[Bugs-r-devel] SF.net SVN: bugs-r:[101] trunk/R2WinBUGS

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

Revision: 101
          http://bugs-r.svn.sourceforge.net/bugs-r/?rev=101&view=rev
Author:   ligges
Date:     2009-02-12 12:26:22 +0000 (Thu, 12 Feb 2009)

Log Message:
-----------
as.mcmc.list.bugs method implemented (contributed by Mike Meredith)

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

Added Paths:
-----------
    trunk/R2WinBUGS/R/as.mcmc.list.bugs.R

Modified: trunk/R2WinBUGS/NAMESPACE
===================================================================
--- trunk/R2WinBUGS/NAMESPACE	2009-02-12 11:17:21 UTC (rev 100)
+++ trunk/R2WinBUGS/NAMESPACE	2009-02-12 12:26:22 UTC (rev 101)
@@ -15,4 +15,4 @@
 
 S3method(print, bugs)
 S3method(plot, bugs)
-
+S3method(as.mcmc.list, bugs)

Added: trunk/R2WinBUGS/R/as.mcmc.list.bugs.R
===================================================================
--- trunk/R2WinBUGS/R/as.mcmc.list.bugs.R	                        (rev 0)
+++ trunk/R2WinBUGS/R/as.mcmc.list.bugs.R	2009-02-12 12:26:22 UTC (rev 101)
@@ -0,0 +1,18 @@
+## Function as.mcmc.list.bugs contributed by Mike Meredith, 12 Feb 2009:
+as.mcmc.list.bugs <- function(x, ...) {
+    if(!inherits(x, "bugs")) 
+        stop("Method as.mcmc.list.bugs() is only intended for bugs objects.")
+    if(dim(x$sims.array)[2] != x$n.chains)
+        stop("Inconsistancy in bug object regarding the number of chains.")
+    mclis <- vector("list", x$n.chains)
+    strt <- x$n.burnin%/%x$n.thin + 1
+    end <- x$n.iter%/%x$n.thin
+    ord <- order(dimnames(x$sims.array)[[3]])
+    if(end - strt + 1 < nrow(x$sims.array[,1,ord])) end <- end + 1
+    for(i in 1:x$n.chains) {
+        tmp1 <- x$sims.array[,i,ord]
+        rownames(tmp1) <- strt:end
+        mclis[[i]] <- mcmc(tmp1, strt, end, 1)
+    }
+    as.mcmc.list(mclis)
+} 

Modified: trunk/R2WinBUGS/R/bugs.sims.R
===================================================================
--- trunk/R2WinBUGS/R/bugs.sims.R	2009-02-12 11:17:21 UTC (rev 100)
+++ trunk/R2WinBUGS/R/bugs.sims.R	2009-02-12 12:26:22 UTC (rev 101)
@@ -123,7 +123,7 @@
   if(DIC) {
      ## Read DIC from BUGS log
      LOG <- bugs.log("log.txt")$DIC
-     if(any(is.na(LOG))) { ## Something went wrong --> Use Gelmans tweak
+     if(any(is.na(LOG))) { ## Something went wrong --> Use Gelman's tweak
         deviance <- all$sims.array[, , dim(sims.array)[3], drop = FALSE]
         if(!is.R()) dimnames(deviance) <- NULL
         dim(deviance) <- dim(deviance)[1:2]

Modified: trunk/R2WinBUGS/man/bugs.Rd
===================================================================
--- trunk/R2WinBUGS/man/bugs.Rd	2009-02-12 11:17:21 UTC (rev 100)
+++ trunk/R2WinBUGS/man/bugs.Rd	2009-02-12 12:26:22 UTC (rev 101)
@@ -71,7 +71,10 @@
   \item{codaPkg}{logical; if \code{FALSE} (default) a \code{bugs} object
     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"}).}
+    \code{\link{read.bugs}} (not used if \code{program="OpenBUGS"}).
+    A \code{bugs} object can be converted to an \code{mcmc.list} object as 
+    used by the \pkg{coda} package with the method \code{\link[coda]{as.mcmc.list}} 
+    (for which a method is provided by R2WinBUGS).}
   \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.}


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