 1. Parameters saved in order of the "parameters.to.save" vector
+ (not alphabetical order).
+ 2. Output saved in both matrix and list form.
+ 3. 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
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <li...@us...> - 2008-02-01 09:42:53
|
Revision: 85
http://bugs-r.svn.sourceforge.net/bugs-r/?rev=85&view=rev
Author: ligges
Date: 2008-02-01 01:42:28 -0800 (Fri, 01 Feb 2008)
Log Message:
-----------
bugfix if DIC is not available ...
Modified Paths:
--------------
trunk/R2WinBUGS/DESCRIPTION
trunk/R2WinBUGS/R/bugs.log.R
Modified: trunk/R2WinBUGS/DESCRIPTION
===================================================================
--- trunk/R2WinBUGS/DESCRIPTION 2008-01-22 12:27:56 UTC (rev 84)
+++ trunk/R2WinBUGS/DESCRIPTION 2008-02-01 09:42:28 UTC (rev 85)
@@ -1,7 +1,7 @@
Package: R2WinBUGS
Title: Running WinBUGS and OpenBUGS from R / S-PLUS
-Date: 2008-01-18
-Version: 2.1-7
+Date: 2008-02-01
+Version: 2.1-8
Author: originally written by Andrew Gelman <ge...@st...>;
changes and packaged by Sibylle Sturtz <st...@st...>
and Uwe Ligges <li...@st...>.
Modified: trunk/R2WinBUGS/R/bugs.log.R
===================================================================
--- trunk/R2WinBUGS/R/bugs.log.R 2008-01-22 12:27:56 UTC (rev 84)
+++ trunk/R2WinBUGS/R/bugs.log.R 2008-02-01 09:42:28 UTC (rev 85)
@@ -11,10 +11,11 @@
log.txt <- readLines(file)
extract <- function (m, line.match, skip=0, empty.left.col=TRUE) {
start <- (skip + which(m == line.match)[1])
- if(is.na(start)) return(NULL)
- if(length(start) < 1) return(NULL)
+ if(is.na(start)) return(NA)
+ if(length(start) < 1) return(NA)
mx <- strsplit(m[-(1:start)], "\t")
n.cols <- length(mx[[1]])
+ if(n.cols < 1) return(NA)
mxlen <- sapply(mx, length)
end <- which(mxlen!=n.cols)[1] - 1
mx <- mx[1:end]
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <li...@us...> - 2007-05-13 11:44:00
|
Revision: 16
http://svn.sourceforge.net/bugs-r/?rev=16&view=rev
Author: ligges
Date: 2007-05-13 04:43:49 -0700 (Sun, 13 May 2007)
Log Message:
-----------
prepare for release
Modified Paths:
--------------
trunk/R2WinBUGS/Changes
trunk/R2WinBUGS/DESCRIPTION
Modified: trunk/R2WinBUGS/Changes
===================================================================
--- trunk/R2WinBUGS/Changes 2007-05-08 22:06:05 UTC (rev 15)
+++ trunk/R2WinBUGS/Changes 2007-05-13 11:43:49 UTC (rev 16)
@@ -70,5 +70,5 @@
- print.bugs / plot.bugs documentation fixes
- write.model() fix
-Update 2.1-1 (07 April 2007):
+Update 2.1-2 (12 May 2007):
- Ported to S-PLUS by Insightful Corp.
Modified: trunk/R2WinBUGS/DESCRIPTION
===================================================================
--- trunk/R2WinBUGS/DESCRIPTION 2007-05-08 22:06:05 UTC (rev 15)
+++ trunk/R2WinBUGS/DESCRIPTION 2007-05-13 11:43:49 UTC (rev 16)
@@ -1,7 +1,7 @@
Package: R2WinBUGS
Title: Running WinBUGS and OpenBUGS from R / S-PLUS
-Date: 2007-04-07
-Version: 2.1-1
+Date: 2007-05-12
+Version: 2.1-2
Author: originally written by Andrew Gelman <ge...@st...>;
changes and packaged by Sibylle Sturtz <st...@st...>
and Uwe Ligges <li...@st...>.
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <li...@us...> - 2007-05-13 16:49:33
|
Revision: 17
http://svn.sourceforge.net/bugs-r/?rev=17&view=rev
Author: ligges
Date: 2007-05-13 09:49:34 -0700 (Sun, 13 May 2007)
Log Message:
-----------
The codetools checks revealed quite a lot of bugs and inconsistencies. Unfortunately we cannot make codetools calm since codetools do not expect S-PLUS.
Again, prepared for release.
Modified Paths:
--------------
trunk/R2WinBUGS/Changes
trunk/R2WinBUGS/DESCRIPTION
trunk/R2WinBUGS/R/attach.all.R
trunk/R2WinBUGS/R/bugs.R
trunk/R2WinBUGS/R/bugs.data.R
trunk/R2WinBUGS/R/bugs.run.R
trunk/R2WinBUGS/R/bugs.script.R
trunk/R2WinBUGS/R/bugs.update.settings.R
trunk/R2WinBUGS/R/openbugs.R
trunk/R2WinBUGS/R/read.bugs.R
trunk/R2WinBUGS/R/wineutils.R
trunk/R2WinBUGS/R/write.model.R
trunk/R2WinBUGS/man/bugs.run.Rd
Modified: trunk/R2WinBUGS/Changes
===================================================================
--- trunk/R2WinBUGS/Changes 2007-05-13 11:43:49 UTC (rev 16)
+++ trunk/R2WinBUGS/Changes 2007-05-13 16:49:34 UTC (rev 17)
@@ -70,5 +70,7 @@
- print.bugs / plot.bugs documentation fixes
- write.model() fix
-Update 2.1-2 (12 May 2007):
+Update 2.1-3 (13 May 2007):
- Ported to S-PLUS by Insightful Corp.
+- some fixes for codetools checks
+
Modified: trunk/R2WinBUGS/DESCRIPTION
===================================================================
--- trunk/R2WinBUGS/DESCRIPTION 2007-05-13 11:43:49 UTC (rev 16)
+++ trunk/R2WinBUGS/DESCRIPTION 2007-05-13 16:49:34 UTC (rev 17)
@@ -1,7 +1,7 @@
Package: R2WinBUGS
Title: Running WinBUGS and OpenBUGS from R / S-PLUS
-Date: 2007-05-12
-Version: 2.1-2
+Date: 2007-05-13
+Version: 2.1-3
Author: originally written by Andrew Gelman <ge...@st...>;
changes and packaged by Sibylle Sturtz <st...@st...>
and Uwe Ligges <li...@st...>.
Modified: trunk/R2WinBUGS/R/attach.all.R
===================================================================
--- trunk/R2WinBUGS/R/attach.all.R 2007-05-13 11:43:49 UTC (rev 16)
+++ trunk/R2WinBUGS/R/attach.all.R 2007-05-13 16:49:34 UTC (rev 17)
@@ -29,10 +29,7 @@
detach("bugs.sims")}
x$sims.list$n.sims <- x$n.sims # put n.sims into sims.list for convenience
r2 <- attach.all(x$sims.list, overwrite = overwrite, name = "bugs.sims")
- if (is.R())
- invisible (bugs.sims = r2)
- else
- invisible (r2)
+ invisible (r2)
}
detach.all <- function(name = "attach.all"){
Modified: trunk/R2WinBUGS/R/bugs.R
===================================================================
--- trunk/R2WinBUGS/R/bugs.R 2007-05-13 11:43:49 UTC (rev 16)
+++ trunk/R2WinBUGS/R/bugs.R 2007-05-13 16:49:34 UTC (rev 17)
@@ -60,7 +60,7 @@
bugs.script(parameters.to.save, n.chains, n.iter, n.burnin, n.thin,
new.model.file, debug=debug, is.inits=!is.null(inits),
bin = bin, DIC = DIC, useWINE = useWINE, newWINE = newWINE, WINEPATH = WINEPATH)
- bugs.run(n.burnin, bugs.directory, WINE = WINE, useWINE = useWINE)
+ bugs.run(n.burnin, bugs.directory, WINE = WINE, useWINE = useWINE, WINEPATH = WINEPATH)
if(codaPkg)
return(file.path(getwd(), paste("coda", 1:n.chains, ".txt", sep="")))
Modified: trunk/R2WinBUGS/R/bugs.data.R
===================================================================
--- trunk/R2WinBUGS/R/bugs.data.R 2007-05-13 11:43:49 UTC (rev 16)
+++ trunk/R2WinBUGS/R/bugs.data.R 2007-05-13 16:49:34 UTC (rev 17)
@@ -1,29 +1,28 @@
"bugs.data" <-
function(data, dir = getwd(), digits = 5){
if(is.numeric(unlist(data)))
- if(is.R()) {
- write.datafile(lapply(data, formatC, digits = digits, format = "E"),
- file.path(dir, "data.txt"))
- }
- else {
- writeDatafileS4(data, towhere = "data.txt")
- }
+ if(is.R()) {
+ write.datafile(lapply(data, formatC, digits = digits, format = "E"),
+ file.path(dir, "data.txt"))
+ }
+ else {
+ writeDatafileS4(data, towhere = "data.txt")
+ }
else {
- if(is.R()) {
- data.list <- lapply(as.list(data), get, pos = parent.frame(2))
- names(data.list) <- as.list(data)
- write.datafile(lapply(data.list, formatC, digits = digits, format = "E"),
- file.path(dir, "data.txt"))
- }
- else {
- data.list <- lapply(as.list(data), get, where = parent.frame(2))
- names(data.list) <- unlist(data)
- writeDatafileS4(data.list, towhere = "data.txt")
- }
- }
+ if(is.R()) {
+ data.list <- lapply(as.list(data), get, pos = parent.frame(2))
+ names(data.list) <- as.list(data)
+ write.datafile(lapply(data.list, formatC, digits = digits, format = "E"),
+ file.path(dir, "data.txt"))
+ }
+ else {
+ data.list <- lapply(as.list(data), get, where = parent.frame(2))
+ names(data.list) <- unlist(data)
+ writeDatafileS4(data.list, towhere = "data.txt")
+ }
+ }
}
-if (!is.R()) {
"writeDatafileS4" <-
#
@@ -50,128 +49,128 @@
# Revision history: 2002-11-19. Fixed to handle missing values properly.
function(DATA, towhere = "clipboard", fill = TRUE)
{
- formatDataS4 =
- #
- # Prepared DATA for input to WinBUGS.
- function(DATA)
- {
- if(!is.list(DATA))
- stop("DATA must be a named list or data frame.")
- dlnames <- names(DATA)
- if(is.data.frame(DATA))
- DATA <- as.list(DATA)
- #
- # Checking for lists in DATA....
- lind <- sapply(DATA, is.list)
- # Checking for data frames in DATA....
- dfind <- sapply(DATA, is.data.frame)
- # Any lists that are not data frames?...
- if(any(lind & !dfind)) stop("DATA may not contain lists.")
- # Checking for unnamed elements of list that are not data frames....
- if(any(dlnames[!dfind] == "")) stop(
- "When DATA is a list, all its elements that are not data frames must be named."
- )
- # Checking for duplicate names....
- dupnames <- unique(dlnames[duplicated(dlnames)])
- if(length(dupnames) > 0)
- stop(paste(
- "The following names are used more than once in DATA:",
- paste(dupnames, collapse = ", ")))
- if(any(dfind)) {
- dataold <- DATA
- DATA <- vector("list", 0)
- for(i in seq(along = dataold)) {
- if(dfind[i])
- DATA <- c(DATA, as.list(dataold[[i]]))
- else DATA <- c(DATA, dataold[i])
- }
- dataold <- NULL
- }
- dlnames <- names(DATA)
- dupnames <- unique(dlnames[duplicated(dlnames)])
- # Checking for duplicated names again (now that columns of data frames are included)....
- if(length(dupnames) > 0) stop(paste(
- "The following names are used more than once in DATA (at least once within a data frame):",
- paste(dupnames, collapse = ", ")))
- # Checking for factors....
- factorind <- sapply(DATA, is.factor)
- if(any(factorind))
- stop(paste(
- "DATA may not include factors. One or more factor variables were detected:",
- paste(dlnames[factorind], collapse = ", ")))
- # Checking for character vectors....
- charind <- sapply(DATA, is.character)
- if(any(charind))
- stop(paste(
- "WinBUGS does not handle character data. One or more character variables were detected:",
- paste(dlnames[charind], collapse = ", ")))
- # Checking for complex vectors....
- complexind <- sapply(DATA, is.complex)
- if(any(complexind))
- stop(paste(
- "WinBUGS does not handle complex data. One or more complex variables were detected:",
- paste(dlnames[complexind], collapse = ", ")))
- # Checking for values farther from zero than 1E+38 (which is limit of single precision)....
- toobigind <- sapply(DATA, function(x)
- {
- y <- abs(x[!is.na(x)])
- any(y[y > 0] > 9.9999999999999998e+37)
- }
- )
- if(any(toobigind))
- stop(paste(
- "WinBUGS works in single precision. The following variables contain data outside the range +/-1.0E+38: ",
- paste(dlnames[toobigind], collapse = ", "),
- ".\n", sep = ""))
- # Checking for values in range +/-1.0E-38 (which is limit of single precision)....
- toosmallind <- sapply(DATA, function(x)
- {
- y <- abs(x[!is.na(x)])
- any(y[y > 0] < 9.9999999999999996e-39)
- }
- )
- n <- length(dlnames)
- data.string <- as.list(rep(NA, n))
- for(i in 1:n) {
- if(length(DATA[[i]]) == 1) {
- ac <- toSingleS4(DATA[[i]])
- data.string[[i]] <- paste(names(DATA)[i], "=",
- ac, sep = "")
- next
- }
- if(is.vector(DATA[[i]]) & length(DATA[[i]]) > 1) {
- ac <- toSingleS4(DATA[[i]])
- data.string[[i]] <- paste(names(DATA)[i], "=c(",
- paste(ac, collapse = ", "), ")", sep =
- "")
- next
- }
- if(is.array(DATA[[i]])) {
- ac <- toSingleS4(aperm(DATA[[i]]))
- data.string[[i]] <- paste(names(DATA)[i],
- "= structure(.Data= c(", paste(ac,
- collapse = ", "), "), \n .Dim=c(",
- paste(as.character(dim(DATA[[i]])),
- collapse = ", "), "))", sep = "")
- }
- }
- data.tofile <- paste("list(", paste(unlist(data.string),
- collapse = ", "), ")", sep = "")
- if(any(toosmallind))
- warning(paste(
- "WinBUGS works in single precision. The following variables contained nonzero data",
- "\ninside the range +/-1.0E-38 that were set to zero: ",
- paste(dlnames[toosmallind], collapse = ", "),
- ".\n", sep = ""))
- return(data.tofile)
- }
- rslt <- formatDataS4(DATA)
- cat(rslt, file = towhere, fill = fill)
- invisible(0)
+ formatDataS4 =
+ #
+ # Prepared DATA for input to WinBUGS.
+ function(DATA)
+ {
+ if(!is.list(DATA))
+ stop("DATA must be a named list or data frame.")
+ dlnames <- names(DATA)
+ if(is.data.frame(DATA))
+ DATA <- as.list(DATA)
+ #
+ # Checking for lists in DATA....
+ lind <- sapply(DATA, is.list)
+ # Checking for data frames in DATA....
+ dfind <- sapply(DATA, is.data.frame)
+ # Any lists that are not data frames?...
+ if(any(lind & !dfind)) stop("DATA may not contain lists.")
+ # Checking for unnamed elements of list that are not data frames....
+ if(any(dlnames[!dfind] == "")) stop(
+ "When DATA is a list, all its elements that are not data frames must be named."
+ )
+ # Checking for duplicate names....
+ dupnames <- unique(dlnames[duplicated(dlnames)])
+ if(length(dupnames) > 0)
+ stop(paste(
+ "The following names are used more than once in DATA:",
+ paste(dupnames, collapse = ", ")))
+ if(any(dfind)) {
+ dataold <- DATA
+ DATA <- vector("list", 0)
+ for(i in seq(along = dataold)) {
+ if(dfind[i])
+ DATA <- c(DATA, as.list(dataold[[i]]))
+ else DATA <- c(DATA, dataold[i])
+ }
+ dataold <- NULL
+ }
+ dlnames <- names(DATA)
+ dupnames <- unique(dlnames[duplicated(dlnames)])
+ # Checking for duplicated names again (now that columns of data frames are included)....
+ if(length(dupnames) > 0) stop(paste(
+ "The following names are used more than once in DATA (at least once within a data frame):",
+ paste(dupnames, collapse = ", ")))
+ # Checking for factors....
+ factorind <- sapply(DATA, is.factor)
+ if(any(factorind))
+ stop(paste(
+ "DATA may not include factors. One or more factor variables were detected:",
+ paste(dlnames[factorind], collapse = ", ")))
+ # Checking for character vectors....
+ charind <- sapply(DATA, is.character)
+ if(any(charind))
+ stop(paste(
+ "WinBUGS does not handle character data. One or more character variables were detected:",
+ paste(dlnames[charind], collapse = ", ")))
+ # Checking for complex vectors....
+ complexind <- sapply(DATA, is.complex)
+ if(any(complexind))
+ stop(paste(
+ "WinBUGS does not handle complex data. One or more complex variables were detected:",
+ paste(dlnames[complexind], collapse = ", ")))
+ # Checking for values farther from zero than 1E+38 (which is limit of single precision)....
+ toobigind <- sapply(DATA, function(x)
+ {
+ y <- abs(x[!is.na(x)])
+ any(y[y > 0] > 9.9999999999999998e+37)
+ }
+ )
+ if(any(toobigind))
+ stop(paste(
+ "WinBUGS works in single precision. The following variables contain data outside the range +/-1.0E+38: ",
+ paste(dlnames[toobigind], collapse = ", "),
+ ".\n", sep = ""))
+ # Checking for values in range +/-1.0E-38 (which is limit of single precision)....
+ toosmallind <- sapply(DATA, function(x)
+ {
+ y <- abs(x[!is.na(x)])
+ any(y[y > 0] < 9.9999999999999996e-39)
+ }
+ )
+ n <- length(dlnames)
+ data.string <- as.list(rep(NA, n))
+ for(i in 1:n) {
+ if(length(DATA[[i]]) == 1) {
+ ac <- toSingleS4(DATA[[i]])
+ data.string[[i]] <- paste(names(DATA)[i], "=",
+ ac, sep = "")
+ next
+ }
+ if(is.vector(DATA[[i]]) & length(DATA[[i]]) > 1) {
+ ac <- toSingleS4(DATA[[i]])
+ data.string[[i]] <- paste(names(DATA)[i], "=c(",
+ paste(ac, collapse = ", "), ")", sep =
+ "")
+ next
+ }
+ if(is.array(DATA[[i]])) {
+ ac <- toSingleS4(aperm(DATA[[i]]))
+ data.string[[i]] <- paste(names(DATA)[i],
+ "= structure(.Data= c(", paste(ac,
+ collapse = ", "), "), \n .Dim=c(",
+ paste(as.character(dim(DATA[[i]])),
+ collapse = ", "), "))", sep = "")
+ }
+ }
+ data.tofile <- paste("list(", paste(unlist(data.string),
+ collapse = ", "), ")", sep = "")
+ if(any(toosmallind))
+ warning(paste(
+ "WinBUGS works in single precision. The following variables contained nonzero data",
+ "\ninside the range +/-1.0E-38 that were set to zero: ",
+ paste(dlnames[toosmallind], collapse = ", "),
+ ".\n", sep = ""))
+ return(data.tofile)
+ }
+ rslt <- formatDataS4(DATA)
+ cat(rslt, file = towhere, fill = fill)
+ invisible(0)
}
-toSingleS4 =
+toSingleS4 <-
#
# Takes numeric vector and removes digit of exponent in scientific notation (if any)
#
@@ -180,50 +179,48 @@
# Revision history: 2002-11-19. Fixed to handle missing values properly.
function(x)
{
- xdim <- dim(x)
- x <- as.character(as.single(x))
+ xdim <- dim(x)
+ x <- as.character(as.single(x))
- # First to look for positives:
- pplus <- regMatchPos(x, "e\\+0")
- pplusind <- apply(pplus, 1, function(y)
- (!any(is.na(y))))
- if(any(pplusind)) {
- # Making sure that periods are in mantissa...
- init <- substring(x[pplusind], 1, pplus[
- pplusind, 1] - 1)
- #...preceeding exponent
- pper <- regMatchPos(init, "\\.")
- pperind <- apply(pper, 1, function(y)
- (all(is.na(y))))
- if(any(pperind))
- init[pperind] <- paste(init[pperind],
- ".0", sep = "")
- # Changing the format of the exponent...
- x[pplusind] <- paste(init, "E+", substring(
- x[pplusind], pplus[pplusind, 2] + 1),
- sep = "")
- }
- # Then to look for negatives:
- pminus <- regMatchPos(x, "e\\-0")
- pminusind <- apply(pminus, 1, function(y)
- (!any(is.na(y))))
- if(any(pminusind)) {
- # Making sure that periods are in mantissa...
