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From: <woo...@us...> - 2007-05-08 21:50:37
|
Revision: 13
http://svn.sourceforge.net/bugs-r/?rev=13&view=rev
Author: woodard_
Date: 2007-05-08 14:50:38 -0700 (Tue, 08 May 2007)
Log Message:
-----------
Added a note to the documentation for write.model on how to avoid a warning in S-PLUS
Modified Paths:
--------------
trunk/R2WinBUGS/man/write.model.Rd
Modified: trunk/R2WinBUGS/man/write.model.Rd
===================================================================
--- trunk/R2WinBUGS/man/write.model.Rd 2007-04-17 14:21:52 UTC (rev 12)
+++ trunk/R2WinBUGS/man/write.model.Rd 2007-05-08 21:50:38 UTC (rev 13)
@@ -21,6 +21,10 @@
but this is illegal in R / S-PLUS. To overcome this incompatibility, use \code{\%_\%} before \code{I(...)}:
\code{dnorm(...) \%_\% I(...)}.
The dummy operator \code{\%_\%} will be removed before the BUGS code is saved.
+
+In S-PLUS, a warning is generated when the model function is defined if the last statement in the
+model is an assignment. To avoid this warning, add the line "invisible()" to the end of the model
+definition. This line will be removed before the BUGS code is saved.
}
\author{original idea by Jouni Kerman, modified by Uwe Ligges}
\examples{
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: Gregor G. <gre...@bf...> - 2007-04-19 10:56:25
|
Hi, In my opinion Dawn's change make sense also for R side. Does anyone have any objection for not porting this also to R side? Gregor -------- Original Message -------- Subject: [Bugs-r-devel] SF.net SVN: bugs-r: [12] trunk/R2WinBUGS/R/bugs.script.R Date: Tue, 17 Apr 2007 07:21:52 -0700 From: woo...@us... To: bug...@li... Revision: 12 http://svn.sourceforge.net/bugs-r/?rev=12&view=rev Author: woodard_ Date: 2007-04-17 07:21:52 -0700 (Tue, 17 Apr 2007) Log Message: ----------- 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. Modified Paths: -------------- trunk/R2WinBUGS/R/bugs.script.R Modified: trunk/R2WinBUGS/R/bugs.script.R =================================================================== --- trunk/R2WinBUGS/R/bugs.script.R 2007-04-16 11:21:38 UTC (rev 11) +++ trunk/R2WinBUGS/R/bugs.script.R 2007-04-17 14:21:52 UTC (rev 12) @@ -21,6 +21,24 @@ 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{ ... + thinUpdateCommand <- paste("update (", n.burnin, ")\n", + "thin.samples (", n.thin, ")\n", sep = "") + bin = bin * n.thin + } + cat( "display ('log')\n", "check ('", native2win(model), "')\n", @@ -28,8 +46,7 @@ "compile (", n.chains, ")\n", if(is.inits) initlist, "gen.inits()\n", - "thin.updater (", n.thin, ")\n", - "update (", ceiling(n.burnin/n.thin), ")\n", + thinUpdateCommand, savelist, if(DIC) "dic.set()\n", rep( This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. ------------------------------------------------------------------------- This SF.net email is sponsored by DB2 Express Download DB2 Express C - the FREE version of DB2 express and take control of your XML. No limits. Just data. Click to get it now. http://sourceforge.net/powerbar/db2/ _______________________________________________ Bugs-r-devel mailing list Bug...@li... https://lists.sourceforge.net/lists/listinfo/bugs-r-devel -- Lep pozdrav / With regards, Gregor Gorjanc ---------------------------------------------------------------------- University of Ljubljana PhD student Biotechnical Faculty www: http://www.bfro.uni-lj.si/MR/ggorjan Zootechnical Department blog: http://ggorjan.blogspot.com Groblje 3 mail: gregor.gorjanc <at> bfro.uni-lj.si SI-1230 Domzale fax: +386 (0)1 72 17 888 Slovenia, Europe tel: +386 (0)1 72 17 861 ---------------------------------------------------------------------- |
|
From: <woo...@us...> - 2007-04-17 14:21:51
|
Revision: 12
http://svn.sourceforge.net/bugs-r/?rev=12&view=rev
Author: woodard_
Date: 2007-04-17 07:21:52 -0700 (Tue, 17 Apr 2007)
Log Message:
-----------
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.
