[Bugs-r-devel] SF.net SVN: bugs-r: [79] trunk/R2WinBUGS

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

Revision: 79
          http://bugs-r.svn.sourceforge.net/bugs-r/?rev=79&view=rev
Author:   ligges
Date:     2008-01-08 13:11:35 -0800 (Tue, 08 Jan 2008)

Log Message:
-----------
bugs in monitor() reported by Andrew Gelman:
- exported from NS (for making code in his book work)
- extracts the default number of chains from the object by default

Modified Paths:
--------------
    trunk/R2WinBUGS/DESCRIPTION
    trunk/R2WinBUGS/NAMESPACE
    trunk/R2WinBUGS/R/monitor.R
    trunk/R2WinBUGS/man/bugs.log.Rd
    trunk/R2WinBUGS/man/monitor.Rd

Modified: trunk/R2WinBUGS/DESCRIPTION
===================================================================
--- trunk/R2WinBUGS/DESCRIPTION	2008-01-06 18:56:18 UTC (rev 78)
+++ trunk/R2WinBUGS/DESCRIPTION	2008-01-08 21:11:35 UTC (rev 79)
@@ -1,6 +1,6 @@
 Package: R2WinBUGS
 Title: Running WinBUGS and OpenBUGS from R / S-PLUS
-Date: 2008-01-06
+Date: 2008-01-08
 Version: 2.1-7
 Author: originally written by Andrew Gelman <ge...@st...>;
  changes and packaged by Sibylle Sturtz <st...@st...>

Modified: trunk/R2WinBUGS/NAMESPACE
===================================================================
--- trunk/R2WinBUGS/NAMESPACE	2008-01-06 18:56:18 UTC (rev 78)
+++ trunk/R2WinBUGS/NAMESPACE	2008-01-08 21:11:35 UTC (rev 79)
@@ -8,6 +8,7 @@
        bugs.data,
        read.bugs,
        bugs.log,
+       monitor,
        openbugs,
        as.bugs.array,
        write.model)

Modified: trunk/R2WinBUGS/R/monitor.R
===================================================================
--- trunk/R2WinBUGS/R/monitor.R	2008-01-06 18:56:18 UTC (rev 78)
+++ trunk/R2WinBUGS/R/monitor.R	2008-01-08 21:11:35 UTC (rev 79)
@@ -1,15 +1,15 @@
 "monitor" <-
-function (a, n.chains, trans=NULL, keep.all=FALSE, Rupper.keep=FALSE) {
+function (a, n.chains=dim(a)[2], trans=NULL, keep.all=FALSE, Rupper.keep=FALSE) {
 
-# If keep.all=T:  a is a n x m x k array:
-#   m sequences of length n, k variables measured
-# If keep.all=F:  a is a 2n x m x k array (first half will be discarded)
-#
-# trans is a vector of length k:  "" if no transformation, or "log" or "logit"
-# (If trans is not defined, it will be set to "log" for parameters that
-# are all-positive and 0 otherwise.)
-#
-# If Rupper.keep=T:  keep Rupper.  (Otherwise don't display it.)
+## If keep.all=T:  a is a n x m x k array:
+##   m sequences of length n, k variables measured
+## If keep.all=F:  a is a 2n x m x k array (first half will be discarded)
+##
+## trans is a vector of length k:  "" if no transformation, or "log" or "logit"
+## (If trans is not defined, it will be set to "log" for parameters that
+## are all-positive and 0 otherwise.)
+##
+## If Rupper.keep=TRUE:  keep Rupper.  (Otherwise don't display it.)
   invlogit <- function (x) {1 / (1 + exp(-x))}
   nparams <- if(length(dim(a)) < 3) 1 else dim(a)[length(dim(a))]
   # Calculation and initialization of the required matrix "output"
@@ -30,9 +30,9 @@
             confshrink = conv.p$confshrink, n.eff = conv.p$n.eff)
     }
     else if (trans[i]=="logit"){
-    		if (!is.R()){
-    			logit <- function (x) { log(x /(1- x)) }
-    		}
+            if (!is.R()){
+                logit <- function (x) { log(x /(1- x)) }
+            }
         conv.p <- conv.par(logit(ai), n.chains, Rupper.keep=Rupper.keep)
         conv.p <- list(quantiles = invlogit(conv.p$quantiles),
             confshrink = conv.p$confshrink, n.eff = conv.p$n.eff)

Modified: trunk/R2WinBUGS/man/bugs.log.Rd
===================================================================
--- trunk/R2WinBUGS/man/bugs.log.Rd	2008-01-06 18:56:18 UTC (rev 78)
+++ trunk/R2WinBUGS/man/bugs.log.Rd	2008-01-08 21:11:35 UTC (rev 79)
@@ -18,5 +18,6 @@
     \pkg{WinBUGS}.}
 }
 \seealso{The main function that generates the log file is \code{\link{bugs}}.}
+\author{Jouni Kerman}
 \keyword{IO}
 \keyword{file}

Modified: trunk/R2WinBUGS/man/monitor.Rd
===================================================================
--- trunk/R2WinBUGS/man/monitor.Rd	2008-01-06 18:56:18 UTC (rev 78)
+++ trunk/R2WinBUGS/man/monitor.Rd	2008-01-08 21:11:35 UTC (rev 79)
@@ -3,15 +3,13 @@
 \alias{conv.par}
 \title{Special summary statistics}
 
-\description{Special summary statistics of the WinBUGS output - intended
-  for internal use}
+\description{Special summary statistics of the WinBUGS output.}
 
 \usage{
-monitor(a, n.chains, trans = NULL, keep.all = FALSE, Rupper.keep = FALSE)
+monitor(a, n.chains = dim(a)[2], trans = NULL, keep.all = FALSE, Rupper.keep = FALSE)
 conv.par(x, n.chains, Rupper.keep = TRUE)
 }
 \arguments{
-  \item{x}{}
   \item{a}{a \code{n * m * k} array: \code{m} sequences of length
     \code{n}, \code{k} variables measured}
   \item{n.chains}{number of Markov chains}
@@ -21,9 +19,10 @@
   \item{keep.all}{if \code{FALSE} (default), first half of \code{a} will
     be discarded}
   \item{Rupper.keep}{if \code{FALSE}, don't return \code{Rupper}}
+  \item{x}{for internal use only}
 }
 
-\details{See the well documented code for details.}
+\details{\code{conv.par} is intended for internal use only.}
 
 \value{
   for \code{monitor}:


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