- init <- substring(x[pminusind], 1, pminus[
- pminusind, 1] - 1)
- #...preceeding exponent
- pper <- regMatchPos(init, "\\.")
- pperind <- apply(pper, 1, function(y)
- (all(is.na(y))))
- if(any(pperind))
- init[pperind] <- paste(init[pperind],
- ".0", sep = "")
- # Changing the format of the exponent...
- x[pminusind] <- paste(init, "E-", substring(
- x[pminusind], pminus[pminusind, 2] +
- 1), sep = "")
- }
- x
+ # First to look for positives:
+ pplus <- regMatchPos(x, "e\\+0")
+ pplusind <- apply(pplus, 1, function(y)
+ (!any(is.na(y))))
+ if(any(pplusind)) {
+ # Making sure that periods are in mantissa...
+ init <- substring(x[pplusind], 1, pplus[
+ pplusind, 1] - 1)
+ #...preceeding exponent
+ pper <- regMatchPos(init, "\\.")
+ pperind <- apply(pper, 1, function(y)
+ (all(is.na(y))))
+ if(any(pperind))
+ init[pperind] <- paste(init[pperind],
+ ".0", sep = "")
+ # Changing the format of the exponent...
+ x[pplusind] <- paste(init, "E+", substring(
+ x[pplusind], pplus[pplusind, 2] + 1),
+ sep = "")
+ }
+ # Then to look for negatives:
+ pminus <- regMatchPos(x, "e\\-0")
+ pminusind <- apply(pminus, 1, function(y)
+ (!any(is.na(y))))
+ if(any(pminusind)) {
+ # Making sure that periods are in mantissa...
+ init <- substring(x[pminusind], 1, pminus[
+ pminusind, 1] - 1)
+ #...preceeding exponent
+ pper <- regMatchPos(init, "\\.")
+ pperind <- apply(pper, 1, function(y)
+ (all(is.na(y))))
+ if(any(pperind))
+ init[pperind] <- paste(init[pperind],
+ ".0", sep = "")
+ # Changing the format of the exponent...
+ x[pminusind] <- paste(init, "E-", substring(
+ x[pminusind], pminus[pminusind, 2] +
+ 1), sep = "")
+ }
+ x
}
-
-} # ends if (!is.R())
Modified: trunk/R2WinBUGS/R/bugs.run.R
===================================================================
--- trunk/R2WinBUGS/R/bugs.run.R 2007-05-13 11:43:49 UTC (rev 16)
+++ trunk/R2WinBUGS/R/bugs.run.R 2007-05-13 16:49:34 UTC (rev 17)
@@ -1,6 +1,7 @@
"bugs.run" <-
function(n.burnin, bugs.directory, WINE = "",
- useWINE = .Platform$OS.type != "windows", newWINE = TRUE){
+ useWINE = .Platform$OS.type != "windows",
+ newWINE = TRUE, WINEPATH = NULL){
if(useWINE && !is.R())
stop ("Non-Windows platforms not yet supported in R2WinBUGS for S-PLUS")
@@ -26,7 +27,7 @@
stop(paste("WinBUGS executable does not exist in", bugs.directory))
## Call Bugs and have it run with script.txt
bugsCall <- paste("\"", dos.location, "\" /par \"",
- native2win(file.path(getwd(), "script.txt"), newWINE = newWINE),
+ native2win(file.path(getwd(), "script.txt"), newWINE = newWINE, WINEPATH = WINEPATH),
"\"", sep = "")
if (useWINE)
bugsCall <- paste(WINE, bugsCall)
Modified: trunk/R2WinBUGS/R/bugs.script.R
===================================================================
--- trunk/R2WinBUGS/R/bugs.script.R 2007-05-13 11:43:49 UTC (rev 16)
+++ trunk/R2WinBUGS/R/bugs.script.R 2007-05-13 16:49:34 UTC (rev 17)
@@ -17,7 +17,8 @@
coda <- file.path(working.directory, "coda")
logfile <- file.path(working.directory, "log.odc")
logfileTxt <- file.path(working.directory, "log.txt")
- inits <- sapply(paste(working.directory, "/inits", 1:n.chains, ".txt", sep=""), native2win)
+ inits <- sapply(paste(working.directory, "/inits", 1:n.chains, ".txt", sep=""),
+ function(x) native2win(x, , WINEPATH = WINEPATH))
initlist <- paste("inits (", 1:n.chains, ", '", inits, "')\n", sep="")
savelist <- paste("set (", parameters.to.save, ")\n", sep="")
redo <- ceiling((n.iter-n.burnin)/(n.thin*bin))
@@ -34,15 +35,15 @@
## Therefore, if the samples are read into S-PLUS using the coda package,
## the thinning will be correctly labelled in the resulting mcmc object.
## In R, the thinning is always labelled as 1, even if thinning was done.
- thinUpdateCommand <- paste("update (", n.burnin, ")\n",
- "thin.samples (", n.thin, ")\n", sep = "")
- bin = bin * n.thin
+ thinUpdateCommand <- paste("update (", n.burnin, ")\n",
+ "thin.samples (", n.thin, ")\n", sep = "")
+ bin = bin * n.thin
}
cat(
"display ('log')\n",
- "check ('", native2win(model), "')\n",
- "data ('", native2win(data), "')\n",
+ "check ('", native2win(model, WINEPATH=WINEPATH), "')\n",
+ "data ('", native2win(data, WINEPATH=WINEPATH), "')\n",
"compile (", n.chains, ")\n",
if(is.inits) initlist,
"gen.inits()\n",
@@ -51,12 +52,12 @@
if(DIC) "dic.set()\n",
rep(
c("update (", formatC(ceiling(bin), format = "d"), ")\n",
- "coda (*, '", native2win(coda), "')\n"),redo),
+ "coda (*, '", native2win(coda, WINEPATH=WINEPATH), "')\n"),redo),
"stats (*)\n",
if(DIC) "dic.stats()\n",
- "history (*, '", native2win(history), "')\n",
- "save ('", native2win(logfile), "')\n",
- "save ('", native2win(logfileTxt), "')\n",
+ "history (*, '", native2win(history, WINEPATH=WINEPATH), "')\n",
+ "save ('", native2win(logfile, WINEPATH=WINEPATH), "')\n",
+ "save ('", native2win(logfileTxt, WINEPATH=WINEPATH), "')\n",
file=script, sep="", append=FALSE)
if (!debug) cat ("quit ()\n", file=script, append=TRUE)
sims.files <- paste ("coda", 1:n.chains, ".txt", sep="")
Modified: trunk/R2WinBUGS/R/bugs.update.settings.R
===================================================================
--- trunk/R2WinBUGS/R/bugs.update.settings.R 2007-05-13 11:43:49 UTC (rev 16)
+++ trunk/R2WinBUGS/R/bugs.update.settings.R 2007-05-13 16:49:34 UTC (rev 17)
@@ -1,13 +1,13 @@
"bugs.update.settings" <-
function (n.burnin, bugs.directory){
-
+
char.burnin <- as.character(n.burnin - 1)
- if (is.R()){
- file.copy(file.path(bugs.directory, "System/Rsrc/Registry.odc"),
+ if (is.R()){
+ file.copy(file.path(bugs.directory, "System/Rsrc/Registry.odc"),
file.path(bugs.directory, "System/Rsrc/Registry_Rsave.odc"),
overwrite = TRUE)
} else {
- splus.file.copy(file.path(bugs.directory, "System/Rsrc/Registry.odc"),
+ splus.file.copy(file.path(bugs.directory, "System/Rsrc/Registry.odc"),
file.path(bugs.directory, "System/Rsrc/Registry_Rsave.odc"),
overwrite = TRUE)
}
@@ -15,19 +15,19 @@
"character", 400, size = 1, endian = "little")
locale <- Sys.getlocale("LC_CTYPE")
Sys.setlocale("LC_CTYPE", "C")
- if (is.R())
- info <- registry[regexpr("Int", registry, fixed = TRUE, useBytes = TRUE) > 0]
- else
- info <- registry[regexpr("Int", registry, fixed = TRUE) > 0]
+ if (is.R())
+ info <- registry[regexpr("Int", registry, fixed = TRUE, useBytes = TRUE) > 0]
+ else
+ info <- registry[regexpr("Int", registry, fixed = TRUE) > 0]
while(regexpr("\r", info) > 0){
newline <- regexpr("\r", info)
info <- substring(info, newline + 1)
line <- substring(info, 1, regexpr("\r", info) - 1)
if(regexpr("AdaptivePhase", line) > 0){
if (is.R())
- numpos <- regexpr("Int", line, fixed = TRUE, useBytes = TRUE) + 4
+ numpos <- regexpr("Int", line, fixed = TRUE, useBytes = TRUE) + 4
else
- numpos <- regexpr("Int", line, fixed = TRUE) + 4
+ numpos <- regexpr("Int", line, fixed = TRUE) + 4
num <- substring(line, numpos)
if (as.numeric(num) > n.burnin){
@@ -43,8 +43,6 @@
file.path(bugs.directory, "System/Rsrc/Registry.odc"), endian = "little")
}
-if (!is.R()){
-
"splus.file.copy"<-
function(from, to, overwrite = FALSE)
{
@@ -57,5 +55,3 @@
size = 1)
invisible(z)
}
-
-} #ends if (!is.R())
Modified: trunk/R2WinBUGS/R/openbugs.R
===================================================================
--- trunk/R2WinBUGS/R/openbugs.R 2007-05-13 11:43:49 UTC (rev 16)
+++ trunk/R2WinBUGS/R/openbugs.R 2007-05-13 16:49:34 UTC (rev 17)
@@ -33,43 +33,43 @@
model <- readLines(modelFile)
try(writeLines(model, modelFile))
}
- modelCheck(modelFile)
+ BRugs::modelCheck(modelFile)
if(!(is.vector(data) && is.character(data) && all(file.exists(data)))) {
- data <- bugsData(data, digits = digits)
+ data <- BRugs::bugsData(data, digits = digits)
}
- modelData(data)
- modelCompile(numChains)
+ BRugs::modelData(data)
+ BRugs::modelCompile(numChains)
if(missing(inits) || is.null(inits)) {
- modelGenInits()
+ BRugs::modelGenInits()
}
else {
if(is.list(inits) || is.function(inits) || (is.character(inits) &&
!any(file.exists(inits)))){
- inits <- bugsInits(inits = inits, numChains = numChains, digits = digits)
+ inits <- BRugs::bugsInits(inits = inits, numChains = numChains, digits = digits)
}
- modelInits(inits)
- modelGenInits()
+ BRugs::modelInits(inits)
+ BRugs::modelGenInits()
}
- samplesSetThin(nThin)
+ BRugs::samplesSetThin(nThin)
# set the adaptive phases
adaptivelines <- scan(system.file("OpenBUGS", "Bugs", "Rsrc", "Registry.txt", package="BRugs"), what="character")
factories <- sub(".adaptivePhase", "",
adaptivelines[grep("adaptivePhase",adaptivelines)])
- sapply(factories, modelSetAP, max(0, nBurnin-1))
+ sapply(factories, BRugs::modelSetAP, max(0, nBurnin-1))
- modelUpdate(nBurnin)
+ BRugs::modelUpdate(nBurnin)
if(!is.null(DIC)) {
- dicSet()
- on.exit(dicClear(), add = TRUE)
+ BRugs::dicSet()
+ on.exit(BRugs::dicClear(), add = TRUE)
}
- samplesSet(parametersToSave)
- modelUpdate(nIter)
- params <- sort.name(samplesMonitors("*"), parametersToSave)
- samples <- sapply(params, samplesSample)
+ BRugs::samplesSet(parametersToSave)
+ BRugs::modelUpdate(nIter)
+ params <- sort.name(BRugs::samplesMonitors("*"), parametersToSave)
+ samples <- sapply(params, BRugs::samplesSample)
n.saved.per.chain <- nrow(samples)/numChains
samples.array <- array(samples, c(n.saved.per.chain, numChains, ncol(samples)))
dimnames(samples.array)[[3]] <- dimnames(samples)[[2]]
- if(!is.null(DIC)) DIC <- dicStats()
+ if(!is.null(DIC)) DIC <- BRugs::dicStats()
bugs.output <- as.bugs.array(samples.array, modelFile, program="OpenBUGS",
n.iter=n.iter, n.burnin=n.burnin, n.thin=n.thin, DIC=DIC)
return(bugs.output)
Modified: trunk/R2WinBUGS/R/read.bugs.R
===================================================================
--- trunk/R2WinBUGS/R/read.bugs.R 2007-05-13 11:43:49 UTC (rev 16)
+++ trunk/R2WinBUGS/R/read.bugs.R 2007-05-13 16:49:34 UTC (rev 17)
@@ -1,7 +1,7 @@
read.bugs <- function(codafiles, ...){
if(!require(coda))
stop("package 'coda' is required to use this function")
- mcmc.list(lapply(codafiles, read.coda,
+ coda::mcmc.list(lapply(codafiles, coda::read.coda,
index.file = file.path(dirname(codafiles[1]), "codaIndex.txt"),
...))
}
Modified: trunk/R2WinBUGS/R/wineutils.R
===================================================================
--- trunk/R2WinBUGS/R/wineutils.R 2007-05-13 11:43:49 UTC (rev 16)
+++ trunk/R2WinBUGS/R/wineutils.R 2007-05-13 16:49:34 UTC (rev 17)
@@ -52,7 +52,7 @@
} # end if (is.R())
-native2win <- function(x, useWINE=.Platform$OS.type != "windows", newWINE=TRUE) { # native -> win
+native2win <- function(x, useWINE=.Platform$OS.type != "windows", newWINE=TRUE, WINEPATH=NULL) { # native -> win
if(is.R()){
if (useWINE && !newWINE) return(winedriveRTr(x))
if (useWINE && newWINE) {
Modified: trunk/R2WinBUGS/R/write.model.R
===================================================================
--- trunk/R2WinBUGS/R/write.model.R 2007-05-13 11:43:49 UTC (rev 16)
+++ trunk/R2WinBUGS/R/write.model.R 2007-05-13 16:49:34 UTC (rev 17)
@@ -21,8 +21,6 @@
writeLines(model.text, con = con)
}
-if (!is.R()){
-
replaceScientificNotation <- function(text){
## Change the format of any numbers in "text" that are in S-PLUS
## scientific notation to WinBUGS scientific notation
@@ -31,7 +29,7 @@
## Find the first instance
## Note that the number may or may not have a decimal point.
sciNoteLoc <- regexpr("[0-9]*\\.{0,1}[0-9]*e\\+0[0-9]{2}", text)
-
+
## For every instance, replace the number
while(sciNoteLoc > -1){
sciNoteEnd <- sciNoteLoc + attr(sciNoteLoc, "match.length")-1
@@ -54,4 +52,3 @@
text
}
-} ## ends if (!is.R())
Modified: trunk/R2WinBUGS/man/bugs.run.Rd
===================================================================
--- trunk/R2WinBUGS/man/bugs.run.Rd 2007-05-13 11:43:49 UTC (rev 16)
+++ trunk/R2WinBUGS/man/bugs.run.Rd 2007-05-13 16:49:34 UTC (rev 17)
@@ -6,7 +6,8 @@
calls WinBUGS and runs it with \file{script.txt}. Intended for internal use only}
\usage{
bugs.run(n.burnin, bugs.directory, WINE = "",
- useWINE = .Platform$OS.type != "windows", newWINE = TRUE)
+ useWINE = .Platform$OS.type != "windows",
+ newWINE = TRUE, WINEPATH = NULL)
}
\arguments{
\item{n.burnin}{length of burn in}
@@ -16,6 +17,8 @@
defaults to \code{TRUE} on Windows, and \code{FALSE} otherwise.
The \code{useWINE = TRUE} option is not available in S-PLUS.}
\item{newWINE}{set this one to \code{TRUE} for new versions of WINE.}
+ \item{WINEPATH}{Path the WINE, \code{bugs} tries hard to get the information automatically and
+ pass it to this function, if not given.}
}
\value{
Does not return anything.
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <gg...@us...> - 2007-06-12 09:12:58
|
Revision: 23
http://svn.sourceforge.net/bugs-r/?rev=23&view=rev
Author: ggorjan
Date: 2007-06-12 02:12:59 -0700 (Tue, 12 Jun 2007)
Log Message:
-----------
bugs.script.R
- using Dawn's solution for proper indexing of CODA files also for R side
- removed one commented and useless line at the top
read.bugs.Rd
- documented Dawn's solution
Modified Paths:
--------------
trunk/R2WinBUGS/R/bugs.script.R
trunk/R2WinBUGS/man/read.bugs.Rd
Modified: trunk/R2WinBUGS/R/bugs.script.R
===================================================================
--- trunk/R2WinBUGS/R/bugs.script.R 2007-05-23 17:44:29 UTC (rev 22)
+++ trunk/R2WinBUGS/R/bugs.script.R 2007-06-12 09:12:59 UTC (rev 23)
@@ -3,7 +3,6 @@
n.thin, model.file, debug=FALSE, is.inits, bin,
DIC = FALSE, useWINE = FALSE, newWINE = FALSE, WINEPATH = NULL){
### Write file script.txt for Bugs to read
-### if (n.chains<2) stop ("n.chains must be at least 2")
if((ceiling(n.iter/n.thin) - ceiling(n.burnin/n.thin)) < 2)
stop ("(n.iter-n.burnin)/n.thin must be at least 2")
@@ -17,29 +16,16 @@
coda <- file.path(working.directory, "coda")
logfile <- file.path(working.directory, "log.odc")
logfileTxt <- file.path(working.directory, "log.txt")
- inits <- sapply(paste(working.directory, "/inits", 1:n.chains, ".txt", sep=""),
+ inits <- sapply(paste(working.directory, "/inits", 1:n.chains, ".txt", sep=""),
function(x) native2win(x, , WINEPATH = WINEPATH))
initlist <- paste("inits (", 1:n.chains, ", '", inits, "')\n", sep="")
savelist <- paste("set (", parameters.to.save, ")\n", sep="")
redo <- ceiling((n.iter-n.burnin)/(n.thin*bin))
-
- if (is.R()){
- thinUpdateCommand <- paste("thin.updater (", n.thin, ")\n",
- "update (", ceiling(n.burnin/n.thin), ")\n", sep = "")
- } else{
- ## In S-PLUS, the handling of the thinning is done differently than in R.
- ## bin represents the number of iterations between saves, before thinning,
- ## where in R it is the number of iterations between saves, after thinning.
- ## This alternative handling of the thinning is done so that the resulting
- ## samples have the correct iteration indexes in the output (coda) files.
- ## Therefore, if the samples are read into S-PLUS using the coda package,
- ## the thinning will be correctly labelled in the resulting mcmc object.
- ## In R, the thinning is always labelled as 1, even if thinning was done.
- thinUpdateCommand <- paste("update (", n.burnin, ")\n",
- "thin.samples (", n.thin, ")\n", sep = "")
- bin = bin * n.thin
- }
-
+
+ thinUpdateCommand <- paste("update (", n.burnin, ")\n",
+ "thin.samples (", n.thin, ")\n", sep = "")
+ bin = bin * n.thin
+
cat(
"display ('log')\n",
"check ('", native2win(model, WINEPATH=WINEPATH), "')\n",
@@ -56,7 +42,7 @@
"stats (*)\n",
if(DIC) "dic.stats()\n",
"history (*, '", native2win(history, WINEPATH=WINEPATH), "')\n",
- "save ('", native2win(logfile, WINEPATH=WINEPATH), "')\n",
+ "save ('", native2win(logfile, WINEPATH=WINEPATH), "')\n",
"save ('", native2win(logfileTxt, WINEPATH=WINEPATH), "')\n",
file=script, sep="", append=FALSE)
if (!debug) cat ("quit ()\n", file=script, append=TRUE)
Modified: trunk/R2WinBUGS/man/read.bugs.Rd
===================================================================
--- trunk/R2WinBUGS/man/read.bugs.Rd 2007-05-23 17:44:29 UTC (rev 22)
+++ trunk/R2WinBUGS/man/read.bugs.Rd 2007-06-12 09:12:59 UTC (rev 23)
@@ -1,19 +1,34 @@
\name{read.bugs}
\alias{read.bugs}
\title{Read output files in CODA format}
-\description{This function reads Markov Chain Monte Carlo output in the CODA format produced by WinBUGS
- and returns an object of class \code{\link[coda]{mcmc.list}} for further output analysis
- using the \sQuote{coda} package.}
+
+\description{This function reads Markov Chain Monte Carlo output in the
+ CODA format produced by WinBUGS and returns an object of class
+ \code{\link[coda]{mcmc.list}} for further output analysis using the
+ \pkg{coda} package.}
+
\usage{
read.bugs(codafiles, ...)