Modified Paths:
--------------
trunk/R2WinBUGS/R/bugs.script.R
Modified: trunk/R2WinBUGS/R/bugs.script.R
===================================================================
--- trunk/R2WinBUGS/R/bugs.script.R 2007-04-16 11:21:38 UTC (rev 11)
+++ trunk/R2WinBUGS/R/bugs.script.R 2007-04-17 14:21:52 UTC (rev 12)
@@ -21,6 +21,24 @@
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
+ }
+
cat(
"display ('log')\n",
"check ('", native2win(model), "')\n",
@@ -28,8 +46,7 @@
"compile (", n.chains, ")\n",
if(is.inits) initlist,
"gen.inits()\n",
- "thin.updater (", n.thin, ")\n",
- "update (", ceiling(n.burnin/n.thin), ")\n",
+ thinUpdateCommand,
savelist,
if(DIC) "dic.set()\n",
rep(
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <gg...@us...> - 2007-04-16 11:21:36
|
Revision: 11
http://svn.sourceforge.net/bugs-r/?rev=11&view=rev
Author: ggorjan
Date: 2007-04-16 04:21:38 -0700 (Mon, 16 Apr 2007)
Log Message:
-----------
fixed link markup, removed some spaces
Modified Paths:
--------------
trunk/R2WinBUGS/man/write.model.Rd
Modified: trunk/R2WinBUGS/man/write.model.Rd
===================================================================
--- trunk/R2WinBUGS/man/write.model.Rd 2007-04-16 11:18:27 UTC (rev 10)
+++ trunk/R2WinBUGS/man/write.model.Rd 2007-04-16 11:21:38 UTC (rev 11)
@@ -7,7 +7,7 @@
}
\arguments{
\item{model}{R / S-PLUS function containing the BUGS model in the BUGS model language, for minor differences see Section Details.}
- \item{con}{passed to \code{link{writeLines}} which actually writes the model file}
+ \item{con}{passed to \code{\link{writeLines}} which actually writes the model file}
}
\value{
Nothing, but as a side effect, the model file is written.
@@ -40,7 +40,7 @@
## some temporary filename:
filename <- file.path(tempdir(), "schoolsmodel.bug")
} else{ # for S-PLUS
- ## put the file in the working directory:
+ ## put the file in the working directory:
filename <- "schoolsmodel.bug"
}
@@ -51,5 +51,4 @@
}
\seealso{\code{\link{bugs}}}
\keyword{IO}
-\concept{model}
-
+\concept{model}
\ No newline at end of file
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <gg...@us...> - 2007-04-16 11:18:27
|
Revision: 10
http://svn.sourceforge.net/bugs-r/?rev=10&view=rev
Author: ggorjan
Date: 2007-04-16 04:18:27 -0700 (Mon, 16 Apr 2007)
Log Message:
-----------
better formatting in SysReq. field
Modified Paths:
--------------
trunk/R2WinBUGS/DESCRIPTION
Modified: trunk/R2WinBUGS/DESCRIPTION
===================================================================
--- trunk/R2WinBUGS/DESCRIPTION 2007-04-07 18:04:11 UTC (rev 9)
+++ trunk/R2WinBUGS/DESCRIPTION 2007-04-16 11:18:27 UTC (rev 10)
@@ -10,12 +10,12 @@
Ported to S-PLUS by Insightful Corp.
Description: Using this package,
it is possible to call a BUGS model, summarize inferences and
- convergence in a table and graph, and save the simulations in arrays for easy access
- in R / S-PLUS. In S-PLUS, the openbugs functionality and the windows emulation
+ convergence in a table and graph, and save the simulations in arrays for easy access
+ in R / S-PLUS. In S-PLUS, the openbugs functionality and the windows emulation
functionality is not yet available.
