[Bugs-r-devel] SF.net SVN: bugs-r:[253] trunk/R2OpenBUGS

[<snt...@us...>]

Revision: 253
          http://bugs-r.svn.sourceforge.net/bugs-r/?rev=253&view=rev
Author:   snthomas99
Date:     2012-07-12 02:22:12 +0000 (Thu, 12 Jul 2012)
Log Message:
-----------
V3.2.2.1

Modified Paths:
--------------
    trunk/R2OpenBUGS/DESCRIPTION
    trunk/R2OpenBUGS/R/bugs.log.R
    trunk/R2OpenBUGS/R/bugs.sims.R
    trunk/R2OpenBUGS/inst/NEWS
    trunk/R2OpenBUGS/man/bugs.Rd
    trunk/R2OpenBUGS/man/bugs.log.Rd

Modified: trunk/R2OpenBUGS/DESCRIPTION
===================================================================
--- trunk/R2OpenBUGS/DESCRIPTION	2012-05-01 12:57:10 UTC (rev 252)
+++ trunk/R2OpenBUGS/DESCRIPTION	2012-07-12 02:22:12 UTC (rev 253)
@@ -1,7 +1,7 @@
 Package: R2OpenBUGS
 Title: Running OpenBUGS from R 
-Date: 2012-2-04
-Version: 3.2-1.4
+Date: 2012-4-20
+Version: 3.2-2.1
 Author: originally written as R2WinBUGS by Andrew Gelman <ge...@st...>;
  changes and packaged by Sibylle Sturtz <st...@st...>
  and Uwe Ligges <li...@st...>.
@@ -14,6 +14,6 @@
  in R. 
 Depends: R (>= 2.11.0)
 Imports: coda (>= 0.11-0), boot
-SystemRequirements: OpenBUGS (>= 3.2.1)
+SystemRequirements: OpenBUGS (>= 3.2.2)
 Maintainer: Neal Thomas <snt...@ya...>
 License: GPL-2

Modified: trunk/R2OpenBUGS/R/bugs.log.R
===================================================================
--- trunk/R2OpenBUGS/R/bugs.log.R	2012-05-01 12:57:10 UTC (rev 252)
+++ trunk/R2OpenBUGS/R/bugs.log.R	2012-07-12 02:22:12 UTC (rev 253)
@@ -18,7 +18,9 @@
     if(n.cols < 1) return(NA)
     mxlen <- sapply(mx, length)
     end <- which(mxlen!=n.cols)[1] - 1
-    mx <- mx[1:end]
+    if(!is.na(end)){  ### if output block does not end mx
+        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"

Modified: trunk/R2OpenBUGS/R/bugs.sims.R
===================================================================
--- trunk/R2OpenBUGS/R/bugs.sims.R	2012-05-01 12:57:10 UTC (rev 252)
+++ trunk/R2OpenBUGS/R/bugs.sims.R	2012-07-12 02:22:12 UTC (rev 253)
@@ -4,7 +4,7 @@
   ## Read the simulations from Bugs into R, format them, and monitor convergence
   sims.files <- paste ("CODAchain", 1:n.chains, ".txt", sep="")
   ## read in the names of the parameters and the indices of their samples
-  index <- read.table("CODAindex.txt", header = FALSE, sep = " ")
+  index <- read.table("CODAindex.txt", header = FALSE, sep = "")
   parameter.names <- as.vector(index[, 1])
   n.keep <- index[1, 3] - index[1, 2] + 1
   n.parameters <- length(parameter.names)

Modified: trunk/R2OpenBUGS/inst/NEWS
===================================================================
--- trunk/R2OpenBUGS/inst/NEWS	2012-05-01 12:57:10 UTC (rev 252)
+++ trunk/R2OpenBUGS/inst/NEWS	2012-07-12 02:22:12 UTC (rev 253)
@@ -1,6 +1,11 @@
 Changes to R2OpenBUGS:
 ======================
 
+Update 3.2-2.1
+- Updated reading of CODA file formats for version 3.2.2 of OpenBUGS, which
+  now consistently uses tab delimiters.  Problems with reading the log
+  file were corrected as part of the new version of OpenBUGS.
+
 Update 3.2-1.4
 - Corrected printing of pD and DIC, which were reversed
 - Updated documentation to note difference in DIC reporting between Windows and Linux, and the lack of support for the bugs.log function under Linux

Modified: trunk/R2OpenBUGS/man/bugs.Rd
===================================================================
--- trunk/R2OpenBUGS/man/bugs.Rd	2012-05-01 12:57:10 UTC (rev 252)
+++ trunk/R2OpenBUGS/man/bugs.Rd	2012-07-12 02:22:12 UTC (rev 253)
@@ -75,11 +75,11 @@
     when the script has finished running, otherwise \pkg{OpenBUGS} remains open
     for further investigation.  The debug option is not available for linux execution.}
   \item{DIC}{logical; if \code{TRUE} (default), compute deviance, pD,
-    and DIC.  For Windows execution, the results are extracted directly
+    and DIC.  The results are extracted directly
     from the \pkg{OpenBUGS} log, which uses the rule \code{pD =
-    Dbar - Dhat}.  For linux execution, or 
+    Dbar - Dhat}.  If extraction fails or 
     if there are less iterations than required for the
-    adaptive phase, the rule \code{pD=var(deviance) / 2} is 
+    adaptive phase, the rule \code{pD=var(deviance) / 2} 
     is computed in R.  See \code{\link{bugs.log}} for more 
     information on extracting results from the log file.}
   \item{digits}{number of significant digits used for \pkg{OpenBUGS} input, see

Modified: trunk/R2OpenBUGS/man/bugs.log.Rd
===================================================================
--- trunk/R2OpenBUGS/man/bugs.log.Rd	2012-05-01 12:57:10 UTC (rev 252)
+++ trunk/R2OpenBUGS/man/bugs.log.Rd	2012-07-12 02:22:12 UTC (rev 253)
@@ -17,8 +17,8 @@
   \item{DIC}{A matrix containing the DIC statistics as returned from
     \pkg{OpenBUGS}.}
 }
-\details{ The function is only supported under Windows execution because the \code{OpenBUGS} log file under Linux execution has a different format.  The function
-returns \code{NA} for both elements of the list under Linux.
+\details{Returns the OpenBUGS summary statistics and DIC extracted directly
+from the log file.
 }
 \seealso{The main function that generates the log file is \code{\link{bugs}}.}
 \author{Jouni Kerman}

This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.