[Bugs-r-devel] SF.net SVN: bugs-r: [37] trunk/R2WinBUGS

[<gg...@us...>]

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}


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