}
+
\arguments{
- \item{codafiles}{character vector of filenames (e.g. returned from \code{\link{bugs}}
- in call such as \code{bugs(....., codaPkg = TRUE, .....)}).
- Each of the files contains coda output for one chain produced by WinBUGS,
- the \emph{directory} name of the corresponding file \file{codaIndex.txt}
- is extracted from the first element of \code{codafiles}.}
- \item{...}{further arguments to be passed to \code{\link[coda]{read.coda}}}
+ \item{codafiles}{character vector of filenames (e.g. returned from
+ \code{\link{bugs}} in call such as \code{bugs(....., codaPkg=TRUE,
+ .....)}). Each of the files contains coda output for one chain
+ produced by WinBUGS, the \emph{directory} name of the corresponding
+ file \file{codaIndex.txt} is extracted from the first element of
+ \code{codafiles}.}
+ \item{...}{further arguments to be passed to
+ \code{\link[coda]{read.coda}}}
}
-\seealso{\code{\link{bugs}}, \code{\link[coda]{read.coda}}, \code{\link[coda]{mcmc.list}}}
+
+\details{
+ \code{\link{bugs}} (actually it is \code{\link{bugs.script}}) writes
+ BUGS script in such a way that iteration numbers in resulting CODA
+ files correspond to iteration numbers before burnin and thinning.
+}
+
+\seealso{\code{\link{bugs}}, \code{\link[coda]{read.coda}},
+\code{\link[coda]{mcmc.list}}}
+
\keyword{file}
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|
|
From: <gg...@us...> - 2007-06-12 09:57:26
|
Revision: 25
http://svn.sourceforge.net/bugs-r/?rev=25&view=rev
Author: ggorjan
Date: 2007-06-12 02:57:21 -0700 (Tue, 12 Jun 2007)
Log Message:
-----------
some formatting
Modified Paths:
--------------
trunk/R2WinBUGS/R/bugs.log.R
trunk/R2WinBUGS/R/print.bugs.R
trunk/R2WinBUGS/man/bugs.log.Rd
Modified: trunk/R2WinBUGS/R/bugs.log.R
===================================================================
--- trunk/R2WinBUGS/R/bugs.log.R 2007-06-12 09:55:29 UTC (rev 24)
+++ trunk/R2WinBUGS/R/bugs.log.R 2007-06-12 09:57:21 UTC (rev 25)
@@ -3,44 +3,47 @@
if(!file.exists(file))
stop("Log file", file, "does not exist")
logfile <- readLines(file)
-
+
+ ## --- Stats ---
+
statsStart <- which(logfile == "Node statistics") + 2
if(!length(statsStart))
stop("Log file", file, "does not contain node statistics.")
## + 2 to remove
## "Node statistics"
## "\t node\t mean\t sd\t MC error\t2.5%\tmedian\t97.5%\tstart\tsample"
-
+
statsEnd <- which(logfile == "dic.stats()") - 1
- ## + 1 to remove
+ ## - 1 to remove
## "dic.stats()"
-
+
statsTable <- logfile[statsStart:statsEnd]
statsTable <- sub("\t", "", statsTable)
statsTable <- sapply(strsplit(statsTable, "\t"), "[")
colnames(statsTable) <- statsTable[1,]
statsTable <- t(apply(statsTable[-1,], 2, as.numeric))
colnames(statsTable) <- c("mean", "sd", "MC error", "2.5%", "median", "97.5%", "start", "sample")
-
- ## DIC
+
+ ## --- DIC ---
+
DICStart <- which(logfile == "DIC") + 3
## + 3 to remove
## "DIC"
## "Dbar = post.mean of -2logL; Dhat = -2LogL at post.mean of stochastic nodes"
## "\tDbar\tDhat\tpD\tDIC\t"
-
- DICEnd <- grep("history(", logfile, fixed = TRUE) - 1
+
+ DICEnd <- grep("history(", logfile, fixed=TRUE) - 1
## - 1 to remove
## "history(+, ..."
-
- if(!length(DICEnd) || !length(DICStart) || (DICEnd < DICStart)){
+
+ if(!length(DICEnd) || !length(DICStart) || (DICEnd < DICStart)){
DICTable <- NA
- }else{
+ } else {
DICTable <- logfile[DICStart:DICEnd]
DICTable <- sapply(strsplit(DICTable, "\t"), "[")
colnames(DICTable) <- DICTable[1,]
DICTable <- t(apply(DICTable[-1,], 2, as.numeric))
colnames(DICTable) <- c("Dbar", "Dhat", "pD", "DIC")
}
- return(list(stats = statsTable, DIC = DICTable))
+ list(stats=statsTable, DIC=DICTable)
}
Modified: trunk/R2WinBUGS/R/print.bugs.R
===================================================================
--- trunk/R2WinBUGS/R/print.bugs.R 2007-06-12 09:55:29 UTC (rev 24)
+++ trunk/R2WinBUGS/R/print.bugs.R 2007-06-12 09:57:21 UTC (rev 25)
@@ -1,29 +1,33 @@
-fround <- function(x, digits)
+fround <- function(x, digits)
format(round(x, digits), nsmall=digits)
-
-print.bugs <- function(x, digits.summary = 1, ...){
+
+print.bugs <- function(x, digits.summary = 1, ...)
+{
if(!is.null(x$model.file))
cat("Inference for Bugs model at \"", x$model.file, "\", ", sep="")
if(!is.null(x$program))
cat("fit using ", x$program, ",", sep="")
- cat("\n ", x$n.chains, " chains, each with ", x$n.iter,
+ cat("\n ", x$n.chains, " chains, each with ", x$n.iter,
" iterations (first ", x$n.burnin, " discarded)", sep = "")
if(x$n.thin > 1) cat(", n.thin =", x$n.thin)
cat("\n n.sims =", x$n.sims, "iterations saved\n")
print(round(x$summary, digits.summary), ...)
- if(x$n.chains > 1){
+ if(x$n.chains > 1) {
cat("\nFor each parameter, n.eff is a crude measure of effective sample size,")
cat("\nand Rhat is the potential scale reduction factor (at convergence, Rhat=1).\n")
}
- if(length(x$DIC)==1 && x$DIC){
- cat("\npD =", fround(x$pD, 1), "and DIC =", fround(x$DIC, 1),
- if(x$DICbyR) "(using the rule, pD = var(deviance)/2)\n" else "(using the rule, pD = Dbar-Dhat)\n")
- cat("DIC is an estimate of expected predictive error (lower deviance is better).\n")
+ msgDICrule <- ifelse(x$DICbyR,
+ "(using the rule, pD = var(deviance)/2)\n",
+ "(using the rule, pD = Dbar-Dhat)\n")
+ msgDIC <- "DIC is an estimate of expected predictive error (lower deviance is better).\n"
+ if(length(x$DIC) == 1 && x$DIC) {
+ cat("\npD =", fround(x$pD, 1), "and DIC =", fround(x$DIC, 1), msgDICrule)
+ cat(msgDIC)
}
else if(length(x$DIC)>1) {
- cat("\n")
- print(round(x$DIC, 1))
- cat("DIC is an estimate of expected predictive error (lower deviance is better).\n")
+ cat("\n")
+ print(round(x$DIC, 1))
+ cat(msgDIC)
}
invisible(x)
}
Modified: trunk/R2WinBUGS/man/bugs.log.Rd
===================================================================
--- trunk/R2WinBUGS/man/bugs.log.Rd 2007-06-12 09:55:29 UTC (rev 24)
+++ trunk/R2WinBUGS/man/bugs.log.Rd 2007-06-12 09:57:21 UTC (rev 25)
@@ -1,23 +1,26 @@
\name{bugs.log}
\alias{bugs.log}
\title{Read data from WinBUGS logfile}
-\description{Read data such as summary statistics and DIC information from the WinBUGS logfile.}
+\description{Read data such as summary statistics and DIC information
+ from the WinBUGS logfile}
\usage{
bugs.log(file)
}
\arguments{
- \item{file}{Location of the WinBUGS logfile.}
+ \item{file}{Location of the WinBUGS logfile}
}
\value{
A list with components
- \item{stats}{A matrix containing summary statistics for each element of each saved parameter.
- Comparable to the information in the element \code{summary} of a bugs object as returned by \code{\link{bugs}}.}
- \item{DIC}{A matrix containg the DIC statistics as returned from WinBUGS
- (which is different from the way \code{\link{bugs}} calculates it).}
+ \item{stats}{A matrix containing summary statistics for each saved
+ parameter. Comparable to the information in the element
+ \code{summary} of a bugs object as returned by \code{\link{bugs}}.}
+ \item{DIC}{A matrix containing the DIC statistics as returned from
+ WinBUGS.}
}
\details{
-In later releases of R2WiNBUGS, this function is considered to read the relevant data from the log file rather than
-analysing and calculating the relevant data in R / S-PLUS again.
+In later releases of R2WiNBUGS, this function is considered to read the
+relevant data from the log file rather than analysing and calculating
+the relevant data in R / S-PLUS again.
}
\seealso{The main function that generates the log file is \code{\link{bugs}}.}
\keyword{IO}
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <gg...@us...> - 2007-06-12 09:58:15
|
Revision: 26
http://svn.sourceforge.net/bugs-r/?rev=26&view=rev
Author: ggorjan
Date: 2007-06-12 02:58:15 -0700 (Tue, 12 Jun 2007)
Log Message:
-----------
bugs.Rd
- fixed useWINE documentation
- some formatting
bugs.R
- fixed use of is.null(DIC)
- some formatting
Modified Paths:
--------------
trunk/R2WinBUGS/R/bugs.R
trunk/R2WinBUGS/man/bugs.Rd
Modified: trunk/R2WinBUGS/R/bugs.R
===================================================================
--- trunk/R2WinBUGS/R/bugs.R 2007-06-12 09:57:21 UTC (rev 25)
+++ trunk/R2WinBUGS/R/bugs.R 2007-06-12 09:58:15 UTC (rev 26)
@@ -1,81 +1,83 @@
"bugs" <-
-function(data, inits, parameters.to.save, model.file = "model.bug",
- n.chains = 3, n.iter = 2000, n.burnin = floor(n.iter / 2),
- n.thin = max(1, floor(n.chains * (n.iter - n.burnin) / 1000)),
- bin = (n.iter - n.burnin) / n.thin,
- debug = FALSE, DIC = TRUE, digits = 5, codaPkg = FALSE,
- bugs.directory = "c:/Program Files/WinBUGS14/",
- program = c("winbugs", "openbugs", "WinBugs", "OpenBugs"),
- working.directory = NULL,
- clearWD = FALSE, useWINE = .Platform$OS.type != "windows", WINE = Sys.getenv("WINE"),
- newWINE = FALSE, WINEPATH = NULL){
-
+function(data, inits, parameters.to.save, model.file="model.bug",
+ n.chains=3, n.iter=2000, n.burnin=floor(n.iter / 2),
+ n.thin=max(1, floor(n.chains * (n.iter - n.burnin) / 1000)),
+ bin=(n.iter - n.burnin) / n.thin,
+ debug=FALSE, DIC=TRUE, digits=5, codaPkg=FALSE,
+ bugs.directory="c:/Program Files/WinBUGS14/",
+ program=c("winbugs", "openbugs", "WinBugs", "OpenBugs"),
+ working.directory=NULL,
+ clearWD=FALSE, useWINE=.Platform$OS.type != "windows", WINE=Sys.getenv("WINE"),
+ newWINE=FALSE, WINEPATH=NULL)
+{
program <- match.arg(program)
- if (program %in% c("openbugs", "OpenBugs"))
- if (is.R()){
- ## If OpenBUGS, we only call openbugs() and exit...
- return(openbugs(data, inits, parameters.to.save, model.file,
- n.chains, n.iter, n.burnin, n.thin, DIC, bugs.directory,
- working.directory, digits))
+ if(program %in% c("openbugs", "OpenBugs")) {
+ if(is.R()) {
+ ## If OpenBUGS, we only call openbugs() and exit...
+ return(openbugs(data, inits, parameters.to.save, model.file,
+ n.chains, n.iter, n.burnin, n.thin, DIC, bugs.directory,
+ working.directory, digits))
} else {
- stop ("OpenBUGS is not yet available in S-PLUS")
+ stop ("OpenBUGS is not yet available in S-PLUS")
}
+ }
## Checking number of inits, which is NOT save here:
if(!missing(inits) && !is.function(inits) && !is.null(inits) && (length(inits) != n.chains))
stop("Number of initialized chains (length(inits)) != n.chains")
- if(useWINE) {
- if (!is.R())
- stop ("Non-Windows platforms not yet supported in R2WinBUGS for S-PLUS")
+ if(useWINE) {
+ if(!is.R())
+ stop ("Non-Windows platforms not yet supported in R2WinBUGS for S-PLUS")
## attempt to find wine and winepath
- if (!nchar(WINE)) {
- WINE <- system("locate wine | grep bin/wine$", intern = TRUE)
- WINE <- WINE[length(WINE)]
+ if(!nchar(WINE)) {
+ WINE <- system("locate wine | grep bin/wine$", intern=TRUE)
+ WINE <- WINE[length(WINE)]
}
- if (!length(WINE)) stop("couldn't locate WINE binary")
- if (!nchar(WINEPATH)) {
- WINEPATH <- system("locate winepath | grep bin/winepath$", intern = TRUE)
- WINEPATH <- WINEPATH[length(WINEPATH)]
+ if(!length(WINE)) stop("couldn't locate WINE binary")
+ if(!nchar(WINEPATH)) {
+ WINEPATH <- system("locate winepath | grep bin/winepath$", intern=TRUE)
+ WINEPATH <- WINEPATH[length(WINEPATH)]
}
- if (!length(WINEPATH)) stop("couldn't locate WINEPATH binary")
- }
- if(!is.null(working.directory)){
- savedWD <- getwd()
- setwd(working.directory)
- on.exit(setwd(savedWD))
+ if(!length(WINEPATH)) stop("couldn't locate WINEPATH binary")
}
- if(!file.exists(model.file)) stop(paste(model.file, "does not exist."))
- if(file.info(model.file)$isdir) stop(paste(model.file, "is a directory, but a file is required."))
- if(!(length(data) == 1 && is.vector(data) && is.character(data) && data == "data.txt")){
- bugs.data(data, dir = getwd(), digits)
+ if(!is.null(working.directory)) {
+ savedWD <- getwd()
+ setwd(working.directory)
+ on.exit(setwd(savedWD))
+ }
+ if(!file.exists(model.file))
+ stop(paste(model.file, "does not exist."))
+ if(file.info(model.file)$isdir)
+ stop(paste(model.file, "is a directory, but a file is required."))
+ if(!(length(data) == 1 && is.vector(data) && is.character(data) && data == "data.txt")) {
+ bugs.data(data, dir=getwd(), digits)
} else if(!file.exists(data))
stop("File data.txt does not exist.")
bugs.inits(inits, n.chains, digits)
if(DIC) parameters.to.save <- c(parameters.to.save, "deviance")
## Model files with extension ".bug" need to be renamed to ".txt"
- if(length(grep("[.]bug$", model.file))){
+ if(length(grep("[.]bug$", model.file))) {
new.model.file <- sub("[.]bug$", ".txt", model.file)
- file.copy(model.file, new.model.file, overwrite = TRUE)
- on.exit(try(file.remove(new.model.file)), add = TRUE)
- } else new.model.file <- model.file
+ file.copy(model.file, new.model.file, overwrite=TRUE)
+ on.exit(try(file.remove(new.model.file)), add=TRUE)
+ } else {
+ new.model.file <- model.file
+ }
bugs.script(parameters.to.save, n.chains, n.iter, n.burnin, n.thin,
- new.model.file, debug=debug, is.inits=!is.null(inits),
- bin = bin, DIC = DIC, useWINE = useWINE, newWINE = newWINE, WINEPATH = WINEPATH)
- bugs.run(n.burnin, bugs.directory, WINE = WINE, useWINE = useWINE, WINEPATH = WINEPATH)
-
+ new.model.file, debug=debug, is.inits=!is.null(inits),
+ bin=bin, DIC=DIC, useWINE=useWINE, newWINE=newWINE,
+ WINEPATH=WINEPATH)
+ bugs.run(n.burnin, bugs.directory, WINE=WINE, useWINE=useWINE,
+ WINEPATH=WINEPATH)
if(codaPkg)
return(file.path(getwd(), paste("coda", 1:n.chains, ".txt", sep="")))
-
- if (is.R()){
- sims <- c(bugs.sims(parameters.to.save, n.chains, n.iter, n.burnin, n.thin, DIC),
- model.file = model.file, is.DIC = !is.null(DIC), program = program)
- } else {
- sims <- c(bugs.sims(parameters.to.save, n.chains, n.iter, n.burnin, n.thin, DIC),
- model.file = model.file, is.DIC = DIC, program = program)
+ sims <- c(bugs.sims(parameters.to.save, n.chains, n.iter, n.burnin,
+ n.thin, DIC),
+ model.file=model.file, is.DIC=DIC, program=program)
+ if(clearWD) {
+ file.remove(c("data.txt", "log.odc", "log.txt", "codaIndex.txt",
+ paste("inits", 1:n.chains, ".txt", sep=""),
+ paste("coda", 1:n.chains, ".txt", sep="")))
}
- if(clearWD)
- file.remove(c("data.txt", "log.odc", "log.txt", "codaIndex.txt",
- paste("inits", 1:n.chains, ".txt", sep=""),
- paste("coda", 1:n.chains, ".txt", sep="")))
class(sims) <- "bugs"
- return(sims)
+ sims
}
Modified: trunk/R2WinBUGS/man/bugs.Rd
===================================================================
--- trunk/R2WinBUGS/man/bugs.Rd 2007-06-12 09:57:21 UTC (rev 25)
+++ trunk/R2WinBUGS/man/bugs.Rd 2007-06-12 09:58:15 UTC (rev 26)
@@ -5,143 +5,172 @@
It automatically writes a WinBUGS script, calls the model,
and saves the simulations for easy access in R or S-PLUS.}
\usage{
-bugs(data, inits, parameters.to.save, model.file = "model.bug",
- n.chains = 3, n.iter = 2000, n.burnin = floor(n.iter/2),
- n.thin = max(1, floor(n.chains * (n.iter - n.burnin)/1000)),
- bin = (n.iter - n.burnin) / n.thin,
- debug = FALSE, DIC = TRUE, digits = 5, codaPkg = FALSE,
- bugs.directory = "c:/Program Files/WinBUGS14/",
- program = c("winbugs", "openbugs", "WinBugs", "OpenBugs"),
- working.directory = NULL, clearWD = FALSE,
- useWINE = .Platform$OS.type != "windows", WINE = Sys.getenv("WINE"),
- newWINE = FALSE, WINEPATH = NULL)
+bugs(data, inits, parameters.to.save, model.file="model.bug",
+ n.chains=3, n.iter=2000, n.burnin=floor(n.iter/2),
+ n.thin=max(1, floor(n.chains * (n.iter - n.burnin)/1000)),
+ bin=(n.iter - n.burnin) / n.thin,
+ debug=FALSE, DIC=TRUE, digits=5, codaPkg=FALSE,
+ bugs.directory="c:/Program Files/WinBUGS14/",
+ program=c("winbugs", "openbugs", "WinBugs", "OpenBugs"),
+ working.directory=NULL, clearWD=FALSE,
+ useWINE=.Platform$OS.type != "windows", WINE=Sys.getenv("WINE"),
+ newWINE=FALSE, WINEPATH=NULL)
}
\arguments{
- \item{data}{either a named list (names corresponding to variable names in the \code{model.file})
- of the data for the WinBUGS model, \emph{or}
- a vector or list of the names of the data objects used by the model.
- If \code{data = "data.txt"}, it is assumed that data have already been written to the working directory
- in a file called \file{data.txt}, e.g. by the function \code{\link{bugs.data}}.}
- \item{inits}{a list with \code{n.chains} elements; each element of the list is
- itself a list of starting values for the WinBUGS model, \emph{or}
- a function creating (possibly random) initial values.
- Alternatively, if \code{inits = NULL}, initial values are generated by WinBUGS}
- \item{parameters.to.save}{character vector of the names of the parameters to save which should be monitored}
+ \item{data}{either a named list (names corresponding to variable names
+ in the \code{model.file}) of the data for the WinBUGS model,
+ \emph{or} a vector or list of the names of the data objects used by
+ the model. If \code{data="data.txt"}, it is assumed that data have
+ already been written to the working directory in a file called
+ \file{data.txt}, e.g. by the function \code{\link{bugs.data}}.}
+ \item{inits}{a list with \code{n.chains} elements; each element of the
+ list is itself a list of starting values for the WinBUGS model,
+ \emph{or} a function creating (possibly random) initial values.
