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[Bugs-r-devel] SF.net SVN: bugs-r:[174] trunk/R2OpenBUGS
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From: <snt...@us...> - 2010-10-02 12:53:22
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Revision: 174
http://bugs-r.svn.sourceforge.net/bugs-r/?rev=174&view=rev
Author: snthomas99
Date: 2010-10-02 12:53:15 +0000 (Sat, 02 Oct 2010)
Log Message:
-----------
trying to add validation code to R2OpenBUGS respository
Modified Paths:
--------------
trunk/R2OpenBUGS/DESCRIPTION
trunk/R2OpenBUGS/NAMESPACE
trunk/R2OpenBUGS/R/bugs.R
trunk/R2OpenBUGS/R/bugs.run.R
trunk/R2OpenBUGS/R/bugs.script.R
trunk/R2OpenBUGS/man/bugs.Rd
trunk/R2OpenBUGS/man/bugs.inits.Rd
Added Paths:
-----------
trunk/R2OpenBUGS/CreatevalidateOpenBUGS.R
Added: trunk/R2OpenBUGS/CreatevalidateOpenBUGS.R
===================================================================
--- trunk/R2OpenBUGS/CreatevalidateOpenBUGS.R (rev 0)
+++ trunk/R2OpenBUGS/CreatevalidateOpenBUGS.R 2010-10-02 12:53:15 UTC (rev 174)
@@ -0,0 +1,49 @@
+library(R2OpenBUGS)
+
+## Selected examples which take a few seconds in total to run
+
+test.models <- c("Air", "Asia", "Beetles", "BiRats", "Camel",
+ "Dugongs", "Dyes", "Equiv", "Eyes",
+ "Line", "OtreesMVN", "Rats", "Stacks",
+ "Surgical", "Surgicalrand")
+
+test.params <- list(Air = c("X", "theta"),
+ Asia = c("bronchitis", "either", "lung.cancer"),
+ Beetles = c("alpha", "beta", "rhat"),
+ BiRats = c("mu.beta", "sigma"),
+ Camel = c("Sigma2", "rho", "tau"),
+ Dugongs = c("U3","alpha", "beta", "gamma", "sigma"),
+ Dyes = c("sigma2.btw", "sigma2.with", "theta"),
+ Equiv = c("equiv", "mu", "phi", "pi","sigma1", "sigma2", "theta"),
+ Eyes = c("P", "lambda", "sigma"),
+ Line = c("alpha", "beta", "sigma"),
+ OtreesMVN = c("mu","sigma", "sigmaC"),
+ Rats = c("alpha0", "beta.c", "sigma"),
+ Stacks = c("b", "b0", "outlier[21]","outlier[3]", "outlier[4]", "sigma"),
+ Surgical = "p",
+ Surgicalrand = c("p","pop.mean", "sigma")
+ )
+
+test.modelfile = paste(test.models,"model.txt",sep="")
+test.modelfile<-file.path('C:/Program Files/OpenBUGS/OpenBUGS312/Examples',test.modelfile)
+test.datafile = paste(test.models,"data.txt",sep="")
+test.datafile<-file.path('C:/Program Files/OpenBUGS/OpenBUGS312/Examples',test.datafile)
+test.inits = paste(test.models,"inits.txt",sep="")
+test.inits<-file.path('C:/Program Files/OpenBUGS/OpenBUGS312/Examples',test.inits)
+
+### Test for posterior means within 1 percent of previously saved values
+
+res.true <- vector(mode="list",length=length(test.modelfile))
+for (i in seq(along=test.models)) {
+ res.true[[i]]<-round(bugs(data=test.datafile[i], inits=test.inits[i],
+ para=test.params[[test.models[i]]],model.file=test.modelfile[i],
+ n.burnin=5000, n.iter=20000, n.thin=1, n.chains=1, DIC=FALSE)$summary,5)
+
+}
+
+dput(res.true,'validOpenBUGSResults.R')
+
+
+
+
+
Property changes on: trunk/R2OpenBUGS/CreatevalidateOpenBUGS.R
___________________________________________________________________
Added: svn:executable
+ *
Modified: trunk/R2OpenBUGS/DESCRIPTION
===================================================================
--- trunk/R2OpenBUGS/DESCRIPTION 2010-10-02 12:50:38 UTC (rev 173)
+++ trunk/R2OpenBUGS/DESCRIPTION 2010-10-02 12:53:15 UTC (rev 174)
@@ -1,7 +1,7 @@
Package: R2OpenBUGS
Title: Running OpenBUGS from R / S-PLUS
-Date: 2010-08-5
-Version: 3.0-1
+Date: 2010-09-30
+Version: 3.1-2
Author: originally written as R2WinBUGS by Andrew Gelman <ge...@st...>;
changes and packaged by Sibylle Sturtz <st...@st...>
and Uwe Ligges <li...@st...>.
