[Bugs-r-devel] SF.net SVN: bugs-r:[100] trunk/R2WinBUGS

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

Revision: 100
          http://bugs-r.svn.sourceforge.net/bugs-r/?rev=100&view=rev
Author:   ligges
Date:     2009-02-12 11:17:21 +0000 (Thu, 12 Feb 2009)

Log Message:
-----------
- bugfix: plot.bugs() did not reset par(mfrow)
- bugfix: adaptive phase stuff cannot be read anymore by openbugs(), files are no longer shipped, feature has been removed
- openbugs now displays messages before starting the sampling (essentially using flush.console())

Modified Paths:
--------------
    trunk/R2WinBUGS/DESCRIPTION
    trunk/R2WinBUGS/R/openbugs.R
    trunk/R2WinBUGS/R/plot.bugs.R
    trunk/R2WinBUGS/inst/NEWS

Modified: trunk/R2WinBUGS/DESCRIPTION
===================================================================
--- trunk/R2WinBUGS/DESCRIPTION	2009-02-02 14:30:50 UTC (rev 99)
+++ trunk/R2WinBUGS/DESCRIPTION	2009-02-12 11:17:21 UTC (rev 100)
@@ -1,7 +1,7 @@
 Package: R2WinBUGS
 Title: Running WinBUGS and OpenBUGS from R / S-PLUS
-Date: 2009-02-02
-Version: 2.1-11
+Date: 2009-02-11
+Version: 2.1-12
 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/openbugs.R
===================================================================
--- trunk/R2WinBUGS/R/openbugs.R	2009-02-02 14:30:50 UTC (rev 99)
+++ trunk/R2WinBUGS/R/openbugs.R	2009-02-12 11:17:21 UTC (rev 100)
@@ -57,13 +57,18 @@
   }
   BRugs::samplesSetThin(nThin)
   ## set the adaptive phases
-  adaptivelines <- scan(system.file("OpenBUGS", "Bugs", "Rsrc",
-                                    "Registry.txt", package="BRugs"),
-                        what="character", quiet = TRUE)
-  factories <- sub(".adaptivePhase", "",
-                   adaptivelines[grep("adaptivePhase",adaptivelines)])
-  sapply(factories, BRugs::modelSetAP, max(0, nBurnin-1))
 
+## We do no longer have any Registry.txt file availabe, 
+## hence not resetting the adaptive phase any more.
+## People should move to BRugs directly.
+#  adaptivelines <- scan(system.file("OpenBUGS", "Bugs", "Rsrc",
+#                                    "Registry.txt", package="BRugs"),
+#                        what="character", quiet = TRUE)
+#  factories <- sub(".adaptivePhase", "",
+#                   adaptivelines[grep("adaptivePhase",adaptivelines)])
+#  sapply(factories, BRugs::modelSetAP, max(0, nBurnin-1))
+  cat("Start to sample ...\n")
+  flush.console()
   BRugs::modelUpdate(nBurnin)
   ## BRugs::samplesSetThin(nThin)
   if(DIC) {

Modified: trunk/R2WinBUGS/R/plot.bugs.R
===================================================================
--- trunk/R2WinBUGS/R/plot.bugs.R	2009-02-02 14:30:50 UTC (rev 99)
+++ trunk/R2WinBUGS/R/plot.bugs.R	2009-02-12 11:17:21 UTC (rev 100)
@@ -1,11 +1,12 @@
 plot.bugs <- function (x, display.parallel = FALSE, ...){
     mar.old <- par("mar")
     pty.old <- par(pty = "m")
+    mfrow.old <- par("mfrow")
     if (is.R())
-    	layout(matrix(c(1,2),1,2))
+        layout(matrix(c(1,2),1,2))
     else
-    	par(mfrow = c(1,2))
-    	
+        par(mfrow = c(1,2))
+        
     bugs.plot.summary (x, ...)
     bugs.plot.inferences (x, display.parallel, ...)
     header <- ""
@@ -16,8 +17,8 @@
     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)
-    if (is.R())  par(pty = pty.old[[1]], mar = mar.old)
-    else  invisible(par(pty = pty.old[[1]], mar = mar.old))
+    if (is.R())  par(pty = pty.old[[1]], mar = mar.old, mfrow = mfrow.old)
+    else  invisible(par(pty = pty.old[[1]], mar = mar.old, mfrow = mfrow.old))
 }
 
 if (!is.R()) {

Modified: trunk/R2WinBUGS/inst/NEWS
===================================================================
--- trunk/R2WinBUGS/inst/NEWS	2009-02-02 14:30:50 UTC (rev 99)
+++ trunk/R2WinBUGS/inst/NEWS	2009-02-12 11:17:21 UTC (rev 100)
@@ -1,6 +1,14 @@
 Changes to R2WinBUGS:
 =====================
 
+Update 2.1-12
+- bugfix: plot.bugs() did not reset par(mfrow)
+- bugfix: adaptive phase stuff cannot read from files anymore by openbugs(),
+          feature has been removed
+- openbugs now displays messages before starting the sampling 
+  (essentially using flush.console())
+
+
 Update 2.1-11
 - bugfix: if working.directory was unset and files are assumed to be in R's 
   former wd, these are copied to the tempdir that is set as new working 


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