+ Alternatively, if \code{inits=NULL}, initial values are generated
+ by WinBUGS.}
+ \item{parameters.to.save}{character vector of the names of the
+ parameters to save which should be monitored}
\item{model.file}{file containing the model written in WinBUGS code.
The extension can be either \file{.bug} or \file{.txt}.
-
- If the extension is \file{.bug} and \code{program=="winbugs"},
+ If the extension is \file{.bug} and \code{program=="winbugs"},
a copy of the file with extension \file{.txt} will be created
- in the \code{bugs()} call and removed afterwards.
- Note that similarly named \file{.txt} files will be overwritten.}
+ in the \code{bugs()} call and removed afterwards. Note that
+ similarly named \file{.txt} files will be overwritten.}
\item{n.chains}{number of Markov chains (default: 3)}
- \item{n.iter}{number of total iterations per chain (including burn in; default: 2000)}
- \item{n.burnin}{length of burn in, i.e. number of iterations to discard at the beginning.
- Default is \code{n.iter/2}, that is, discarding the first half of the simulations.}
- \item{n.thin}{thinning rate. Must be a positive integer.
- Set \code{n.thin} > 1 to save memory and computation time if \code{n.iter} is large.
- Default is \code{max(1, floor(n.chains * (n.iter-n.burnin) / 1000))}
- which will only thin if there are at least 2000 simulations.}
- \item{bin}{number of iterations between saving of results
- (i.e. the coda files are saved after each \code{bin} iterations);
+ \item{n.iter}{number of total iterations per chain (including burn in;
+ default: 2000)}
+ \item{n.burnin}{length of burn in, i.e. number of iterations to
+ discard at the beginning. Default is \code{n.iter/2}, that is,
+ discarding the first half of the simulations.}
+ \item{n.thin}{thinning rate. Must be a positive integer. Set
+ \code{n.thin} > 1 to save memory and computation time if
+ \code{n.iter} is large. Default is \code{max(1, floor(n.chains *
+ (n.iter-n.burnin) / 1000))} which will only thin if there are at
+ least 2000 simulations.}
+ \item{bin}{number of iterations between saving of results
+ (i.e. the coda files are saved after each \code{bin} iterations);
default is to save only at the end.}
\item{debug}{if \code{FALSE} (default), WinBUGS is closed automatically
- when the script has finished running, otherwise WinBUGS remains open for further investigation}
- \item{DIC}{logical; if \code{TRUE} (default), compute deviance, pD, and DIC.
- This is done in WinBUGS directly using the rule \code{pD = Dbar - Dhat}.
- If there are less iterations than required for the adaptive phase,
- the rule \code{pD = var(deviance) / 2} is used.}
- \item{digits}{number of significant digits used for WinBUGS input, see \code{\link{formatC}}}
- \item{codaPkg}{logical; if \code{FALSE} (default) a \code{bugs} object is returned,
- if \code{TRUE} file names of WinBUGS output are returned for easy access by the \pkg{coda} package
- through function \code{\link{read.bugs}}. (not used if \code{program = "openbugs"})}
+ when the script has finished running, otherwise WinBUGS remains open
+ for further investigation}
+ \item{DIC}{logical; if \code{TRUE} (default), compute deviance, pD,
+ and DIC. This is done in WinBUGS directly using the rule \code{pD =
+ Dbar - Dhat}. If there are less iterations than required for the
+ adaptive phase, the rule \code{pD=var(deviance) / 2} is used.}
+ \item{digits}{number of significant digits used for WinBUGS input, see
+ \code{\link{formatC}}}
+ \item{codaPkg}{logical; if \code{FALSE} (default) a \code{bugs} object
+ is returned, if \code{TRUE} file names of WinBUGS output are
+ returned for easy access by the \pkg{coda} package through function
+ \code{\link{read.bugs}} (not used if \code{program="openbugs"}).}
\item{bugs.directory}{directory that contains the WinBUGS executable}
- \item{program}{the program to use, either \code{winbugs}/\code{WinBugs} or \code{openbugs}/\code{OpenBugs},
- the latter makes use of function \code{\link{openbugs}} and requires the CRAN package \pkg{BRugs}.
- The \code{openbugs}/\code{OpenBugs} choice is not available in S-PLUS.}
- \item{working.directory}{sets working directory during execution of this function;
- WinBUGS' in- and output will be stored in this directory;
- if \code{NULL}, the current working directory is chosen.}
- \item{clearWD}{logical; indicating whether the files \file{data.txt},
- \file{inits[1:n.chains].txt}, \file{log.odc}, \file{codaIndex.txt}, and
- \file{coda[1:nchains].txt} should be removed after WinBUGS has finished.
- If set to \code{TRUE}, this argument is only respected if \code{codaPkg = FALSE}.
- }
- \item{useWINE}{logical; attempt to use the WINE emulator to run WinBUGS,
- defaults to \code{TRUE} on Windows, and \code{FALSE} otherwise.
- If WINE is used, the arguments \code{bugs.directory} and \code{working.directory} must be given in form of Linux paths
- rather than Windows paths (if not \code{NULL}).
- The \code{useWINE = TRUE} option is not available in S-PLUS.}
+ \item{program}{the program to use, either
+ \code{winbugs}/\code{WinBugs} or \code{openbugs}/\code{OpenBugs},
+ the latter makes use of function \code{\link{openbugs}} and requires
+ the CRAN package \pkg{BRugs}. The \code{openbugs}/\code{OpenBugs}
+ choice is not available in S-PLUS.}
+ \item{working.directory}{sets working directory during execution of
+ this function; WinBUGS' in- and output will be stored in this
+ directory; if \code{NULL}, the current working directory is chosen.}
+ \item{clearWD}{logical; indicating whether the files \file{data.txt},
+ \file{inits[1:n.chains].txt}, \file{log.odc}, \file{codaIndex.txt},
+ and \file{coda[1:nchains].txt} should be removed after WinBUGS has
+ finished. If set to \code{TRUE}, this argument is only respected if
+ \code{codaPkg=FALSE}.}
+ \item{useWINE}{logical; attempt to use the WINE emulator to run
+ WinBUGS, defaults to \code{FALSE} on Windows, and \code{TRUE}
+ otherwise. If WINE is used, the arguments \code{bugs.directory} and
+ \code{working.directory} must be given in form of Linux paths rather
+ than Windows paths (if not \code{NULL}). The \code{useWINE=TRUE}
+ option is not available in S-PLUS.}
\item{WINE}{character; name of WINE binary file}
\item{newWINE}{Set this one to \code{TRUE} for new versions of WINE.}
- \item{WINEPATH}{Path the WINE, it is tried hard to get the information automatically if not given.}
+ \item{WINEPATH}{Path to WINE binary file, it is tried hard to get the
+ information automatically if not given.}
}
\details{
-To run:
-\enumerate{
-\item Write a WinBUGS model in a ASCII file.
-\item Go into R / S-PLUS.
-\item Prepare the inputs to the \code{bugs} function and run it (see Example).
-\item A WinBUGS window will pop up and R / S-PLUS will freeze up. The model
- will now run in WinBUGS. It might take awhile. You will see
- things happening in the Log window within WinBUGS. When WinBugs
- is done, its window will close and R / S-PLUS will work again.
-\item If an error message appears, re-run with \code{debug = TRUE}.
-}}
+ To run:
+ \enumerate{
+ \item Write a WinBUGS model in a ASCII file.
+ \item Go into R / S-PLUS.
+ \item Prepare the inputs to the \code{bugs} function and run it (see
+ Example).
+ \item A WinBUGS window will pop up and R / S-PLUS will freeze
+ up. The model will now run in WinBUGS. It might take awhile. You
+ will see things happening in the Log window within WinBUGS. When
+ WinBugs is done, its window will close and R / S-PLUS will work
+ again.
+ \item If an error message appears, re-run with \code{debug=TRUE}.
+ }
+}
+
\value{
- If \code{codaPkg = TRUE} the returned values are the names
- of coda output files written by WinBUGS containing
- the Markov Chain Monte Carlo output in the CODA format.
- This is useful for direct access with \code{\link{read.bugs}}.
+ If \code{codaPkg=TRUE} the returned values are the names
+ of coda output files written by WinBUGS containing
+ the Markov Chain Monte Carlo output in the CODA format.
+ This is useful for direct access with \code{\link{read.bugs}}.
- If \code{codaPkg = FALSE}, the following values are returned:
+ If \code{codaPkg=FALSE}, the following values are returned:
\item{n.chains}{see Section \sQuote{Arguments}}
\item{n.iter}{see Section \sQuote{Arguments}}
\item{n.burnin}{see Section \sQuote{Arguments}}
\item{n.thin}{see Section \sQuote{Arguments}}
- \item{n.keep}{number of iterations kept per chain (equal to \code{(n.iter-n.burnin) / n.thin})}
- \item{n.sims}{number of posterior simulations (equal to \code{n.chains * n.keep})}
+ \item{n.keep}{number of iterations kept per chain (equal to
+ \code{(n.iter-n.burnin) / n.thin})}
+ \item{n.sims}{number of posterior simulations (equal to
+ \code{n.chains * n.keep})}
\item{sims.array}{3-way array of simulation output, with dimensions
n.keep, n.chains, and length of combined parameter vector}
- \item{sims.list}{list of simulated parameters:\cr
- for each scalar parameter, a vector of length n.sims\cr
- for each vector parameter, a 2-way array of simulations,\cr
+ \item{sims.list}{list of simulated parameters:
+ for each scalar parameter, a vector of length n.sims
+ for each vector parameter, a 2-way array of simulations,
for each matrix parameter, a 3-way array of simulations, etc.
- (for convenience, the \code{n.keep * n.chains} simulations in
- sims.matrix and sims.list (but NOT sims.array have been randomly permuted)}
- \item{sims.matrix}{matrix of simulation output, with \code{n.chains * n.keep} rows and
- one column for each element of each saved parameter
- (for convenience, the \code{n.keep * n.chains} simulations in
- sims.matrix and sims.list (but NOT sims.array have been randomly permuted)}
- \item{summary}{summary statistics and convergence information for each
- element of each saved parameter.}
+ (for convenience, the \code{n.keep*n.chains} simulations in
+ sims.matrix and sims.list (but NOT sims.array) have been randomly
+ permuted)}
+ \item{sims.matrix}{matrix of simulation output, with
+ \code{n.chains*n.keep} rows and one column for each element of
+ each saved parameter (for convenience, the \code{n.keep*n.chains}
+ simulations in sims.matrix and sims.list (but NOT sims.array) have
+ been randomly permuted)}
+ \item{summary}{summary statistics and convergence information for
+ each saved parameter.}
\item{mean}{a list of the estimated parameter means}
\item{sd}{a list of the estimated parameter standard deviations}
\item{median}{a list of the estimated parameter medians}
- \item{root.short}{names of argument \code{parameters.to.save} and \dQuote{deviance}}
+ \item{root.short}{names of argument \code{parameters.to.save} and
+ \dQuote{deviance}}
\item{long.short}{indexes; programming stuff}
\item{dimension.short}{dimension of \code{indexes.short}}
\item{indexes.short}{indexes of \code{root.short}}
- \item{last.values}{list of simulations from the most recent iteration; they
- can be used as starting points if you wish to run WinBUGS for further iterations}
- \item{pD}{an estimate of the effective number of parameters, for calculations see the section \dQuote{Arguments}.}
+ \item{last.values}{list of simulations from the most recent
+ iteration; they can be used as starting points if you wish to run
+ WinBUGS for further iterations}
+ \item{pD}{an estimate of the effective number of parameters, for
+ calculations see the section \dQuote{Arguments}.}
\item{DIC}{\code{mean(deviance) + pD}}
}
+
\references{
Gelman, A., Carlin, J.B., Stern, H.S., Rubin, D.B. (2003):
\emph{Bayesian Data Analysis}, 2nd edition, CRC Press.
- Sturtz, S., Ligges, U., Gelman, A. (2005):
- R2WinBUGS: A Package for Running WinBUGS from R.
+ Sturtz, S., Ligges, U., Gelman, A. (2005):
+ R2WinBUGS: A Package for Running WinBUGS from R.
\emph{Journal of Statistical Software} 12(3), 1-16.
}
-
-\author{Andrew Gelman, \email{ge...@st...}, \url{http:/www.stat.columbia.edu/~gelman/bugsR/};
- modifications and packaged by Sibylle Sturtz, \email{st...@st...}, and Uwe Ligges.}
-\seealso{\code{\link{print.bugs}}, \code{\link{plot.bugs}}, and the \pkg{coda} package}
+
+\author{Andrew Gelman, \email{ge...@st...},
+ \url{http:/www.stat.columbia.edu/~gelman/bugsR/}; modifications and
+ packaged by Sibylle Sturtz, \email{st...@st...},
+ and Uwe Ligges.}
+
+\seealso{\code{\link{print.bugs}}, \code{\link{plot.bugs}}, and the
+ \pkg{coda} package}
+
\examples{
# An example model file is given in:
-model.file <- system.file(package = "R2WinBUGS", "model", "schools.txt")
+model.file <- system.file(package="R2WinBUGS", "model", "schools.txt")
# Let's take a look:
file.show(model.file)
@@ -154,17 +183,17 @@
sigma.y <- schools$sd
data <- list ("J", "y", "sigma.y")
inits <- function(){
- list(theta = rnorm(J, 0, 100), mu.theta = rnorm(1, 0, 100),
- sigma.theta = runif(1, 0, 100))
+ list(theta=rnorm(J, 0, 100), mu.theta=rnorm(1, 0, 100),
+ sigma.theta=runif(1, 0, 100))
}
## or alternatively something like:
# inits <- list(
-# list(theta = rnorm(J, 0, 90), mu.theta = rnorm(1, 0, 90),
-# sigma.theta = runif(1, 0, 90)),
-# list(theta = rnorm(J, 0, 100), mu.theta = rnorm(1, 0, 100),
-# sigma.theta = runif(1, 0, 100))
-# list(theta = rnorm(J, 0, 110), mu.theta = rnorm(1, 0, 110),
-# sigma.theta = runif(1, 0, 110)))
+# list(theta=rnorm(J, 0, 90), mu.theta=rnorm(1, 0, 90),
+# sigma.theta=runif(1, 0, 90)),
+# list(theta=rnorm(J, 0, 100), mu.theta=rnorm(1, 0, 100),
+# sigma.theta=runif(1, 0, 100))
+# list(theta=rnorm(J, 0, 110), mu.theta=rnorm(1, 0, 110),
+# sigma.theta=runif(1, 0, 110)))
parameters <- c("theta", "mu.theta", "sigma.theta")
@@ -172,9 +201,9 @@
## You may need to edit "bugs.directory",
## also you need write access in the working directory:
schools.sim <- bugs(data, inits, parameters, model.file,
- n.chains = 3, n.iter = 5000,
- bugs.directory = "c:/Program Files/WinBUGS14/",
- working.directory = NULL, clearWD = TRUE)
+ n.chains=3, n.iter=5000,
+ bugs.directory="c:/Program Files/WinBUGS14/",
+ working.directory=NULL, clearWD=TRUE)
print(schools.sim)
plot(schools.sim)
}
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <gg...@us...> - 2007-06-12 10:09:17
|
Revision: 28
http://svn.sourceforge.net/bugs-r/?rev=28&view=rev
Author: ggorjan
Date: 2007-06-12 03:09:18 -0700 (Tue, 12 Jun 2007)
Log Message:
-----------
version bump, merged and reversed ChangeLog files, note about supported BUGS versions
Modified Paths:
--------------
trunk/R2WinBUGS/Changes
trunk/R2WinBUGS/DESCRIPTION
trunk/R2WinBUGS/man/bugs.Rd
Removed Paths:
-------------
trunk/R2WinBUGS/Changes0
Modified: trunk/R2WinBUGS/Changes
===================================================================
--- trunk/R2WinBUGS/Changes 2007-06-12 09:58:57 UTC (rev 27)
+++ trunk/R2WinBUGS/Changes 2007-06-12 10:09:18 UTC (rev 28)
@@ -1,51 +1,37 @@
Changes to R2WinBUGS:
=====================
-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 ...
+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
+- some internal fixes related to is.null(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 0.2-2 (28 Apr 2004):
-- schools data: original (see references) instead of the rounded data
+Update 2.1-3 (13 May 2007):
+- Ported to S-PLUS by Insightful Corp.
+- some fixes for codetools checks
-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 2.0-4 (01 November 2006):
+- print.bugs / plot.bugs documentation fixes
+- write.model() fix
-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 2.0-3 (06 October 2006):
+- \\. -> [.] in regular expressions
-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 2.0-2 (26 July 2006):
+- changes for DIC, making use of BUGS internal calculations
+- some doc fixes
-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 2.0-1 (26 May 2006):
+- some wine patches for 2.2-0 by Gregor Gorjanc
-Update 0.2-8 (30 May 2005):
-- bugs passed DIC to bugs.script in order to be able to disable it
-
-Update 0.2-9 (26 July 2005):
-- bugs has new argument clearWD
-
-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 1.0-1 (14 Nov 2005):
-- make inits=NULL work (again ?)
-
-Update 1.1-0 (14 Dec 2005):
-- Contribution by Ben Bolker and Yun Yan's rbugs package:
- make R2WinBUGS work under WINE
-
-Update 1.1-1 (17 Feb 2006):
-- WINE tweaks (mainly 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)
@@ -56,25 +42,188 @@
Jouni Kerman and Andrew Gelman
- new function write.model() based on ideas from Jouni Kerman
-Update 2.0-1 (26 May 2006):
-- some wine patches for 2.2-0 by Gregor Gorjanc
+Update 1.1-1 (17 Feb 2006):
+- WINE tweaks (mainly by Gregor Gorjanc)
-Update 2.0-2 (26 July 2006):
-- changes for DIC, making use of BUGS internal calculations
-- some doc fixes
+Update 1.1-0 (14 Dec 2005):
+- Contribution by Ben Bolker and Yun Yan's rbugs package:
+ make R2WinBUGS work under WINE
-Update 2.0-3 (06 October 2006):
-- \\. -> [.] in regular expressions
+Update 1.0-1 (14 Nov 2005):
+- make inits=NULL work (again ?)
-Update 2.0-4 (01 November 2006):
-- print.bugs / plot.bugs documentation fixes
-- write.model() fix
+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 2.1-3 (13 May 2007):
-- Ported to S-PLUS by Insightful Corp.
-- some fixes for codetools checks
+Update 0.2-9 (26 July 2005):
+- bugs has new argument clearWD
-Update 2.1-4 (20 May 2007):
-- Depending on coda now (Namespace issues)
-- some more fixes for codetools checks
-- Vignette has been updated
+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:
+ 1. Fixed "bugs.data.inits" function so you can use data that have the
+ same names as R functions.
+ 2. Changed T and F to TRUE and FALSE everywhere in case the variables
+ T and F are used as data in the main program
+ 3. 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.
+ 4. 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:
+ 1. The "attach.all" function (no longer called "attach2") overwrites
+ so that all components of a list or data frame get attached.
+ 2. Program now looks in the directory /winbug~1/ rather than /winbug~2/
+ 3. Graphics parameters for margins are returned to their original state
+ at the end of the program.
+ 4. Added "digits.summary" option to the numerical display.
+ 5. 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:
+ 1. 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!
+ 2. 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).
+ 3. 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:
+ 1. 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.)
+ 2. 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:
+ 1. Fix display.parallel=T option by adding min.width so that very
+ intervals are still visible.
+ 2. 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:
+ 1. Approximate "effective sample size" n.eff given for each parameter.
+ 2. More explanatory material displayed.
+ 3. Use bringToTop() to automatically bring up the graphics window.
+Update 4 Feb 2003:
+ 1. 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.)
+ 2. 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:
+ 1. Fix of bug that occurred with uppercase and lowercase variable names
+ 2. Set default for n.thin so that no more than about 500 iterations
+ will be saved from each sequence
+ 3. 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:
+ 1. Automatic fixing of adaptive phases. Now you no longer need to run
+ for thousands of iterations when slice or Metropolis sampling is used.
+ 2. Various minor fixes
+Update 10 Dec 2002:
+ 1. Cool graphical display of convergence and inferences!
+ 2. New "attach2" function that overwrites so that all components of
+ the list are attached
+Update 29 Nov 2002:
+ 1. Fix of bug in 24 Nov update.
+ 2. Fix of bug in 16 Nov update.
+ 3. 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:
+ 1. Parameters saved in order of the "parameters.to.save" vector
+ (not alphabetical order).
+ 2. Output saved in both matrix and list form.
+ 3. 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
Deleted: trunk/R2WinBUGS/Changes0
===================================================================
--- trunk/R2WinBUGS/Changes0 2007-06-12 09:58:57 UTC (rev 27)
+++ trunk/R2WinBUGS/Changes0 2007-06-12 10:09:18 UTC (rev 28)
@@ -1,142 +0,0 @@
-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:
- 1. Fixed "bugs.data.inits" function so you can use data that have the
- same names as R functions.