Depends: R (>= 2.4.0)
Suggests: coda (>= 0.9-0), BRugs (>= 0.3-0)
-SystemRequirements: WinBUGS 1.4 on Windows
+SystemRequirements: WinBUGS 1.4
URL: http://www.stat.columbia.edu/~gelman/bugsR/
Maintainer: Sibylle Sturtz <st...@st...>
License: GPL version 2
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: Uwe L. <li...@st...> - 2007-04-10 20:01:07
|
Dawn Woodard wrote: > Uwe, > > Sorry about that. I just created an account with username woodard_ > > Let me know if you have any more problems. Dawn, got it done. You are in the role of a developer with full access to the Bugs-R SVN repository now. Thanks for your contributions to R2WinBUGS. Best, Uwe > Thank you! > Dawn |
|
From: Gregor G. <gre...@bf...> - 2007-04-08 15:02:31
|
li...@us... wrote: > Revision: 9 > http://svn.sourceforge.net/bugs-r/?rev=9&view=rev > Author: ligges > Date: 2007-04-07 11:04:11 -0700 (Sat, 07 Apr 2007) > > Log Message: > ----------- > R2WinBUGS has been ported to S-PLUS by Insightful Corp. > Special thanks to Dawn Woodard! Great. It is nice to see some development going on. Unfortunately, I did not have any time since setting up SF project to work on R2BUGS stuff. I hope this will change in near future. -- Lep pozdrav / With regards, Gregor Gorjanc ---------------------------------------------------------------------- University of Ljubljana PhD student Biotechnical Faculty www: http://www.bfro.uni-lj.si/MR/ggorjan Zootechnical Department blog: http://ggorjan.blogspot.com Groblje 3 mail: gregor.gorjanc <at> bfro.uni-lj.si SI-1230 Domzale fax: +386 (0)1 72 17 888 Slovenia, Europe tel: +386 (0)1 72 17 861 ---------------------------------------------------------------------- |
|
From: <li...@us...> - 2007-04-07 18:04:19
|
Revision: 9
http://svn.sourceforge.net/bugs-r/?rev=9&view=rev
Author: ligges
Date: 2007-04-07 11:04:11 -0700 (Sat, 07 Apr 2007)
Log Message:
-----------
R2WinBUGS has been ported to S-PLUS by Insightful Corp.
Special thanks to Dawn Woodard!
Modified Paths:
--------------
trunk/R2WinBUGS/Changes
trunk/R2WinBUGS/DESCRIPTION
trunk/R2WinBUGS/R/as.bugs.array.R
trunk/R2WinBUGS/R/attach.all.R
trunk/R2WinBUGS/R/bugs.R
trunk/R2WinBUGS/R/bugs.data.R
trunk/R2WinBUGS/R/bugs.inits.R
trunk/R2WinBUGS/R/bugs.plot.inferences.R
trunk/R2WinBUGS/R/bugs.plot.summary.R
trunk/R2WinBUGS/R/bugs.run.R
trunk/R2WinBUGS/R/bugs.sims.R
trunk/R2WinBUGS/R/bugs.update.settings.R
trunk/R2WinBUGS/R/conv.par.R
trunk/R2WinBUGS/R/monitor.R
trunk/R2WinBUGS/R/openbugs.R
trunk/R2WinBUGS/R/plot.bugs.R
trunk/R2WinBUGS/R/wineutils.R
trunk/R2WinBUGS/R/write.model.R
trunk/R2WinBUGS/man/bugs.Rd
trunk/R2WinBUGS/man/bugs.log.Rd
trunk/R2WinBUGS/man/bugs.run.Rd
trunk/R2WinBUGS/man/bugs.script.Rd
trunk/R2WinBUGS/man/bugs.sims.Rd
trunk/R2WinBUGS/man/openbugs.Rd
trunk/R2WinBUGS/man/write.model.Rd
Modified: trunk/R2WinBUGS/Changes
===================================================================
--- trunk/R2WinBUGS/Changes 2006-12-29 16:10:15 UTC (rev 8)
+++ trunk/R2WinBUGS/Changes 2007-04-07 18:04:11 UTC (rev 9)
@@ -69,3 +69,6 @@
Update 2.0-4 (01 November 2006):
- print.bugs / plot.bugs documentation fixes
- write.model() fix
+
+Update 2.1-1 (07 April 2007):
+- Ported to S-PLUS by Insightful Corp.