Modified: trunk/R2OpenBUGS/NAMESPACE
===================================================================
--- trunk/R2OpenBUGS/NAMESPACE 2010-10-02 12:50:38 UTC (rev 173)
+++ trunk/R2OpenBUGS/NAMESPACE 2010-10-02 12:53:15 UTC (rev 174)
@@ -10,7 +10,8 @@
bugs.log,
monitor,
as.bugs.array,
- write.model)
+ write.model,
+ validateInstallOpenBUGS)
S3method(print, bugs)
S3method(plot, bugs)
Modified: trunk/R2OpenBUGS/R/bugs.R
===================================================================
--- trunk/R2OpenBUGS/R/bugs.R 2010-10-02 12:50:38 UTC (rev 173)
+++ trunk/R2OpenBUGS/R/bugs.R 2010-10-02 12:53:15 UTC (rev 174)
@@ -5,7 +5,7 @@
OpenBUGS.pgm=ifelse(.Platform$OS.type == "windows" | useWINE==TRUE,
paste("C:/Program Files/OpenBUGS/OpenBUGS",
version,"/OpenBUGS.exe",sep=""),"OpenBUGS"),
- version='311',
+ version='312',
working.directory=NULL,
clearWD=FALSE, useWINE=FALSE, WINE=NULL,
newWINE=TRUE, WINEPATH=NULL, bugs.seed=1, summary.only=FALSE,
Modified: trunk/R2OpenBUGS/R/bugs.run.R
===================================================================
--- trunk/R2OpenBUGS/R/bugs.run.R 2010-10-02 12:50:38 UTC (rev 173)
+++ trunk/R2OpenBUGS/R/bugs.run.R 2010-10-02 12:53:15 UTC (rev 174)
@@ -27,6 +27,7 @@
native2win(file.path(getwd(), "script.txt"),
useWINE=useWINE, newWINE=newWINE, WINEPATH=WINEPATH),
"\" /", sep="")
+ if(!debug)bugsCall<-paste(bugsCall,"HEADLESS",sep="")
if(useWINE) bugsCall <- paste(WINE, bugsCall)
}else{
bugsCall <- paste(OpenBUGS.pgm, "<", "script.txt", ">", file.path(getwd(), "log.txt"))
Modified: trunk/R2OpenBUGS/R/bugs.script.R
===================================================================
--- trunk/R2OpenBUGS/R/bugs.script.R 2010-10-02 12:50:38 UTC (rev 173)
+++ trunk/R2OpenBUGS/R/bugs.script.R 2010-10-02 12:53:15 UTC (rev 174)
@@ -46,7 +46,8 @@
bugs.seed.cmd <- paste("modelSetRN(", bugs.seed, ")\n", sep="")
}
- thinUpdate <- paste("modelUpdate(", n.burnin, ",", n.thin, ")\n", sep="")
+ thinUpdate <- paste("modelUpdate(", formatC(n.burnin, format='d'), ",", n.thin,
+ ",",formatC(n.burnin, format='d'), ")\n", sep="")
cat(
if(.Platform$OS.type == "windows" | useWINE) "modelDisplay('log')\n",
@@ -61,7 +62,8 @@
savelist,
summarylist,
if(DIC) "dicSet()\n",
- "modelUpdate(", n.iter-n.burnin, ",", n.thin, ")\n",
+ "modelUpdate(", formatC(n.iter-n.burnin, format='d'), ",", n.thin,
+ ",",formatC(n.iter-n.burnin, format='d'),")\n",
"samplesCoda('*', '", coda, "')\n",
"summaryStats('*')\n",
if(DIC) "dicStats()\n",
Modified: trunk/R2OpenBUGS/man/bugs.Rd
===================================================================
--- trunk/R2OpenBUGS/man/bugs.Rd 2010-10-02 12:50:38 UTC (rev 173)
+++ trunk/R2OpenBUGS/man/bugs.Rd 2010-10-02 12:53:15 UTC (rev 174)
@@ -13,7 +13,7 @@
OpenBUGS.pgm=ifelse(.Platform$OS.type == "windows" | useWINE==TRUE,
paste("C:/Program Files/OpenBUGS/OpenBUGS",
version,"/OpenBUGS.exe",sep=""),"OpenBUGS"),
- version='311',
+ version='312',
working.directory=NULL,
clearWD=FALSE, useWINE=FALSE, WINE=NULL,
newWINE=TRUE, WINEPATH=NULL, bugs.seed=1, summary.only=FALSE,
@@ -100,7 +100,9 @@
\item{WINEPATH}{Character, path to \file{winepath} binary file, it is
tried hard (by a guess and the utilities \code{which} and \code{locate})
to get the information automatically if not given.}
- \item{bugs.seed}{Random seed for \pkg{OpenBUGS}}.
+ \item{bugs.seed}{Random seed for \pkg{OpenBUGS}. Must be an integer between 1-14. Seed
+ specification changed between WinBUGS and OpenBUGS; see the OpenBUGS documentation for
+ details}.
\item{summary.only}{If \code{TRUE}, only a parameter summary for very quick analyses is given,
temporary created files are not removed in that case.}
\item{save.history}{If \code{TRUE} (the default), trace plots are generated at the end.}
Modified: trunk/R2OpenBUGS/man/bugs.inits.Rd
===================================================================
--- trunk/R2OpenBUGS/man/bugs.inits.Rd 2010-10-02 12:50:38 UTC (rev 173)
+++ trunk/R2OpenBUGS/man/bugs.inits.Rd 2010-10-02 12:53:15 UTC (rev 174)
@@ -16,7 +16,7 @@
\item{n.chains}{number of Markov chains}
\item{digits}{number of significant digits used for \pkg{OpenBUGS}
input, see \code{\link{formatC}}}
- \item{inits.file}{name for the inits files R write the inits into.}
+ \item{inits.files}{name for the inits files R write the inits into.}
}
\value{Vector of names of \code{inits.files}; as a side effect, the inits files \file{inits*.txt}
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