- 2. Changed T and F to TRUE and FALSE everywhere in case the variables
- T and F are used as data in the main program
- 3. 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.
- 4. 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:
- 1. The "attach.all" function (no longer called "attach2") overwrites
- so that all components of a list or data frame get attached.
- 2. Program now looks in the directory /winbug~1/ rather than /winbug~2/
- 3. Graphics parameters for margins are returned to their original state
- at the end of the program.
- 4. Added "digits.summary" option to the numerical display.
- 5. 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:
- 1. 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!
- 2. 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).
- 3. 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:
- 1. 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.)
- 2. 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:
- 1. Fix display.parallel=T option by adding min.width so that very
- intervals are still visible.
- 2. 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:
- 1. Approximate "effective sample size" n.eff given for each parameter.
- 2. More explanatory material displayed.
- 3. Use bringToTop() to automatically bring up the graphics window.
-Update 4 Feb 2003:
- 1. 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.)
- 2. 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:
- 1. Fix of bug that occurred with uppercase and lowercase variable names
- 2. Set default for n.thin so that no more than about 500 iterations
- will be saved from each sequence
- 3. 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:
- 1. Automatic fixing of adaptive phases. Now you no longer need to run
- for thousands of iterations when slice or Metropolis sampling is used.
- 2. Various minor fixes
-Update 10 Dec 2002:
- 1. Cool graphical display of convergence and inferences!
- 2. New "attach2" function that overwrites so that all components of
- the list are attached
-Update 29 Nov 2002:
- 1. Fix of bug in 24 Nov update.
- 2. Fix of bug in 16 Nov update.
- 3. 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:
- 1. Parameters saved in order of the "parameters.to.save" vector
- (not alphabetical order).
- 2. Output saved in both matrix and list form.
- 3. 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
Modified: trunk/R2WinBUGS/DESCRIPTION
===================================================================
--- trunk/R2WinBUGS/DESCRIPTION 2007-06-12 09:58:57 UTC (rev 27)
+++ trunk/R2WinBUGS/DESCRIPTION 2007-06-12 10:09:18 UTC (rev 28)
@@ -1,7 +1,7 @@
Package: R2WinBUGS
Title: Running WinBUGS and OpenBUGS from R / S-PLUS
Date: 2007-05-20
-Version: 2.1-4
+Version: 2.1-5
Author: originally written by Andrew Gelman <ge...@st...>;
changes and packaged by Sibylle Sturtz <st...@st...>
and Uwe Ligges <li...@st...>.
Modified: trunk/R2WinBUGS/man/bugs.Rd
===================================================================
--- trunk/R2WinBUGS/man/bugs.Rd 2007-06-12 09:58:57 UTC (rev 27)
+++ trunk/R2WinBUGS/man/bugs.Rd 2007-06-12 10:09:18 UTC (rev 28)
@@ -102,6 +102,12 @@
again.
\item If an error message appears, re-run with \code{debug=TRUE}.
}
+
+ BUGS version support:
+ \itemize{
+ \item WinBUGS 1.4* (this is the only version that works under Linux)
+ \item OpenBUGS 2.* (via argument \code{program="OpenBUGS"})
+ }
}
\value{
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <gg...@us...> - 2007-08-23 07:44:09
|
Revision: 37
http://bugs-r.svn.sourceforge.net/bugs-r/?rev=37&view=rev
Author: ggorjan
Date: 2007-08-23 00:44:10 -0700 (Thu, 23 Aug 2007)
Log Message:
-----------
now default argument values should also work for Linux side using WINE + some code cleanup; hold your breath plase until I test this on Windows machine
Modified Paths:
--------------
trunk/R2WinBUGS/Changes
trunk/R2WinBUGS/DESCRIPTION
trunk/R2WinBUGS/R/bugs.R
trunk/R2WinBUGS/R/bugs.run.R
trunk/R2WinBUGS/R/bugs.script.R
trunk/R2WinBUGS/R/wineutils.R
trunk/R2WinBUGS/man/bugs.Rd
trunk/R2WinBUGS/man/bugs.run.Rd
trunk/R2WinBUGS/man/bugs.script.Rd
Modified: trunk/R2WinBUGS/Changes
===================================================================
--- trunk/R2WinBUGS/Changes 2007-08-08 11:31:43 UTC (rev 36)
+++ trunk/R2WinBUGS/Changes 2007-08-23 07:44:10 UTC (rev 37)
@@ -1,6 +1,13 @@
Changes to R2WinBUGS:
=====================
+Update 2.1-6 (23 August 2007):
+- reverting back to use thin.updater since it is faster, however CODA files
+ have "wrong" indexes
+- WINE arguments are now set in such a way that defaults work on Windows
+ and Linux
+- minor formatting in the code and help files
+
Update 2.1-5 (12 June 2007):
- proper indexing of CODA files also in R version
- fixed useWINE documentation in bugs help page
Modified: trunk/R2WinBUGS/DESCRIPTION
===================================================================
--- trunk/R2WinBUGS/DESCRIPTION 2007-08-08 11:31:43 UTC (rev 36)
+++ trunk/R2WinBUGS/DESCRIPTION 2007-08-23 07:44:10 UTC (rev 37)
@@ -1,7 +1,7 @@
Package: R2WinBUGS
Title: Running WinBUGS and OpenBUGS from R / S-PLUS
Date: 2007-05-20
-Version: 2.1-5
+Version: 2.1-6
Author: originally written by Andrew Gelman <ge...@st...>;
changes and packaged by Sibylle Sturtz <st...@st...>
and Uwe Ligges <li...@st...>.
Modified: trunk/R2WinBUGS/R/bugs.R
===================================================================
--- trunk/R2WinBUGS/R/bugs.R 2007-08-08 11:31:43 UTC (rev 36)
+++ trunk/R2WinBUGS/R/bugs.R 2007-08-23 07:44:10 UTC (rev 37)
@@ -7,38 +7,30 @@
bugs.directory="c:/Program Files/WinBUGS14/",
program=c("WinBUGS", "OpenBUGS", "winbugs", "openbugs"),
working.directory=NULL,
- clearWD=FALSE, useWINE=.Platform$OS.type != "windows", WINE=Sys.getenv("WINE"),
- newWINE=FALSE, WINEPATH=NULL)
+ clearWD=FALSE, useWINE=.Platform$OS.type != "windows", WINE=NULL,
+ newWINE=TRUE, WINEPATH=NULL)
{
program <- match.arg(program)
if(program %in% c("openbugs", "OpenBUGS", "OpenBugs")) {
- if(is.R()) {
- ## If OpenBUGS, we only call openbugs() and exit...
- return(openbugs(data, inits, parameters.to.save, model.file,
- n.chains, n.iter, n.burnin, n.thin, DIC=DIC,
- bugs.directory, working.directory, digits))
- } else {
- stop ("OpenBUGS is not yet available in S-PLUS")
- }
+ if(!is.R()) stop("OpenBUGS is not yet available in S-PLUS")
+ ## If OpenBUGS, we only call openbugs() and exit...
+ return(openbugs(data, inits, parameters.to.save, model.file,
+ n.chains, n.iter, n.burnin, n.thin, DIC=DIC,
+ bugs.directory, working.directory, digits))
}
## Checking number of inits, which is NOT save here:
if(!missing(inits) && !is.function(inits) && !is.null(inits) && (length(inits) != n.chains))
stop("Number of initialized chains (length(inits)) != n.chains")
+
+ ## Wine
if(useWINE) {
if(!is.R())
- stop ("Non-Windows platforms not yet supported in R2WinBUGS for S-PLUS")
- ## attempt to find wine and winepath
- if(!nchar(WINE)) {
- WINE <- system("locate wine | grep bin/wine$", intern=TRUE)
- WINE <- WINE[length(WINE)]
- }
- if(!length(WINE)) stop("couldn't locate WINE binary")
- if(!nchar(WINEPATH)) {
- WINEPATH <- system("locate winepath | grep bin/winepath$", intern=TRUE)
- WINEPATH <- WINEPATH[length(WINEPATH)]
- }
- if(!length(WINEPATH)) stop("couldn't locate WINEPATH binary")
+ stop("Non-Windows platforms not yet supported in R2WinBUGS for S-PLUS")
+ ## Attempt to find wine and winepath
+ if(is.null(WINE)) WINE <- findUnixBinary(x="wine")
+ if(is.null(WINEPATH)) WINEPATH <- findUnixBinary(x="winepath")
}
+
if(!is.null(working.directory)) {
savedWD <- getwd()
setwd(working.directory)
@@ -50,8 +42,9 @@
stop(paste(model.file, "is a directory, but a file is required."))
if(!(length(data) == 1 && is.vector(data) && is.character(data) && data == "data.txt")) {
bugs.data(data, dir=getwd(), digits)
- } else if(!file.exists(data))
- stop("File data.txt does not exist.")
+ } else {
+ if(!file.exists(data)) stop("File data.txt does not exist.")
+ }
bugs.inits(inits, n.chains, digits)
if(DIC) parameters.to.save <- c(parameters.to.save, "deviance")
## Model files with extension ".bug" need to be renamed to ".txt"
@@ -67,7 +60,7 @@
bin=bin, DIC=DIC, useWINE=useWINE, newWINE=newWINE,
WINEPATH=WINEPATH)
bugs.run(n.burnin, bugs.directory, WINE=WINE, useWINE=useWINE,
- WINEPATH=WINEPATH)
+ newWINE=newWINE, WINEPATH=WINEPATH)
if(codaPkg)
return(file.path(getwd(), paste("coda", 1:n.chains, ".txt", sep="")))
sims <- c(bugs.sims(parameters.to.save, n.chains, n.iter, n.burnin,
Modified: trunk/R2WinBUGS/R/bugs.run.R
===================================================================
--- trunk/R2WinBUGS/R/bugs.run.R 2007-08-08 11:31:43 UTC (rev 36)
+++ trunk/R2WinBUGS/R/bugs.run.R 2007-08-23 07:44:10 UTC (rev 37)
@@ -1,51 +1,55 @@
"bugs.run" <-
- function(n.burnin, bugs.directory, WINE = "",
- useWINE = .Platform$OS.type != "windows",
- newWINE = TRUE, WINEPATH = NULL){
-
-if(useWINE && !is.R())
- stop ("Non-Windows platforms not yet supported in R2WinBUGS for S-PLUS")
-if(useWINE && !newWINE) bugs.directory <- win2native(bugs.directory)
+ function(n.burnin, bugs.directory,
+ useWINE=.Platform$OS.type != "windows", WINE=NULL,
+ newWINE=TRUE, WINEPATH=NULL)
+{
-## Update the lengths of the adaptive phases in the Bugs updaters
+ if(useWINE && !is.R())
+ stop("Non-Windows platforms not yet supported in R2WinBUGS for S-PLUS")
+
+ ## Is bugs.directory defined in Windows (where second character is :
+ ## i.e. C:\Program...) or Unix style path?
+ test <- substr(bugs.directory, start=2, stop=2) == ":"
+ if(useWINE && test) {
+ bugs.directory <- win2native(bugs.directory, newWINE=newWINE, WINEPATH=WINEPATH)
+ }
+
+ ## Update the lengths of the adaptive phases in the Bugs updaters
try(bugs.update.settings(n.burnin, bugs.directory))
-## Return the lengths of the adaptive phases to their original settings
- if (is.R()){
- on.exit(try(file.copy(file.path(bugs.directory, "System/Rsrc/Registry_Rsave.odc"),
- file.path(bugs.directory, "System/Rsrc/Registry.odc"),
- overwrite = TRUE)))
- } else {
- on.exit(try(splus.file.copy(file.path(bugs.directory, "System/Rsrc/Registry_Rsave.odc"),
- file.path(bugs.directory, "System/Rsrc/Registry.odc"),
- overwrite = TRUE)))
- }
-
-## Search Win*.exe (WinBUGS executable) within bugs.directory
- dos.location <- file.path(bugs.directory,
- grep("^Win[[:alnum:]]*[.]exe$", list.files(bugs.directory), value = TRUE)[1])
- if(!file.exists(dos.location))
+
+ ## Return the lengths of the adaptive phases to their original settings
+ if(is.R()) {
+ .fileCopy <- file.copy
+ } else {
+ .fileCopy <- splus.file.copy
+ }
+ on.exit(try(.fileCopy(file.path(bugs.directory, "System/Rsrc/Registry_Rsave.odc"),
+ file.path(bugs.directory, "System/Rsrc/Registry.odc"),
+ overwrite=TRUE)))
+
+ ## Search Win*.exe (WinBUGS executable) within bugs.directory
+ dos.location <- file.path(bugs.directory,
+ grep("^Win[[:alnum:]]*[.]exe$",
+ list.files(bugs.directory), value=TRUE)[1])
+ if(!file.exists(dos.location))
stop(paste("WinBUGS executable does not exist in", bugs.directory))
-## Call Bugs and have it run with script.txt
+
+ ## Call Bugs and have it run with script.txt
bugsCall <- paste("\"", dos.location, "\" /par \"",
- native2win(file.path(getwd(), "script.txt"), newWINE = newWINE, WINEPATH = WINEPATH),
- "\"", sep = "")
- if (useWINE)
- bugsCall <- paste(WINE, bugsCall)
+ native2win(file.path(getwd(), "script.txt"),
+ useWINE=useWINE, newWINE=newWINE, WINEPATH=WINEPATH),
+ "\"", sep="")
+ if(useWINE) bugsCall <- paste(WINE, bugsCall)
temp <- system(bugsCall)
+ if(temp == -1)
+ stop("Error in bugs.run().\nCheck that WinBUGS is in the specified directory.")
- if(temp == -1)
- stop("Error in bugs.run().\nCheck that WinBUGS is in the specified directory.")
-## Stop and print an error message if Bugs did not run correctly
+ ## Stop and print an error message if Bugs did not run correctly
if(is.R()) {
- if(length(grep("Bugs did not run correctly",
- scan("coda1.txt", character(), quiet=TRUE, sep="\n"))) > 0)
- stop("Look at the log file and\ntry again with debug=TRUE and figure out what went wrong within Bugs.")
+ tmp <- scan("coda1.txt", character(), quiet=TRUE, sep="\n")
} else {
- if (length(grep("Bugs did not run correctly",
- scan("coda1.txt", character(), sep="\n"))) > 0)
- stop("Look at the log file and\ntry again with debug=TRUE and figure out what went wrong within Bugs.")
+ tmp <- scan("coda1.txt", character(), sep="\n")
}
+ if(length(grep("Bugs did not run correctly", tmp)) > 0)
+ stop("Look at the log file and\ntry again with 'debug=TRUE' to figure out what went wrong within Bugs.")
}
-
-
-
Modified: trunk/R2WinBUGS/R/bugs.script.R
===================================================================
--- trunk/R2WinBUGS/R/bugs.script.R 2007-08-08 11:31:43 UTC (rev 36)
+++ trunk/R2WinBUGS/R/bugs.script.R 2007-08-23 07:44:10 UTC (rev 37)
@@ -1,50 +1,65 @@
"bugs.script" <-
-function (parameters.to.save, n.chains, n.iter, n.burnin,
- n.thin, model.file, debug=FALSE, is.inits, bin,
- DIC = FALSE, useWINE = FALSE, newWINE = FALSE, WINEPATH = NULL){
-### Write file script.txt for Bugs to read
+ function(parameters.to.save, n.chains, n.iter, n.burnin,
+ n.thin, model.file, debug=FALSE, is.inits, bin,
+ DIC=FALSE, useWINE=.Platform$OS.type != "windows",
+ newWINE=TRUE, WINEPATH=NULL)
+{
+ ## Write file script.txt for Bugs
if((ceiling(n.iter/n.thin) - ceiling(n.burnin/n.thin)) < 2)
stop ("(n.iter-n.burnin)/n.thin must be at least 2")
working.directory <- getwd()
script <- "script.txt"
- model <- if(length(grep("\\\\", model.file)) || length(grep("/", model.file))){
- model.file
- } else file.path(working.directory, model.file)
+
+ test <- length(grep("\\\\", model.file)) || length(grep("/", model.file))
+ model <- ifelse(test, model.file, file.path(working.directory, model.file))
+ model <- native2win(model, useWINE=useWINE, newWINE=newWINE, WINEPATH=WINEPATH)
+
data <- file.path(working.directory, "data.txt")
+ data <- native2win(data, useWINE=useWINE, newWINE=newWINE, WINEPATH=WINEPATH)
+
coda <- file.path(working.directory, "coda")
- logfile <- file.path(working.directory, "log.odc")
- logfileTxt <- file.path(working.directory, "log.txt")
- inits <- sapply(paste(working.directory, "/inits", 1:n.chains, ".txt", sep=""),
- function(x) native2win(x, , WINEPATH = WINEPATH))
+ coda <- native2win(coda, useWINE=useWINE, newWINE=newWINE, WINEPATH=WINEPATH)
+
+ logFile <- file.path(working.directory, "log.odc")
+ logFile <- native2win(logFile, useWINE=useWINE, newWINE=newWINE, WINEPATH=WINEPATH)
+ logFileTxt <- file.path(working.directory, "log.txt")
+ logFileTxt <- native2win(logFileTxt, useWINE=useWINE, newWINE=newWINE, WINEPATH=WINEPATH)
+
+ inits <- paste(working.directory, "/inits", 1:n.chains, ".txt", sep="")
+ inits <- sapply(inits, function(x) native2win(x, useWINE=useWINE, newWINE=newWINE, WINEPATH=WINEPATH))
+
initlist <- paste("inits (", 1:n.chains, ", '", inits, "')\n", sep="")
+
savelist <- paste("set (", parameters.to.save, ")\n", sep="")
redo <- ceiling((n.iter-n.burnin)/(n.thin*bin))
- thinUpdateCommand <- paste("thin.updater (", n.thin, ")\n",
- "update (", ceiling(n.burnin/n.thin), ")\n", sep = "")
+ thinUpdate <- paste("thin.updater (", n.thin, ")\n",
+ "update (", ceiling(n.burnin/n.thin), ")\n", sep="")
cat(
"display ('log')\n",
- "check ('", native2win(model, WINEPATH=WINEPATH), "')\n",
- "data ('", native2win(data, WINEPATH=WINEPATH), "')\n",
+ "check ('", model, "')\n",
+ "data ('", data, "')\n",
"compile (", n.chains, ")\n",
if(is.inits) initlist,
"gen.inits()\n",
- thinUpdateCommand,
+ thinUpdate,
savelist,
if(DIC) "dic.set()\n",
rep(
- c("update (", formatC(ceiling(bin), format = "d"), ")\n",
- "coda (*, '", native2win(coda, WINEPATH=WINEPATH), "')\n"),redo),
+ c("update (", formatC(ceiling(bin), format="d"), ")\n",
+ "coda (*, '", coda, "')\n"),redo),
"stats (*)\n",
if(DIC) "dic.stats()\n",
"history (*)\n",
- "save ('", native2win(logfile, WINEPATH=WINEPATH), "')\n",
- "save ('", native2win(logfileTxt, WINEPATH=WINEPATH), "')\n",
+ "save ('", logFile, "')\n",
+ "save ('", logFileTxt, "')\n",
file=script, sep="", append=FALSE)
- if (!debug) cat ("quit ()\n", file=script, append=TRUE)
- sims.files <- paste ("coda", 1:n.chains, ".txt", sep="")
- for (i in 1:n.chains) cat ("WinBUGS did not run correctly.\n",
- file=sims.files[i], append=FALSE)
+
+ if(!debug) cat("quit ()\n", file=script, append=TRUE)
+
+ sims.files <- paste("coda", 1:n.chains, ".txt", sep="")
+ for(i in 1:n.chains)
+ cat("WinBUGS did not run correctly.\n", file=sims.files[i], append=FALSE)
}
Modified: trunk/R2WinBUGS/R/wineutils.R
===================================================================
--- trunk/R2WinBUGS/R/wineutils.R 2007-08-08 11:31:43 UTC (rev 36)
+++ trunk/R2WinBUGS/R/wineutils.R 2007-08-23 07:44:10 UTC (rev 37)
@@ -1,65 +1,110 @@
-## from Jun Yan's rbugs package, extended
+findUnixBinary <- function(x)
+{
+ ## --- Environmental variable ---
+ tmp <- Sys.getenv(toupper(x))
+ if(nchar(tmp) != 0) return(tmp)
+ ## else
-if (is.R()){
+ ## --- Standard place ---
+ tmp <- paste("/usr/bin", x, sep="")
+ if(file.exists(tmp)) return(tmp)
+ ## else ...
