[Bugs-r-devel] SF.net SVN: bugs-r:[103] trunk/R2WinBUGS

[<li...@us...>]

Revision: 103
          http://bugs-r.svn.sourceforge.net/bugs-r/?rev=103&view=rev
Author:   ligges
Date:     2009-02-12 18:51:52 +0000 (Thu, 12 Feb 2009)

Log Message:
-----------
let openbugs work in the temporary directory as well, and update the docs

Modified Paths:
--------------
    trunk/R2WinBUGS/R/bugs.R
    trunk/R2WinBUGS/R/openbugs.R
    trunk/R2WinBUGS/man/openbugs.Rd

Modified: trunk/R2WinBUGS/R/bugs.R
===================================================================
--- trunk/R2WinBUGS/R/bugs.R	2009-02-12 12:28:59 UTC (rev 102)
+++ trunk/R2WinBUGS/R/bugs.R	2009-02-12 18:51:52 UTC (rev 103)
@@ -80,7 +80,7 @@
        (regexpr("\\.txt$", data) > 0))) {
     bugs.data.file <- bugs.data(data, dir = getwd(), digits)
   } else {
-    if(inTempDir && basename(data) == data)
+    if(inTempDir && all(basename(data) == data))
         try(file.copy(file.path(savedWD, data), data, overwrite = TRUE))
     if(!file.exists(data))
         stop("File", data, "does not exist.")

Modified: trunk/R2WinBUGS/R/openbugs.R
===================================================================
--- trunk/R2WinBUGS/R/openbugs.R	2009-02-12 12:28:59 UTC (rev 102)
+++ trunk/R2WinBUGS/R/openbugs.R	2009-02-12 18:51:52 UTC (rev 103)
@@ -21,11 +21,14 @@
   ## Move to working drirectory or temporary directory when NULL
   if(is.null(working.directory)) {
     working.directory <- tempdir()
+    inTempDir <- TRUE
   }
   savedWD <- getwd()
   setwd(working.directory)
   on.exit(setwd(savedWD))
 
+  if(inTempDir && basename(model.file) == model.file)
+    try(file.copy(file.path(savedWD, model.file), model.file, overwrite = TRUE))
   if(!file.exists(modelFile)) {
     stop(modelFile, " does not exist")
   }
@@ -42,6 +45,8 @@
   if(!(is.vector(data) && is.character(data) && all(file.exists(data)))) {
     data <- BRugs::bugsData(data, digits = digits)
   }
+  if(inTempDir && all(basename(data) == data))
+    try(file.copy(file.path(savedWD, data), data, overwrite = TRUE))
   BRugs::modelData(data)
   BRugs::modelCompile(numChains)
   if(missing(inits) || is.null(inits)) {
@@ -52,6 +57,8 @@
       inits <- BRugs::bugsInits(inits = inits, numChains = numChains,
                                 digits = digits)
     }
+    if(inTempDir && all(basename(inits) == inits))
+        try(file.copy(file.path(savedWD, inits), inits, overwrite = TRUE))
     BRugs::modelInits(inits)
     BRugs::modelGenInits()
   }
@@ -67,8 +74,10 @@
 #  factories <- sub(".adaptivePhase", "",
 #                   adaptivelines[grep("adaptivePhase",adaptivelines)])
 #  sapply(factories, BRugs::modelSetAP, max(0, nBurnin-1))
-  cat("Start to sample ...\n")
-  flush.console()
+  if(getOption("BRugsVerbose")){   
+    cat("Sampling has been started ...\n")
+    flush.console()
+  }
   BRugs::modelUpdate(nBurnin)
   ## BRugs::samplesSetThin(nThin)
   if(DIC) {

Modified: trunk/R2WinBUGS/man/openbugs.Rd
===================================================================
--- trunk/R2WinBUGS/man/openbugs.Rd	2009-02-12 12:28:59 UTC (rev 102)
+++ trunk/R2WinBUGS/man/openbugs.Rd	2009-02-12 18:51:52 UTC (rev 103)
@@ -55,7 +55,8 @@
     - currently unused}
   \item{working.directory}{sets working directory during execution of
     this function; \pkg{WinBUGS} in- and output will be stored in this
-    directory; if \code{NULL}, the current working directory is chosen.}
+    directory; if \code{NULL}, a temporary working directory via
+    \code{\link{tempdir}} is used.}
 
 }
 
@@ -68,7 +69,7 @@
 }
 
 \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}})
+    This can be controlled for the whole BRugs package by the option \sQuote{BRugsVerbose} (see \code{\link{options}})
     which is set to \code{TRUE} by default.
 }
 


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