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[Bugs-r-devel] SF.net SVN: bugs-r: [77] trunk/R2WinBUGS
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From: <li...@us...> - 2008-01-06 18:17:53
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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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