-## get drive mapping table from ~/.wine/config
-winedriveMap <- function(config="~/.wine/config") {
- if (!file.exists(config)) return (NULL);
- con <- readLines(config)
- con <- con[- grep("^;", con)]
- drive <- con[grep("^\\[Drive ", con)]
- drive <- substr(drive, 8, 8)
- drive <- paste(drive, ":", sep="")
- path <- con[grep("Path", con)]
- len <- length(drive)
- path <- path[1:len]
- dir <- sapply(path,
- function(x) {
- foo <- unlist(strsplit(x, "\""))
- foo[length(foo)]
- })
- dir <- sub("%HOME%",tools::file_path_as_absolute("~"),dir)
- data.frame(drive = I(drive), path = I(dir), row.names=NULL)
-}
+ ## --- Which ---
+ tmp <- system(paste("which ", x, sep=""), intern=TRUE)
+ if(length(tmp) != 0) return(tmp)
+ ## else ..
-## translate windows dir to native dir
-winedriveTr <- function(windir, DriveTable=winedriveMap()) {
- win.dr <- substr(windir, 1, 2)
- ind <- pmatch(toupper(win.dr), DriveTable$drive)
- native.dr <- DriveTable$path[ind]
- sub(win.dr, native.dr, windir)
+ ## --- Locate ---
+ tmp <- system(paste("locate ", x, " | grep bin/", x, "$", sep=""), intern=TRUE)
+ tmp <- tmp[length(tmp)] ## keep only last hit
+ if(length(tmp) > 0) return(tmp)
+
+ stop(paste("couldn't find", x, "binary file"))
}
-## translate full Unix path to Wine path
-winedriveRTr <- function(unixpath, DriveTable=winedriveMap()) {
- blocks <- strsplit(unixpath,"/")[[1]]
- cblocks <- c("/",sapply(1+seq(along=blocks[-1]),
- function(n) paste(blocks[1:n],collapse="/")))
- path <- match(cblocks,DriveTable$path)
- if (any(!is.na(path))) {
- unixdir <- cblocks[which.min(path)]
- windrive <- paste(DriveTable$drive[min(path,na.rm=TRUE)],"/",sep="")
- winpath <- sub("//","/",sub(unixdir,windrive,unixpath)) ## kluge
- } else stop("can't find equivalent Windows path: file may be inaccessible")
- winpath
+native2win <- function(x, useWINE=.Platform$OS.type != "windows",
+ newWINE=TRUE, WINEPATH=NULL)
+{
+ ## Translate Unix path to Windows (wine) path
+ if(useWINE) {
+ if(newWINE) {
+ if(is.null(WINEPATH)) WINEPATH <- findUnixBinary(x="winepath")
+ x <- system(paste(WINEPATH, "-w", x), intern=TRUE)
+ gsub("\\\\", "/", x) ## under wine BUGS cannot use \ or \\
+ } else {
+ winedriveRTr(x)
+ }
+ } else {
+ x
+ }
}
+## TODO: why are we masking these functions in S-PLUS
-win2native <- function(x, useWINE=.Platform$OS.type != "windows") { # win -> native
- if (useWINE) winedriveTr(x)
- else x
-}
+if(is.R()) {
-} # end if (is.R())
+ win2native <- function(x, useWINE=.Platform$OS.type != "windows",
+ newWINE=TRUE, WINEPATH=NULL)
+ {
+ ## Translate Windows path to native (unix) path
+ if(useWINE) {
+ if(newWINE) {
+ if(is.null(WINEPATH)) WINEPATH <- findUnixBinary(x="winepath")
+ system(paste(WINEPATH, " \"", x, "\"", sep=""), intern=TRUE)
+ } else {
+ winedriveTr(x)
+ }
+ } else {
+ x
+ }
+ }
-native2win <- function(x, useWINE=.Platform$OS.type != "windows", newWINE=TRUE, WINEPATH=NULL) { # native -> win
- if(is.R()){
- if (useWINE && !newWINE) return(winedriveRTr(x))
- if (useWINE && newWINE) {
- x <- system(paste(WINEPATH, "-w", x), intern = TRUE)
- return(gsub("\\\\", "/", x)) ## under wine BUGS cannot use \ or \\
- } else x
- } else { #S-PLUS
- gsub("\\\\", "/", x)
+ winedriveMap <- function(config="~/.wine/config")
+ {
+ ## Get drive mapping table from ~/.wine/config
+ if(!file.exists(config)) return(NULL);
+ con <- readLines(config)
+ con <- con[- grep("^;", con)]
+ drive <- con[grep("^\\[Drive ", con)]
+ drive <- substr(drive, 8, 8)
+ drive <- paste(drive, ":", sep="")
+ path <- con[grep("Path", con)]
+ len <- length(drive)
+ path <- path[1:len]
+ dir <- sapply(path,
+ function(x) {
+ foo <- unlist(strsplit(x, "\""))
+ foo[length(foo)]
+ })
+ dir <- sub("%HOME%",tools::file_path_as_absolute("~"),dir)
+ data.frame(drive=I(drive), path=I(dir), row.names=NULL)
}
-}
+
+ winedriveTr <- function(windir, DriveTable=winedriveMap())
+ {
+ ## Translate Windows path to native (Unix) path
+ win.dr <- substr(windir, 1, 2)
+ ind <- pmatch(toupper(win.dr), DriveTable$drive)
+ native.dr <- DriveTable$path[ind]
+ sub(win.dr, native.dr, windir)
+ }
+
+ winedriveRTr <- function(unixpath, DriveTable=winedriveMap())
+ {
+ ## Translate Unix path to Windows (wine) path
+ blocks <- strsplit(unixpath,"/")[[1]]
+ cblocks <- c("/",sapply(1+seq(along=blocks[-1]),
+ function(n) paste(blocks[1:n],collapse="/")))
+ path <- match(cblocks,DriveTable$path)
+ if(any(!is.na(path))) {
+ unixdir <- cblocks[which.min(path)]
+ windrive <- paste(DriveTable$drive[min(path,na.rm=TRUE)],"/",sep="")
+ winpath <- sub("//","/",sub(unixdir,windrive,unixpath)) ## kludge
+ } else {
+ stop("can't find equivalent Windows path: file may be inaccessible")
+ }
+ winpath
+ }
+
+} # end of if(is.R())
Modified: trunk/R2WinBUGS/man/bugs.Rd
===================================================================
--- trunk/R2WinBUGS/man/bugs.Rd 2007-08-08 11:31:43 UTC (rev 36)
+++ trunk/R2WinBUGS/man/bugs.Rd 2007-08-23 07:44:10 UTC (rev 37)
@@ -3,8 +3,8 @@
\title{Run WinBUGS and OpenBUGS from R or S-PLUS}
\description{The \code{bugs} function takes data and starting values as
- input. It automatically writes a WinBUGS script, calls the model, and
- saves the simulations for easy access in R or S-PLUS.}
+ input. It automatically writes a \pkg{WinBUGS} script, calls the model, and
+ saves the simulations for easy access in \R or S-PLUS.}
\usage{
bugs(data, inits, parameters.to.save, model.file="model.bug",
@@ -15,25 +15,25 @@
bugs.directory="c:/Program Files/WinBUGS14/",
program=c("WinBUGS", "OpenBUGS", "winbugs", "openbugs"),
working.directory=NULL, clearWD=FALSE,
- useWINE=.Platform$OS.type != "windows", WINE=Sys.getenv("WINE"),
- newWINE=FALSE, WINEPATH=NULL)
+ useWINE=.Platform$OS.type != "windows", WINE=NULL,
+ newWINE=TRUE, WINEPATH=NULL)
}
\arguments{
\item{data}{either a named list (names corresponding to variable names
- in the \code{model.file}) of the data for the WinBUGS model,
+ in the \code{model.file}) of the data for the \pkg{WinBUGS} model,
\emph{or} a vector or list of the names of the data objects used by
the model. If \code{data="data.txt"}, it is assumed that data have
already been written to the working directory in a file called
\file{data.txt}, e.g. by the function \code{\link{bugs.data}}.}
\item{inits}{a list with \code{n.chains} elements; each element of the
- list is itself a list of starting values for the WinBUGS model,
+ list is itself a list of starting values for the \pkg{WinBUGS} model,
\emph{or} a function creating (possibly random) initial values.
Alternatively, if \code{inits=NULL}, initial values are generated
- by WinBUGS.}
+ by \pkg{WinBUGS}.}
\item{parameters.to.save}{character vector of the names of the
parameters to save which should be monitored}
- \item{model.file}{file containing the model written in WinBUGS code.
+ \item{model.file}{file containing the model written in \pkg{WinBUGS} code.
The extension can be either \file{.bug} or \file{.txt}.
If the extension is \file{.bug} and \code{program=="WinBUGS"},
a copy of the file with extension \file{.txt} will be created
@@ -53,69 +53,76 @@
\item{bin}{number of iterations between saving of results
(i.e. the coda files are saved after each \code{bin} iterations);
default is to save only at the end.}
- \item{debug}{if \code{FALSE} (default), WinBUGS is closed automatically
- when the script has finished running, otherwise WinBUGS remains open
+ \item{debug}{if \code{FALSE} (default), \pkg{WinBUGS} is closed automatically
+ when the script has finished running, otherwise \pkg{WinBUGS} remains open
for further investigation}
\item{DIC}{logical; if \code{TRUE} (default), compute deviance, pD,
- and DIC. This is done in WinBUGS directly using the rule \code{pD =
+ and DIC. This is done in \pkg{WinBUGS} directly using the rule \code{pD =
Dbar - Dhat}. If there are less iterations than required for the
adaptive phase, the rule \code{pD=var(deviance) / 2} is used.}
- \item{digits}{number of significant digits used for WinBUGS input, see
+ \item{digits}{number of significant digits used for \pkg{WinBUGS} input, see
\code{\link{formatC}}}
\item{codaPkg}{logical; if \code{FALSE} (default) a \code{bugs} object
- is returned, if \code{TRUE} file names of WinBUGS output are
+ is returned, if \code{TRUE} file names of \pkg{WinBUGS} output are
returned for easy access by the \pkg{coda} package through function
\code{\link{read.bugs}} (not used if \code{program="OpenBUGS"}).}
- \item{bugs.directory}{directory that contains the WinBUGS executable}
+ \item{bugs.directory}{directory that contains the \pkg{WinBUGS} executable}
\item{program}{the program to use, either
\code{winbugs}/\code{WinBUGS} or \code{openbugs}/\code{OpenBUGS},
the latter makes use of function \code{\link{openbugs}} and requires
the CRAN package \pkg{BRugs}. The \code{openbugs}/\code{OpenBUGS}
choice is not available in S-PLUS.}
\item{working.directory}{sets working directory during execution of
- this function; WinBUGS' in- and output will be stored in this
+ this function; \pkg{WinBUGS}' in- and output will be stored in this
directory; if \code{NULL}, the current working directory is chosen.}
\item{clearWD}{logical; indicating whether the files \file{data.txt},
\file{inits[1:n.chains].txt}, \file{log.odc}, \file{codaIndex.txt},
- and \file{coda[1:nchains].txt} should be removed after WinBUGS has
+ and \file{coda[1:nchains].txt} should be removed after \pkg{WinBUGS} has
finished. If set to \code{TRUE}, this argument is only respected if
\code{codaPkg=FALSE}.}
+
\item{useWINE}{logical; attempt to use the WINE emulator to run
- WinBUGS, defaults to \code{FALSE} on Windows, and \code{TRUE}
- otherwise. If WINE is used, the arguments \code{bugs.directory} and
- \code{working.directory} must be given in form of Linux paths rather
- than Windows paths (if not \code{NULL}). The \code{useWINE=TRUE}
- option is not available in S-PLUS.}
- \item{WINE}{character; name of WINE binary file}
- \item{newWINE}{Set this one to \code{TRUE} for new versions of WINE.}
- \item{WINEPATH}{Path to WINE binary file, it is tried hard to get the
- information automatically if not given.}
+ \pkg{WinBUGS}, defaults to \code{FALSE} on Windows, and \code{TRUE}
+ otherwise. Not available in S-PLUS.}
+ \item{WINE}{character, path to \file{wine} binary file, it is
+ tried hard to get the information automatically if not given.}
+ \item{newWINE}{Use new versions of WINE that have \file{winepath}
+ utility}
+ \item{WINEPATH}{character, path to \file{winepath} binary file, it is
+ tried hard to get the information automatically if not given.}
}
\details{
To run:
\enumerate{
- \item Write a WinBUGS model in a ASCII file.
- \item Go into R / S-PLUS.
- \item Prepare the inputs to the \code{bugs} function and run it (see
- Example).
- \item A WinBUGS window will pop up and R / S-PLUS will freeze
- up. The model will now run in WinBUGS. It might take awhile. You
- will see things happening in the Log window within WinBUGS. When
- WinBUGS is done, its window will close and R / S-PLUS will work
+ \item Write a \pkg{WinBUGS} model in an ASCII file (hint: use
+ \code{\link{write.model}}).
+ \item Go into \R / S-PLUS.
+ \item Prepare the inputs for the \code{bugs} function and run it (see
+ Example section).
+ \item A \pkg{WinBUGS} window will pop up and \R / S-PLUS will freeze
+ up. The model will now run in \pkg{WinBUGS}. It might take awhile. You
+ will see things happening in the Log window within \pkg{WinBUGS}. When
+ \pkg{WinBUGS} is done, its window will close and \R / S-PLUS will work
again.
\item If an error message appears, re-run with \code{debug=TRUE}.
}
BUGS version support:
\itemize{
- \item WinBUGS 1.4* (this is the only version that works under Linux)
- \item OpenBUGS 2.* (via argument \code{program="OpenBUGS"})
+ \item \pkg{WinBUGS} 1.4* (this is the only version that works under Linux)
+ \item \pkg{OpenBUGS} 2.* (via argument \code{program="OpenBUGS"})
}
+
+ If \code{useWINE=TRUE} is used, all paths (such as
+ \code{working.directory} and \code{model.file}, must be given in
+ native (Unix) style, but \code{working.directory} can be given as
+ native(Unix) or Windows path style. This is done to achieve greatest
+ portability with default argument value for \code{working.directory}.
}
\value{
If \code{codaPkg=TRUE} the returned values are the names
- of coda output files written by WinBUGS containing
+ of coda output files written by \pkg{WinBUGS} containing
the Markov Chain Monte Carlo output in the CODA format.
This is useful for direct access with \code{\link{read.bugs}}.
@@ -154,7 +161,7 @@
\item{indexes.short}{indexes of \code{root.short}}
\item{last.values}{list of simulations from the most recent
iteration; they can be used as starting points if you wish to run
- WinBUGS for further iterations}
+ \pkg{WinBUGS} for further iterations}
\item{pD}{an estimate of the effective number of parameters, for
calculations see the section \dQuote{Arguments}.}
\item{DIC}{\code{mean(deviance) + pD}}
Modified: trunk/R2WinBUGS/man/bugs.run.Rd
===================================================================
--- trunk/R2WinBUGS/man/bugs.run.Rd 2007-08-08 11:31:43 UTC (rev 36)
+++ trunk/R2WinBUGS/man/bugs.run.Rd 2007-08-23 07:44:10 UTC (rev 37)
@@ -2,30 +2,27 @@
\alias{bugs.run}
\title{Calling WinBUGS}
-\description{Updates the lengths of the adaptive phases in the WinBUGS
- registry (using \code{\link{bugs.update.settings}}), calls WinBUGS and
- runs it with \file{script.txt} - intended for internal use}
+\description{Updates the lengths of the adaptive phases in the
+ \pkg{WinBUGS} registry (using \code{\link{bugs.update.settings}}),
+ calls \pkg{WinBUGS} and runs it with \file{script.txt} - intended for
+ internal use}
\usage{
-bugs.run(n.burnin, bugs.directory, WINE = "",
- useWINE = .Platform$OS.type != "windows",
- newWINE = TRUE, WINEPATH = NULL)
+bugs.run(n.burnin, bugs.directory,
+ useWINE=.Platform$OS.type != "windows", WINE=NULL,
+ newWINE=TRUE, WINEPATH=NULL)
}
\arguments{
\item{n.burnin}{length of burn in}
- \item{bugs.directory}{directory that contains the WinBUGS executable}
- \item{WINE}{name of WINE binary, for Windows emulation}
- \item{useWINE}{logical; attempt to use the WINE emulator to run WinBUGS,
- defaults to \code{TRUE} on Windows, and \code{FALSE} otherwise.
- The \code{useWINE = TRUE} option is not available in S-PLUS.}
- \item{newWINE}{set this one to \code{TRUE} for new versions of WINE.}
- \item{WINEPATH}{Path the WINE, \code{bugs} tries hard to get the
- information automatically and pass it to this function, if not
- given.}
+ \item{bugs.directory}{directory that contains the \pkg{WinBUGS} executable}
+ \item{useWINE}{as in \code{\link{bugs}} meta function}
+ \item{WINE}{as in \code{\link{bugs}} meta function}
+ \item{newWINE}{as in \code{\link{bugs}} meta function}
+ \item{WINEPATH}{as in \code{\link{bugs}} meta function}
}
\value{Nothing, but has side effects as documented in
- \code{\link{bugs.update.settings}} and calls WinBUGS.}
+ \code{\link{bugs.update.settings}} and calls \pkg{WinBUGS}.}
\seealso{The main function to be called by the user is \code{\link{bugs}}.}
\keyword{internal}
Modified: trunk/R2WinBUGS/man/bugs.script.Rd
===================================================================
--- trunk/R2WinBUGS/man/bugs.script.Rd 2007-08-08 11:31:43 UTC (rev 36)
+++ trunk/R2WinBUGS/man/bugs.script.Rd 2007-08-23 07:44:10 UTC (rev 37)
@@ -3,13 +3,13 @@
\title{Writes script for running WinBUGS}
-\description{Write file \file{script.txt} for WinBUGS to read - intended
- for internal use}
+\description{Write file \file{script.txt} for \pkg{WinBUGS} to read -
+ intended for internal use}
\usage{
bugs.script(parameters.to.save, n.chains, n.iter, n.burnin, n.thin,
- model.file, debug = FALSE, is.inits, bin, DIC = FALSE,
- useWINE = FALSE, newWINE = FALSE, WINEPATH = NULL)
+ model.file, debug=FALSE, is.inits, bin, DIC=FALSE,
+ useWINE=.Platform$OS.type != "windows", newWINE=TRUE, WINEPATH=NULL)
}
\arguments{
\item{parameters.to.save}{parameters that should be monitored}
@@ -17,20 +17,17 @@
\item{n.iter}{number of total iterations (including burn in)}
\item{n.burnin}{length of burn in}
\item{n.thin}{size of thinning parameter}
- \item{model.file}{file containing the model written in WinBUGS code}
- \item{debug}{if \code{FALSE}, WinBUGS is closed automatically,
- otherwise WinBUGS remains open for further investigation}
+ \item{model.file}{file containing the model written in \pkg{WinBUGS} code}
+ \item{debug}{if \code{FALSE}, \pkg{WinBUGS} is closed automatically,
+ otherwise \pkg{WinBUGS} remains open for further investigation}
\item{is.inits}{logical; whether initial values are given by the user
- (\code{TRUE}) or have to be generated by WinBUGS}
+ (\code{TRUE}) or have to be generated by \pkg{WinBUGS}}
\item{bin}{number of iterations between saving of results}
\item{DIC}{logical; if \code{TRUE}, compute deviance, pD, and DIC
- automatically in WinBUGS}
- \item{useWINE}{logical; use WINE to run WinBUGS under Linux.
- The \code{useWINE = TRUE} option is not available in S-PLUS.}
- \item{newWINE}{set this one to \code{TRUE} for new versions of WINE.}
- \item{WINEPATH}{Path the WINE, \code{bugs} tries hard to get the
- information automatically and pass it to this function, if not
- given.}
+ automatically in \pkg{WinBUGS}}
+ \item{useWINE}{as in \code{\link{bugs}} meta function}
+ \item{newWINE}{as in \code{\link{bugs}} meta function}
+ \item{WINEPATH}{as in \code{\link{bugs}} meta function}
}
\value{Nothing, but as a side effect, the script file \file{script.txt}
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <li...@us...> - 2007-09-17 09:18:10
|
Revision: 65
http://bugs-r.svn.sourceforge.net/bugs-r/?rev=65&view=rev
Author: ligges
Date: 2007-09-17 02:18:14 -0700 (Mon, 17 Sep 2007)
Log Message:
-----------
as for BRugs:
allow model.file to be a function containing a BUGS model that is written to a temporary model file
Modified Paths:
--------------
trunk/R2WinBUGS/R/bugs.R
trunk/R2WinBUGS/man/bugs.Rd
Modified: trunk/R2WinBUGS/R/bugs.R
===================================================================
--- trunk/R2WinBUGS/R/bugs.R 2007-09-17 09:08:38 UTC (rev 64)
+++ trunk/R2WinBUGS/R/bugs.R 2007-09-17 09:18:14 UTC (rev 65)
@@ -36,6 +36,17 @@
setwd(working.directory)
on.exit(setwd(savedWD))
}
+ if(is.function(model.file)){
+ temp <-
+ if(is.R()){
+ paste(tempfile("model"), "txt", sep=".")
