[Bugs-r-devel] SF.net SVN: bugs-r: [23] trunk/R2WinBUGS

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

Revision: 23
          http://svn.sourceforge.net/bugs-r/?rev=23&view=rev
Author:   ggorjan
Date:     2007-06-12 02:12:59 -0700 (Tue, 12 Jun 2007)

Log Message:
-----------
bugs.script.R
 - using Dawn's solution for proper indexing of CODA files also for R side
 - removed one commented and useless line at the top

read.bugs.Rd
 - documented Dawn's solution

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

Modified: trunk/R2WinBUGS/R/bugs.script.R
===================================================================
--- trunk/R2WinBUGS/R/bugs.script.R	2007-05-23 17:44:29 UTC (rev 22)
+++ trunk/R2WinBUGS/R/bugs.script.R	2007-06-12 09:12:59 UTC (rev 23)
@@ -3,7 +3,6 @@
     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
-###  if (n.chains<2) stop ("n.chains must be at least 2")
 
   if((ceiling(n.iter/n.thin) - ceiling(n.burnin/n.thin)) < 2)
     stop ("(n.iter-n.burnin)/n.thin must be at least 2")
@@ -17,29 +16,16 @@
   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=""), 
+  inits <- sapply(paste(working.directory, "/inits", 1:n.chains, ".txt", sep=""),
                   function(x) native2win(x, , 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))
-  
-  if (is.R()){
-    thinUpdateCommand <- paste("thin.updater (", n.thin, ")\n",
-      "update (", ceiling(n.burnin/n.thin), ")\n", sep = "")
-  } else{
-    ## In S-PLUS, the handling of the thinning is done differently than in R.
-    ## bin represents the number of iterations between saves, before thinning,
-    ## where in R it is the number of iterations between saves, after thinning.
-    ## This alternative handling of the thinning is done so that the resulting 
-    ## samples have the correct iteration indexes in the output (coda) files.
-    ## Therefore, if the samples are read into S-PLUS using the coda package,
-    ## the thinning will be correctly labelled in the resulting mcmc object.
-    ## In R, the thinning is always labelled as 1, even if thinning was done.
-    thinUpdateCommand <- paste("update (", n.burnin, ")\n",
-            "thin.samples (", n.thin, ")\n", sep = "")
-        bin = bin * n.thin
-  }
-  
+
+  thinUpdateCommand <- paste("update (", n.burnin, ")\n",
+                             "thin.samples (", n.thin, ")\n", sep = "")
+  bin = bin * n.thin
+
   cat(
     "display ('log')\n",
     "check ('", native2win(model, WINEPATH=WINEPATH), "')\n",
@@ -56,7 +42,7 @@
     "stats (*)\n",
     if(DIC) "dic.stats()\n",
     "history (*, '", native2win(history, WINEPATH=WINEPATH), "')\n",
-    "save ('", native2win(logfile, WINEPATH=WINEPATH), "')\n", 
+    "save ('", native2win(logfile, WINEPATH=WINEPATH), "')\n",
     "save ('", native2win(logfileTxt, WINEPATH=WINEPATH), "')\n",
     file=script, sep="", append=FALSE)
   if (!debug) cat ("quit ()\n", file=script, append=TRUE)

Modified: trunk/R2WinBUGS/man/read.bugs.Rd
===================================================================
--- trunk/R2WinBUGS/man/read.bugs.Rd	2007-05-23 17:44:29 UTC (rev 22)
+++ trunk/R2WinBUGS/man/read.bugs.Rd	2007-06-12 09:12:59 UTC (rev 23)
@@ -1,19 +1,34 @@
 \name{read.bugs}
 \alias{read.bugs}
 \title{Read output files in CODA format}
-\description{This function reads Markov Chain Monte Carlo output in the CODA format produced by WinBUGS
-    and returns an object of class \code{\link[coda]{mcmc.list}} for further output analysis 
-    using the \sQuote{coda} package.}
+
+\description{This function reads Markov Chain Monte Carlo output in the
+  CODA format produced by WinBUGS and returns an object of class
+  \code{\link[coda]{mcmc.list}} for further output analysis using the
+  \pkg{coda} package.}
+
 \usage{
 read.bugs(codafiles, ...)
 }
+
 \arguments{
-  \item{codafiles}{character vector of filenames (e.g. returned from \code{\link{bugs}} 
-    in call such as \code{bugs(....., codaPkg = TRUE, .....)}). 
-    Each of the files contains coda output for one chain produced by WinBUGS,
-    the \emph{directory} name of the corresponding file \file{codaIndex.txt} 
-    is extracted from the first element of \code{codafiles}.}
-  \item{...}{further arguments to be passed to \code{\link[coda]{read.coda}}}
+  \item{codafiles}{character vector of filenames (e.g. returned from
+    \code{\link{bugs}} in call such as \code{bugs(....., codaPkg=TRUE,
+    .....)}). Each of the files contains coda output for one chain
+    produced by WinBUGS, the \emph{directory} name of the corresponding
+    file \file{codaIndex.txt} is extracted from the first element of
+    \code{codafiles}.}
+  \item{...}{further arguments to be passed to
+    \code{\link[coda]{read.coda}}}
 }
-\seealso{\code{\link{bugs}}, \code{\link[coda]{read.coda}}, \code{\link[coda]{mcmc.list}}}
+
+\details{
+  \code{\link{bugs}} (actually it is \code{\link{bugs.script}}) writes
+  BUGS script in such a way that iteration numbers in resulting CODA
+  files correspond to iteration numbers before burnin and thinning.
+}
+
+\seealso{\code{\link{bugs}}, \code{\link[coda]{read.coda}},
+\code{\link[coda]{mcmc.list}}}
+
 \keyword{file}


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