+ } else {
+ gsub(".tmp$", ".txt", tempfile("model"))
+ }
+ write.model(model.file, con = temp)
+ model.file <- gsub("\\\\", "/", temp)
+ if(!is.R()) on.exit(file.remove(model.file), add = TRUE)
+ }
if(!file.exists(model.file))
stop(paste(model.file, "does not exist."))
if(file.info(model.file)$isdir)
Modified: trunk/R2WinBUGS/man/bugs.Rd
===================================================================
--- trunk/R2WinBUGS/man/bugs.Rd 2007-09-17 09:08:38 UTC (rev 64)
+++ trunk/R2WinBUGS/man/bugs.Rd 2007-09-17 09:18:14 UTC (rev 65)
@@ -38,7 +38,9 @@
If the extension is \file{.bug} and \code{program=="WinBUGS"},
a copy of the file with extension \file{.txt} will be created
in the \code{bugs()} call and removed afterwards. Note that
- similarly named \file{.txt} files will be overwritten.}
+ similarly named \file{.txt} files will be overwritten.
+ Alternatively, \code{model.file} can be an R function that contains a BUGS model that is written to a
+ temporary model file (see \code{\link{tempfile}}) using \code{\link{write.model}}.}
\item{n.chains}{number of Markov chains (default: 3)}
\item{n.iter}{number of total iterations per chain (including burn in;
default: 2000)}
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <li...@us...> - 2008-01-06 18:17:53
|
Revision: 77
http://bugs-r.svn.sourceforge.net/bugs-r/?rev=77&view=rev
Author: ligges
Date: 2008-01-06 10:17:57 -0800 (Sun, 06 Jan 2008)
Log Message:
-----------
Some major changes contributed by Jouni Kerman, citing from his message the relevant changes:
(In function bugs:)
- Add bugs.seed parameter and the corresponding bugs script entry to specify random seed in WinBUGS
- Add summary.only parameter (default FALSE) which prevents outputting the coda and only returns the parameter summary
- Add save.history parameter (default TRUE) which controls whether the trace plots are generated at end
- Add n.sims parameter (number of simulations to keep). I often specify this and n.iter only.
- Fix definition of n.thin which assumes output of 1000 simulations (divide by n.sims instead)
- If the global option 'R2WinBUGS.bugs.directory' exists, bugs uses it for the R2WinBUGS directory
- Allow specification of data file that can be named something else than data.txt
- Allow specification of inits file names
I have also rewritten the bugs.log routine so it does not crash if DIC is not specified; it also does not make assumptions about the column names.
Modified Paths:
--------------
trunk/R2WinBUGS/DESCRIPTION
trunk/R2WinBUGS/R/bugs.R
trunk/R2WinBUGS/R/bugs.data.R
trunk/R2WinBUGS/R/bugs.inits.R
trunk/R2WinBUGS/R/bugs.log.R
trunk/R2WinBUGS/R/bugs.script.R
trunk/R2WinBUGS/R/openbugs.R
trunk/R2WinBUGS/man/bugs.Rd
trunk/R2WinBUGS/man/bugs.data.Rd
trunk/R2WinBUGS/man/bugs.inits.Rd
trunk/R2WinBUGS/man/bugs.log.Rd
trunk/R2WinBUGS/man/bugs.script.Rd
trunk/R2WinBUGS/man/openbugs.Rd
Modified: trunk/R2WinBUGS/DESCRIPTION
===================================================================
--- trunk/R2WinBUGS/DESCRIPTION 2007-10-17 10:09:41 UTC (rev 76)
+++ trunk/R2WinBUGS/DESCRIPTION 2008-01-06 18:17:57 UTC (rev 77)
@@ -1,6 +1,6 @@
Package: R2WinBUGS
Title: Running WinBUGS and OpenBUGS from R / S-PLUS
-Date: 2007-09-25
+Date: 2008-01-06
Version: 2.1-7
Author: originally written by Andrew Gelman <ge...@st...>;
changes and packaged by Sibylle Sturtz <st...@st...>
Modified: trunk/R2WinBUGS/R/bugs.R
===================================================================
--- trunk/R2WinBUGS/R/bugs.R 2007-10-17 10:09:41 UTC (rev 76)
+++ trunk/R2WinBUGS/R/bugs.R 2008-01-06 18:17:57 UTC (rev 77)
@@ -1,21 +1,26 @@
"bugs" <-
function(data, inits, parameters.to.save, model.file="model.bug",
n.chains=3, n.iter=2000, n.burnin=floor(n.iter / 2),
- n.thin=max(1, floor(n.chains * (n.iter - n.burnin) / 1000)),
+ n.thin=max(1, floor(n.chains * (n.iter - n.burnin) / n.sims)), n.sims = 1000,
bin=(n.iter - n.burnin) / n.thin,
debug=FALSE, DIC=TRUE, digits=5, codaPkg=FALSE,
bugs.directory="c:/Program Files/WinBUGS14/",
program=c("WinBUGS", "OpenBUGS", "winbugs", "openbugs"),
working.directory=NULL,
clearWD=FALSE, useWINE=.Platform$OS.type != "windows", WINE=NULL,
- newWINE=TRUE, WINEPATH=NULL)
+ newWINE=TRUE, WINEPATH=NULL, bugs.seed=NULL, summary.only=FALSE,
+ save.history=!summary.only)
{
program <- match.arg(program)
+ if (missing(bugs.directory) &&
+ !is.null(bugs.dir <- getOption("R2WinBUGS.bugs.directory"))) { # requested by Jouni Kerman
+ bugs.directory <- bugs.dir
+ }
if(program %in% c("openbugs", "OpenBUGS", "OpenBugs")) {
if(!is.R()) stop("OpenBUGS is not yet available in S-PLUS")
## If OpenBUGS, we only call openbugs() and exit...
return(openbugs(data, inits, parameters.to.save, model.file,
- n.chains, n.iter, n.burnin, n.thin, DIC=DIC,
+ n.chains, n.iter, n.burnin, n.thin, n.sims, DIC=DIC,
bugs.directory, working.directory, digits))
}
## Checking number of inits, which is NOT save here:
@@ -52,12 +57,32 @@
stop(paste(model.file, "does not exist."))
if(file.info(model.file)$isdir)
stop(paste(model.file, "is a directory, but a file is required."))
- if(!(length(data) == 1 && is.vector(data) && is.character(data) && data == "data.txt")) {
- bugs.data(data, dir=getwd(), digits)
+ if (!(length(data) == 1 && is.vector(data) && is.character(data) &&
+ (regexpr("\\.txt$", data) > 0))) {
+ bugs.data.file <- bugs.data(data, dir = getwd(), digits)
} else {
- if(!file.exists(data)) stop("File data.txt does not exist.")
+ if(!file.exists(data))
+ stop("File", data, "does not exist.")
+ bugs.data.file <- data
}
- bugs.inits(inits, n.chains, digits)
+
+
+ if (is.character(inits)) {
+ if (!all(file.exists(inits))) {
+ stop("One or more inits files are missing")
+ }
+ if (length(inits)!=n.chains) {
+ stop("Need one inits file for each chain")
+ }
+ bugs.inits.files <- inits
+ } else {
+ if (!is.function(inits) && !is.null(inits) && (length(inits) != n.chains)) {
+ stop("Number of initialized chains (length(inits)) != n.chains")
+ }
+ bugs.inits.files <- bugs.inits(inits, n.chains, digits)
+ }
+
+
if(DIC) parameters.to.save <- c(parameters.to.save, "deviance")
## Model files with extension ".bug" need to be renamed to ".txt"
if(length(grep("[.]bug$", model.file))) {
@@ -70,17 +95,24 @@
bugs.script(parameters.to.save, n.chains, n.iter, n.burnin, n.thin,
new.model.file, debug=debug, is.inits=!is.null(inits),
bin=bin, DIC=DIC, useWINE=useWINE, newWINE=newWINE,
- WINEPATH=WINEPATH)
+ WINEPATH=WINEPATH, bugs.seed=bugs.seed,
+ summary.only=summary.only, save.history=save.history,
+ bugs.data.file = bugs.data.file,
+ bugs.inits.files = bugs.inits.files)
bugs.run(n.burnin, bugs.directory, WINE=WINE, useWINE=useWINE,
newWINE=newWINE, WINEPATH=WINEPATH)
if(codaPkg)
return(file.path(getwd(), paste("coda", 1:n.chains, ".txt", sep="")))
+ if (summary.only) {
+ return(log("log.txt"))
+ }
+
sims <- c(bugs.sims(parameters.to.save, n.chains, n.iter, n.burnin,
n.thin, DIC),
model.file=model.file, program=program)
if(clearWD) {
- file.remove(c("data.txt", "log.odc", "log.txt", "codaIndex.txt",
- paste("inits", 1:n.chains, ".txt", sep=""),
+ file.remove(c(bugs.data.file, "log.odc", "log.txt", "codaIndex.txt",
+ bugs.inits.files,
paste("coda", 1:n.chains, ".txt", sep="")))
}
class(sims) <- "bugs"
Modified: trunk/R2WinBUGS/R/bugs.data.R
===================================================================
--- trunk/R2WinBUGS/R/bugs.data.R 2007-10-17 10:09:41 UTC (rev 76)
+++ trunk/R2WinBUGS/R/bugs.data.R 2008-01-06 18:17:57 UTC (rev 77)
@@ -1,26 +1,27 @@
"bugs.data" <-
-function(data, dir = getwd(), digits = 5){
+function(data, dir = getwd(), digits = 5, data.file = "data.txt"){
if(is.numeric(unlist(data)))
if(is.R()) {
write.datafile(lapply(data, formatC, digits = digits, format = "E"),
- file.path(dir, "data.txt"))
+ file.path(dir, data.file))
}
else {
- writeDatafileS4(data, towhere = "data.txt")
+ writeDatafileS4(data, towhere = data.file)
}
else {
if(is.R()) {
data.list <- lapply(as.list(data), get, pos = parent.frame(2))
names(data.list) <- as.list(data)
write.datafile(lapply(data.list, formatC, digits = digits, format = "E"),
- file.path(dir, "data.txt"))
+ file.path(dir, data.file))
}
else {
data.list <- lapply(as.list(data), get, where = parent.frame(2))
names(data.list) <- unlist(data)
- writeDatafileS4(data.list, towhere = "data.txt")
+ writeDatafileS4(data.list, towhere = data.file)
}
- }
+ }
+ return(data.file)
}
Modified: trunk/R2WinBUGS/R/bugs.inits.R
===================================================================
--- trunk/R2WinBUGS/R/bugs.inits.R 2007-10-17 10:09:41 UTC (rev 76)
+++ trunk/R2WinBUGS/R/bugs.inits.R 2008-01-06 18:17:57 UTC (rev 77)
@@ -1,22 +1,22 @@
"bugs.inits" <-
-function (inits, n.chains, digits){
+function (inits, n.chains, digits,
+ inits.files = paste("inits", 1:n.chains, ".txt", sep = "")){
if(!is.null(inits)) {
for(i in 1:n.chains) {
if(is.function(inits))
if(is.R()) {
write.datafile(lapply(inits(), formatC, digits = digits, format = "E"),
- paste("inits", i, ".txt", sep = ""))
+ inits.files[i])
} else {
- writeDatafileS4(inits(), towhere =
- paste("inits", i, ".txt", sep = ""))
+ writeDatafileS4(inits(), towhere = inits.files[i])
}
else if(is.R()) {
write.datafile(lapply(inits[[i]], formatC, digits = digits, format = "E"),
- paste("inits", i, ".txt", sep = ""))
+ inits.files[i])
} else {
- writeDatafileS4(inits[[i]], towhere = paste(
- "inits", i, ".txt", sep = ""))
+ writeDatafileS4(inits[[i]], towhere = inits.files[i])
}
}
}
+ return(inits.files)
}
Modified: trunk/R2WinBUGS/R/bugs.log.R
===================================================================
--- trunk/R2WinBUGS/R/bugs.log.R 2007-10-17 10:09:41 UTC (rev 76)
+++ trunk/R2WinBUGS/R/bugs.log.R 2008-01-06 18:17:57 UTC (rev 77)
@@ -1,49 +1,34 @@
-bugs.log <- function(file)
+bugs.log <- function (file)
{
- if(!file.exists(file))
- stop("Log file", file, "does not exist")
- logfile <- readLines(file)
+ # Extracts the summary statistics from log.txt written by WinBUGS.
+ # Jouni Kerman 2007-01-30
+ # does essentially the same thing as bugs.log() but
+ # - won't crash if DIC is not there
+ # - makes fewer assumptions about the structure of the matrix
- ## --- Stats ---
-
- statsStart <- which(logfile == "Node statistics") + 2
- if(!length(statsStart))
- stop("Log file", file, "does not contain node statistics.")
- ## + 2 to remove
- ## "Node statistics"
- ## "\t node\t mean\t sd\t MC error\t2.5%\tmedian\t97.5%\tstart\tsample"
-
- statsEnd <- which(logfile == "dic.stats()") - 1
- ## - 1 to remove
- ## "dic.stats()"
-
- statsTable <- logfile[statsStart:statsEnd]
- statsTable <- sub("\t", "", statsTable)
- statsTable <- sapply(strsplit(statsTable, "\t"), "[")
- colnames(statsTable) <- statsTable[1,]
- statsTable <- t(apply(statsTable[-1,], 2, as.numeric))
- colnames(statsTable) <- c("mean", "sd", "MC error", "2.5%", "median", "97.5%", "start", "sample")
-
- ## --- DIC ---
-
- DICStart <- which(logfile == "DIC") + 3
- ## + 3 to remove
- ## "DIC"
- ## "Dbar = post.mean of -2logL; Dhat = -2LogL at post.mean of stochastic nodes"
- ## "\tDbar\tDhat\tpD\tDIC\t"
-
- DICEnd <- grep("history(", logfile, fixed=TRUE) - 1
- ## - 1 to remove
- ## "history(..."
-
- if(!length(DICEnd) || !length(DICStart) || (DICEnd < DICStart)){
- DICTable <- NA
- } else {
- DICTable <- logfile[DICStart:DICEnd]
- DICTable <- sapply(strsplit(DICTable, "\t"), "[")
- colnames(DICTable) <- DICTable[1,]
- DICTable <- t(apply(DICTable[-1,], 2, as.numeric))
- colnames(DICTable) <- c("Dbar", "Dhat", "pD", "DIC")
- }
- list(stats=statsTable, DIC=DICTable)
+ if(!file.exists(file))
+ stop("Log file", file, "does not exist")
+ log.txt <- readLines(file)
+ extract <- function (m, line.match, skip=0, empty.left.col=TRUE) {
+ start <- (skip + which(log.txt == line.match)[1])
+ if(is.na(start)) return(NULL)
+ if(length(start) < 1) return(NULL)
+ mx <- strsplit(m[-(1:start)], "\t")
+ n.cols <- length(mx[[1]])
+ mxlen <- sapply(mx, length)
+ end <- which(mxlen!=n.cols)[1] - 1
+ mx <- mx[1:end]
+ cm <- matrix(unlist(mx), ncol=n.cols, byrow=TRUE) # character format
+ if(empty.left.col) cm <- cm[,-1] # empty column
+ col.names <- cm[1, -1] # first column is just "node"
+ row.names <- cm[,1][-1] # first row is just ""
+ col.names <- gsub("[[:space:]]+", "", col.names) # get rid of spaces
+ cm <- cm[-1,-1] # delete dimname row/columns
+ m <- matrix(as.numeric(cm), nrow=nrow(cm)) # convert to numeric
+ dimnames(m) <- list(row.names, col.names)
+ return(m)
+ }
+ stats <- extract(log.txt, "Node statistics")
+ DIC <- extract(log.txt, "DIC", skip=1, empty.left.col=FALSE)
+ list(stats=stats, DIC=DIC)
}
Modified: trunk/R2WinBUGS/R/bugs.script.R
===================================================================
--- trunk/R2WinBUGS/R/bugs.script.R 2007-10-17 10:09:41 UTC (rev 76)
+++ trunk/R2WinBUGS/R/bugs.script.R 2008-01-06 18:17:57 UTC (rev 77)
@@ -2,20 +2,28 @@
function(parameters.to.save, n.chains, n.iter, n.burnin,
n.thin, model.file, debug=FALSE, is.inits, bin,
DIC=FALSE, useWINE=.Platform$OS.type != "windows",
- newWINE=TRUE, WINEPATH=NULL)
+ newWINE=TRUE, WINEPATH=NULL, bugs.seed=NULL, summary.only=FALSE,
+ save.history=TRUE, bugs.data.file, bugs.inits.files)
{
+
+ output.coda <- (!summary.only)
## Write file script.txt for Bugs
-
if((ceiling(n.iter/n.thin) - ceiling(n.burnin/n.thin)) < 2)
stop ("(n.iter-n.burnin)/n.thin must be at least 2")
working.directory <- getwd()
script <- "script.txt"
- test <- length(grep("\\\\", model.file)) || length(grep("/", model.file))
- model <- ifelse(test, model.file, file.path(working.directory, model.file))
+ model <-
+ if (length(grep("\\\\", model.file)) || length(grep("/", model.file))) {
+ model.file
+ }
+ else file.path(working.directory, model.file)
model <- native2win(model, useWINE=useWINE, newWINE=newWINE, WINEPATH=WINEPATH)
- data <- file.path(working.directory, "data.txt")
+ history <- file.path(working.directory, "history.odc")
+ history <- native2win(history, useWINE=useWINE, newWINE=newWINE, WINEPATH=WINEPATH)
+
+ data <- file.path(working.directory, bugs.data.file)
data <- native2win(data, useWINE=useWINE, newWINE=newWINE, WINEPATH=WINEPATH)
coda <- file.path(working.directory, "coda")
@@ -26,16 +34,21 @@
logFileTxt <- file.path(working.directory, "log.txt")
logFileTxt <- native2win(logFileTxt, useWINE=useWINE, newWINE=newWINE, WINEPATH=WINEPATH)
- inits <- paste(working.directory, "/inits", 1:n.chains, ".txt", sep="")
+ inits <- paste(working.directory, "/", bugs.inits.files, sep="")
inits <- sapply(inits, useWINE=useWINE, newWINE=newWINE, WINEPATH=WINEPATH,
- function(x, useWINE, newWINE, WINEPATH)
- {native2win(x, useWINE=useWINE, newWINE=newWINE, WINEPATH=WINEPATH)})
+ function(x, useWINE, newWINE, WINEPATH)
+ {native2win(x, useWINE=useWINE, newWINE=newWINE, WINEPATH=WINEPATH)})
initlist <- paste("inits (", 1:n.chains, ", '", inits, "')\n", sep="")
savelist <- paste("set (", parameters.to.save, ")\n", sep="")
redo <- ceiling((n.iter-n.burnin)/(n.thin*bin))
+ bugs.seed.cmd <- ""
+ if (!is.null(bugs.seed)) {
+ bugs.seed.cmd <- paste("set.seed(", bugs.seed, ")\n", sep="")
+ }
+
thinUpdate <- paste("thin.updater (", n.thin, ")\n",
"update (", ceiling(n.burnin/n.thin), ")\n", sep="")
@@ -43,18 +56,19 @@
"display ('log')\n",
"check ('", model, "')\n",
"data ('", data, "')\n",
+ bugs.seed.cmd,
"compile (", n.chains, ")\n",
if(is.inits) initlist,
"gen.inits()\n",
thinUpdate,
- savelist,
+ savelist,
if(DIC) "dic.set()\n",
- rep(
- c("update (", formatC(ceiling(bin), format="d"), ")\n",
- "coda (*, '", coda, "')\n"),redo),
+ rep(c("update (", formatC(ceiling(bin), format = "d"), ")\n",
+ if (output.coda) c("coda (*, '", coda, "')\n")),
+ redo),
"stats (*)\n",
if(DIC) "dic.stats()\n",
- "history (*)\n",
+ if (save.history) c("history (*, '", history, "')\n"),
"save ('", logFile, "')\n",
"save ('", logFileTxt, "')\n",
file=script, sep="", append=FALSE)
Modified: trunk/R2WinBUGS/R/openbugs.R
===================================================================
--- trunk/R2WinBUGS/R/openbugs.R 2007-10-17 10:09:41 UTC (rev 76)
+++ trunk/R2WinBUGS/R/openbugs.R 2008-01-06 18:17:57 UTC (rev 77)
@@ -3,7 +3,7 @@
openbugs <- function(data, inits, parameters.to.save, model.file="model.txt",
n.chains = 3, n.iter = 2000, n.burnin = floor(n.iter/2),
- n.thin = max(1, floor(n.chains *(n.iter - n.burnin)/1000)),
+ n.thin = max(1, floor(n.chains *(n.iter - n.burnin) / n.sims)), n.sims = 1000,
DIC = TRUE, bugs.directory = "c:/Program Files/OpenBUGS/",
working.directory=NULL, digits = 5)
{
Modified: trunk/R2WinBUGS/man/bugs.Rd
===================================================================
--- trunk/R2WinBUGS/man/bugs.Rd 2007-10-17 10:09:41 UTC (rev 76)
+++ trunk/R2WinBUGS/man/bugs.Rd 2008-01-06 18:17:57 UTC (rev 77)
@@ -9,28 +9,31 @@
\usage{
bugs(data, inits, parameters.to.save, model.file="model.bug",
n.chains=3, n.iter=2000, n.burnin=floor(n.iter/2),
- n.thin=max(1, floor(n.chains * (n.iter - n.burnin)/1000)),
- bin=(n.iter - n.burnin) / n.thin,
+ n.thin=max(1, floor(n.chains * (n.iter - n.burnin) / n.sims)),
+ n.sims = 1000, bin=(n.iter - n.burnin) / n.thin,
debug=FALSE, DIC=TRUE, digits=5, codaPkg=FALSE,
bugs.directory="c:/Program Files/WinBUGS14/",
program=c("WinBUGS", "OpenBUGS", "winbugs", "openbugs"),
working.directory=NULL, clearWD=FALSE,
useWINE=.Platform$OS.type != "windows", WINE=NULL,
- newWINE=TRUE, WINEPATH=NULL)
+ newWINE=TRUE, WINEPATH=NULL, bugs.seed=NULL, summary.only=FALSE,
+ save.history=!summary.only)
}
\arguments{
\item{data}{either a named list (names corresponding to variable names
in the \code{model.file}) of the data for the \pkg{WinBUGS} model,
\emph{or} a vector or list of the names of the data objects used by
- the model. If \code{data="data.txt"}, it is assumed that data have
- already been written to the working directory in a file called
- \file{data.txt}, e.g. by the function \code{\link{bugs.data}}.}
+ the model. If \code{data} is a one element character vector (such as \code{"data.txt"}),
+ it is assumed that data have already been written to the working directory into that file,
+ e.g. by the function \code{\link{bugs.data}}.}
\item{inits}{a list with \code{n.chains} elements; each element of the
list is itself a list of starting values for the \pkg{WinBUGS} model,
\emph{or} a function creating (possibly random) initial values.
Alternatively, if \code{inits=NULL}, initial values are generated
- by \pkg{WinBUGS}.}
+ by \pkg{WinBUGS}. If \code{inits} is a character vector with \code{n.chains} elements,
+ it is assumed that inits have already been written to the working directory into those files,
+ e.g. by the function \code{\link{bugs.inits}}.}
\item{parameters.to.save}{character vector of the names of the
parameters to save which should be monitored}
\item{model.file}{file containing the model written in \pkg{WinBUGS} code.
@@ -52,6 +55,7 @@
\code{n.iter} is large. Default is \code{max(1, floor(n.chains *
(n.iter-n.burnin) / 1000))} which will only thin if there are at
least 2000 simulations.}
+ \item{n.sims}{The approximate number of simulations to keep after thinning.}
\item{bin}{number of iterations between saving of results
(i.e. the coda files are saved after each \code{bin} iterations);
default is to save only at the end.}
@@ -68,7 +72,9 @@
is returned, if \code{TRUE} file names of \pkg{WinBUGS} output are
returned for easy access by the \pkg{coda} package through function
\code{\link{read.bugs}} (not used if \code{program="OpenBUGS"}).}
- \item{bugs.directory}{directory that contains the \pkg{WinBUGS} executable}
+ \item{bugs.directory}{directory that contains the \pkg{WinBUGS} executable.
+ If the global option \code{R2WinBUGS.bugs.directory} is not \code{NULL},
+ it will be used as the default.}
\item{program}{the program to use, either
\code{winbugs}/\code{WinBUGS} or \code{openbugs}/\code{OpenBUGS},
the latter makes use of function \code{\link{openbugs}} and requires
@@ -92,6 +98,10 @@
utility}
\item{WINEPATH}{character, path to \file{winepath} binary file, it is
tried hard to get the information automatically if not given.}
+ \item{bugs.seed}{random seed for \pkg{WinBUGS} (default is no seed)}
+ \item{summary.only}{If \code{TRUE}, only a parameter summary for very quick analyses is given,
+ temporary created files are not removed in that case.}
+ \item{save.history}{If \code{TRUE} (the default), trace plots are generated at the end.}
}
\details{
Modified: trunk/R2WinBUGS/man/bugs.data.Rd
===================================================================
--- trunk/R2WinBUGS/man/bugs.data.Rd 2007-10-17 10:09:41 UTC (rev 76)
+++ trunk/R2WinBUGS/man/bugs.data.Rd 2008-01-06 18:17:57 UTC (rev 77)
@@ -2,11 +2,11 @@
\alias{bugs.data}
\title{Writing input for WinBUGS}
-\description{Write file \file{data.txt} for \pkg{WinBUGS} to read - for
+\description{Write file for \pkg{WinBUGS} to read - for
internal use.}
\usage{
-bugs.data(data, dir = getwd(), digits = 5)
+bugs.data(data, dir = getwd(), digits = 5, data.file = "data.txt")
}
\arguments{
\item{data}{either a named list (names corresponding to variable names
@@ -16,10 +16,11 @@
\item{dir}{the directory to write the file \file{data.txt} to}
\item{digits}{number of significant digits used for \pkg{WinBUGS}
input, see \code{\link{formatC}}}
+ \item{data.file}{name for the file R writes the data into.}
}
-\value{Nothing, but as a side effect, the data file \file{data.txt} is
- written}
+\value{The name of \code{data.file} is returned and as a side effect,
+ the data file is written}
\seealso{The main function to be called by the user is \code{\link{bugs}}.}
\keyword{internal}
Modified: trunk/R2WinBUGS/man/bugs.inits.Rd
===================================================================
--- trunk/R2WinBUGS/man/bugs.inits.Rd 2007-10-17 10:09:41 UTC (rev 76)
+++ trunk/R2WinBUGS/man/bugs.inits.Rd 2008-01-06 18:17:57 UTC (rev 77)
@@ -6,7 +6,8 @@
the working directory for \pkg{WinBUGS} to read - for internal use.}
\usage{
-bugs.inits(inits, n.chains, digits)
+bugs.inits(inits, n.chains, digits,
+ inits.files = paste("inits", 1:n.chains, ".txt", sep = ""))
}
\arguments{
\item{inits}{a list with \code{n.chains} elements; each element of the
@@ -15,9 +16,10 @@
\item{n.chains}{number of Markov chains}
\item{digits}{number of significant digits used for \pkg{WinBUGS}
input, see \code{\link{formatC}}}
+ \item{inits.file}{name for the inits files R write the inits into.}
}
-\value{Nothing, but as a side effect, the inits files \file{inits*.txt}
+\value{Vector of names of \code{inits.files}; as a side effect, the inits files \file{inits*.txt}
are written}
\seealso{The main function to be called by the user is \code{\link{bugs}}.}
Modified: trunk/R2WinBUGS/man/bugs.log.Rd
===================================================================
--- trunk/R2WinBUGS/man/bugs.log.Rd 2007-10-17 10:09:41 UTC (rev 76)
+++ trunk/R2WinBUGS/man/bugs.log.Rd 2008-01-06 18:17:57 UTC (rev 77)
@@ -17,11 +17,6 @@
\item{DIC}{A matrix containing the DIC statistics as returned from
\pkg{WinBUGS}.}
}
-
-\details{ In later releases of \pkg{R2WinBUGS}, this function is
-considered to read the relevant data from the log file rather than
-analysing and calculating the relevant data in \R / S-PLUS again. }
-
\seealso{The main function that generates the log file is \code{\link{bugs}}.}
\keyword{IO}
\keyword{file}
Modified: trunk/R2WinBUGS/man/bugs.script.Rd
===================================================================
--- trunk/R2WinBUGS/man/bugs.script.Rd 2007-10-17 10:09:41 UTC (rev 76)
+++ trunk/R2WinBUGS/man/bugs.script.Rd 2008-01-06 18:17:57 UTC (rev 77)
@@ -9,7 +9,9 @@
\usage{
bugs.script(parameters.to.save, n.chains, n.iter, n.burnin, n.thin,
model.file, debug=FALSE, is.inits, bin, DIC=FALSE,
- useWINE=.Platform$OS.type != "windows", newWINE=TRUE, WINEPATH=NULL)
+ useWINE=.Platform$OS.type != "windows", newWINE=TRUE, WINEPATH=NULL,
+ bugs.seed=NULL, summary.only=FALSE, save.history=TRUE,
+ bugs.data.file, bugs.inits.files)
}
\arguments{
\item{parameters.to.save}{parameters that should be monitored}
@@ -28,6 +30,12 @@
\item{useWINE}{as in \code{\link{bugs}} meta function}
\item{newWINE}{as in \code{\link{bugs}} meta function}
\item{WINEPATH}{as in \code{\link{bugs}} meta function}
+ \item{bugs.seed}{random seed for \pkg{WinBUGS} (default is no seed)}
+ \item{summary.only}{If \code{TRUE}, only a parameter summary for very quick analyses is given,
+ temporary created files are not removed in that case.}
+ \item{save.history}{If \code{TRUE} (the default), trace plots are generated at the end.}
+ \item{bugs.data.file}{character name of the data file}
+ \item{bugs.inits.files}{character vector of names of the inits files}
}
\value{Nothing, but as a side effect, the script file \file{script.txt}
Modified: trunk/R2WinBUGS/man/openbugs.Rd
===================================================================
--- trunk/R2WinBUGS/man/openbugs.Rd 2007-10-17 10:09:41 UTC (rev 76)
+++ trunk/R2WinBUGS/man/openbugs.Rd 2008-01-06 18:17:57 UTC (rev 77)
@@ -10,8 +10,9 @@
openbugs(data, inits, parameters.to.save,
model.file = "model.txt", n.chains = 3, n.iter = 2000,
n.burnin = floor(n.iter/2),
- n.thin = max(1, floor(n.chains * (n.iter - n.burnin) / 1000)),
- DIC = TRUE, bugs.directory = "c:/Program Files/OpenBUGS/",
+ n.thin = max(1, floor(n.chains * (n.iter - n.burnin) / n.sims)),
+ n.sims = 1000, DIC = TRUE,
+ bugs.directory = "c:/Program Files/OpenBUGS/",
working.directory = NULL, digits = 5)
}
@@ -19,9 +20,9 @@
\item{data}{either a named list (names corresponding to variable names
in the \code{model.file}) of the data for the \pkg{OpenBUGS} model,
\emph{or} a vector or list of the names of the data objects used by
- the model. If \code{data = "data.txt"}, it is assumed that data
- have already been written to the working directory in a file called
- \file{data.txt}, e.g. by the function \code{\link{bugs.data}}.}
+ the model. If \code{data} is a one element character vector (such as \code{"data.txt"}),
+ it is assumed that data have already been written to the working directory into that file,
+ e.g. by the function \code{\link{bugs.data}}.}
\item{inits}{a list with \code{n.chains} elements; each element of the
list is itself a list of starting values for the \pkg{OpenBUGS} model,
\emph{or} a function creating (possibly random) initial values.
@@ -45,7 +46,8 @@
\code{n.iter} is large. Default is \code{max(1, floor(n.chains *
(n.iter-n.burnin) / 1000))} which will only thin if there are at
least 2000 simulations.}
- \item{DIC}{logical; if \code{TRUE} (default), compute deviance, pD, and
+ \item{n.sims}{The approximate number of simulations to keep after thinning.}
+ \item{DIC}{logical; if \code{TRUE} (default), compute deviance, pD, and
DIC. This is done in \pkg{BRugs} directly.}
\item{digits}{number of significant digits used for \pkg{OpenBUGS} input,
see \code{\link{formatC}}}
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|
|
From: <li...@us...> - 2008-01-08 21:12:15
|
Revision: 79
http://bugs-r.svn.sourceforge.net/bugs-r/?rev=79&view=rev
Author: ligges
Date: 2008-01-08 13:11:35 -0800 (Tue, 08 Jan 2008)
Log Message:
-----------
bugs in monitor() reported by Andrew Gelman:
- exported from NS (for making code in his book work)
- extracts the default number of chains from the object by default
Modified Paths:
--------------
trunk/R2WinBUGS/DESCRIPTION
trunk/R2WinBUGS/NAMESPACE
trunk/R2WinBUGS/R/monitor.R
trunk/R2WinBUGS/man/bugs.log.Rd
trunk/R2WinBUGS/man/monitor.Rd
Modified: trunk/R2WinBUGS/DESCRIPTION
===================================================================
--- trunk/R2WinBUGS/DESCRIPTION 2008-01-06 18:56:18 UTC (rev 78)
+++ trunk/R2WinBUGS/DESCRIPTION 2008-01-08 21:11:35 UTC (rev 79)
@@ -1,6 +1,6 @@
Package: R2WinBUGS
Title: Running WinBUGS and OpenBUGS from R / S-PLUS
-Date: 2008-01-06
+Date: 2008-01-08
Version: 2.1-7
Author: originally written by Andrew Gelman <ge...@st...>;
changes and packaged by Sibylle Sturtz <st...@st...>
Modified: trunk/R2WinBUGS/NAMESPACE
===================================================================
--- trunk/R2WinBUGS/NAMESPACE 2008-01-06 18:56:18 UTC (rev 78)
+++ trunk/R2WinBUGS/NAMESPACE 2008-01-08 21:11:35 UTC (rev 79)
@@ -8,6 +8,7 @@
bugs.data,
read.bugs,
bugs.log,
+ monitor,
openbugs,
as.bugs.array,
write.model)
Modified: trunk/R2WinBUGS/R/monitor.R
===================================================================
--- trunk/R2WinBUGS/R/monitor.R 2008-01-06 18:56:18 UTC (rev 78)
+++ trunk/R2WinBUGS/R/monitor.R 2008-01-08 21:11:35 UTC (rev 79)
@@ -1,15 +1,15 @@
"monitor" <-
-function (a, n.chains, trans=NULL, keep.all=FALSE, Rupper.keep=FALSE) {
+function (a, n.chains=dim(a)[2], trans=NULL, keep.all=FALSE, Rupper.keep=FALSE) {
-# If keep.all=T: a is a n x m x k array:
-# m sequences of length n, k variables measured
-# If keep.all=F: a is a 2n x m x k array (first half will be discarded)
-#
-# trans is a vector of length k: "" if no transformation, or "log" or "logit"
-# (If trans is not defined, it will be set to "log" for parameters that
-# are all-positive and 0 otherwise.)
-#
-# If Rupper.keep=T: keep Rupper. (Otherwise don't display it.)
+## If keep.all=T: a is a n x m x k array:
+## m sequences of length n, k variables measured
+## If keep.all=F: a is a 2n x m x k array (first half will be discarded)
+##
+## trans is a vector of length k: "" if no transformation, or "log" or "logit"
+## (If trans is not defined, it will be set to "log" for parameters that
+## are all-positive and 0 otherwise.)
+##
+## If Rupper.keep=TRUE: keep Rupper. (Otherwise don't display it.)
invlogit <- function (x) {1 / (1 + exp(-x))}
nparams <- if(length(dim(a)) < 3) 1 else dim(a)[length(dim(a))]
# Calculation and initialization of the required matrix "output"
@@ -30,9 +30,9 @@
confshrink = conv.p$confshrink, n.eff = conv.p$n.eff)
}
else if (trans[i]=="logit"){
- if (!is.R()){
- logit <- function (x) { log(x /(1- x)) }
- }
+ if (!is.R()){
+ logit <- function (x) { log(x /(1- x)) }
+ }
conv.p <- conv.par(logit(ai), n.chains, Rupper.keep=Rupper.keep)
conv.p <- list(quantiles = invlogit(conv.p$quantiles),
confshrink = conv.p$confshrink, n.eff = conv.p$n.eff)
Modified: trunk/R2WinBUGS/man/bugs.log.Rd
===================================================================
--- trunk/R2WinBUGS/man/bugs.log.Rd 2008-01-06 18:56:18 UTC (rev 78)
+++ trunk/R2WinBUGS/man/bugs.log.Rd 2008-01-08 21:11:35 UTC (rev 79)
@@ -18,5 +18,6 @@
\pkg{WinBUGS}.}
}
\seealso{The main function that generates the log file is \code{\link{bugs}}.}
+\author{Jouni Kerman}
\keyword{IO}
\keyword{file}
Modified: trunk/R2WinBUGS/man/monitor.Rd
===================================================================
--- trunk/R2WinBUGS/man/monitor.Rd 2008-01-06 18:56:18 UTC (rev 78)
+++ trunk/R2WinBUGS/man/monitor.Rd 2008-01-08 21:11:35 UTC (rev 79)
@@ -3,15 +3,13 @@
\alias{conv.par}
\title{Special summary statistics}
-\description{Special summary statistics of the WinBUGS output - intended
- for internal use}
+\description{Special summary statistics of the WinBUGS output.}
\usage{
-monitor(a, n.chains, trans = NULL, keep.all = FALSE, Rupper.keep = FALSE)
+monitor(a, n.chains = dim(a)[2], trans = NULL, keep.all = FALSE, Rupper.keep = FALSE)
conv.par(x, n.chains, Rupper.keep = TRUE)
}
\arguments{
- \item{x}{}
\item{a}{a \code{n * m * k} array: \code{m} sequences of length
\code{n}, \code{k} variables measured}
\item{n.chains}{number of Markov chains}
@@ -21,9 +19,10 @@
\item{keep.all}{if \code{FALSE} (default), first half of \code{a} will
be discarded}
\item{Rupper.keep}{if \code{FALSE}, don't return \code{Rupper}}
+ \item{x}{for internal use only}
}
-\details{See the well documented code for details.}
+\details{\code{conv.par} is intended for internal use only.}
\value{
for \code{monitor}:
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|
|
From: <li...@us...> - 2008-01-18 16:59:59
|
Revision: 82
http://bugs-r.svn.sourceforge.net/bugs-r/?rev=82&view=rev
Author: ligges
Date: 2008-01-18 09:00:00 -0800 (Fri, 18 Jan 2008)
Log Message:
-----------
- make scan() in openbugs() quiet
- add note on option BRugsVerbose
- increase date for release
Modified Paths:
--------------
trunk/R2WinBUGS/DESCRIPTION
trunk/R2WinBUGS/R/openbugs.R
trunk/R2WinBUGS/man/openbugs.Rd
Modified: trunk/R2WinBUGS/DESCRIPTION
===================================================================
--- trunk/R2WinBUGS/DESCRIPTION 2008-01-17 18:24:14 UTC (rev 81)
+++ trunk/R2WinBUGS/DESCRIPTION 2008-01-18 17:00:00 UTC (rev 82)
@@ -1,6 +1,6 @@
Package: R2WinBUGS
Title: Running WinBUGS and OpenBUGS from R / S-PLUS
-Date: 2008-01-08
+Date: 2008-01-18
Version: 2.1-7
Author: originally written by Andrew Gelman <ge...@st...>;
changes and packaged by Sibylle Sturtz <st...@st...>
Modified: trunk/R2WinBUGS/R/openbugs.R
===================================================================
--- trunk/R2WinBUGS/R/openbugs.R 2008-01-17 18:24:14 UTC (rev 81)
+++ trunk/R2WinBUGS/R/openbugs.R 2008-01-18 17:00:00 UTC (rev 82)
@@ -7,7 +7,7 @@
DIC = TRUE, bugs.directory = "c:/Program Files/OpenBUGS/",
working.directory=NULL, digits = 5)
{
- if(!require(BRugs))
+ if(!require("BRugs"))
stop("BRugs is required")
## switching from bugs() to BRugsFit() notation
modelFile <- model.file
@@ -55,7 +55,7 @@
## set the adaptive phases
adaptivelines <- scan(system.file("OpenBUGS", "Bugs", "Rsrc",
"Registry.txt", package="BRugs"),
- what="character")
+ what="character", quiet = TRUE)
factories <- sub(".adaptivePhase", "",
adaptivelines[grep("adaptivePhase",adaptivelines)])
sapply(factories, BRugs::modelSetAP, max(0, nBurnin-1))
Modified: trunk/R2WinBUGS/man/openbugs.Rd
===================================================================
--- trunk/R2WinBUGS/man/openbugs.Rd 2008-01-17 18:24:14 UTC (rev 81)
+++ trunk/R2WinBUGS/man/openbugs.Rd 2008-01-18 17:00:00 UTC (rev 82)
@@ -67,6 +67,11 @@
and Uwe Ligges.
}
+\note{By default, BRugs (and hence \code{openbugs()}) is quite verbose.
+ This can be controlled for the whole BRugs package by by the option \sQuote{BRugsVerbose} (see \code{\link{options}})
+ which is set to \code{TRUE} by default.
+}
+
\seealso{\code{\link{bugs}} and the \pkg{BRugs} package}
\examples{
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|
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