Modified: trunk/R2WinBUGS/DESCRIPTION
===================================================================
--- trunk/R2WinBUGS/DESCRIPTION 2006-12-29 16:10:15 UTC (rev 8)
+++ trunk/R2WinBUGS/DESCRIPTION 2007-04-07 18:04:11 UTC (rev 9)
@@ -1,18 +1,22 @@
Package: R2WinBUGS
-Title: Running WinBUGS and OpenBUGS from R
-Date: 2006-11-01
-Version: 2.0-4
+Title: Running WinBUGS and OpenBUGS from R / S-PLUS
+Date: 2007-04-07
+Version: 2.1-1
Author: originally written by Andrew Gelman <ge...@st...>;
changes and packaged by Sibylle Sturtz <st...@st...>
and Uwe Ligges <li...@st...>.
With considerable contributions by Gregor Gorjanc <gre...@bf...>
and Jouni Kerman <ke...@st...>.
+ Ported to S-PLUS by Insightful Corp.
Description: Using this package,
it is possible to call a BUGS model, summarize inferences and
- convergence in a table and graph, and save the simulations in arrays for easy access in R.
-Depends: R (>= 2.2.0)
+ convergence in a table and graph, and save the simulations in arrays for easy access
+ in R / S-PLUS. In S-PLUS, the openbugs functionality and the windows emulation
+ functionality is not yet available.
+Depends: R (>= 2.4.0)
Suggests: coda (>= 0.9-0), BRugs (>= 0.3-0)
SystemRequirements: WinBUGS 1.4 on Windows
URL: http://www.stat.columbia.edu/~gelman/bugsR/
Maintainer: Sibylle Sturtz <st...@st...>
License: GPL version 2
+Dialect: R, S-PLUS
Modified: trunk/R2WinBUGS/R/as.bugs.array.R
===================================================================
--- trunk/R2WinBUGS/R/as.bugs.array.R 2006-12-29 16:10:15 UTC (rev 8)
+++ trunk/R2WinBUGS/R/as.bugs.array.R 2007-04-07 18:04:11 UTC (rev 9)
@@ -71,9 +71,11 @@
summary <- monitor(sims.array, n.chains, keep.all = TRUE)
last.values <- as.list(numeric(n.chains))
for (i in 1:n.chains) {
- n.roots.0 <- if (!is.null(DIC))
- n.roots - 1
- else n.roots
+ if (is.R()) {
+ n.roots.0 <- if(!is.null(DIC)) n.roots - 1 else n.roots
+ } else {
+ n.roots.0 <- if(DIC) n.roots - 1 else n.roots
+ }
last.values[[i]] <- as.list(numeric(n.roots.0))
names(last.values[[i]]) <- root.short[1:n.roots.0]
for (j in 1:n.roots.0) {
@@ -111,6 +113,11 @@
}
}
summary <- summary[rank.long, ]
+ if (is.R())
+ is.DIC = !is.null(DIC)
+ else
+ is.DIC = DIC
+
all <- list(n.chains = n.chains, n.iter = n.iter, n.burnin = n.burnin,
n.thin = n.thin, n.keep = n.keep, n.sims = n.sims,
sims.array = sims.array[,,rank.long,drop = FALSE], sims.list = sims.list,
@@ -118,7 +125,7 @@
sd = summary.sd, median = summary.median, root.short = root.short,
long.short = long.short, dimension.short = dimension.short,
indexes.short = indexes.short, last.values = last.values, program=program,
- model.file=model.file, is.DIC=!is.null(DIC), DIC=DIC)
+ model.file=model.file, is.DIC=is.DIC, DIC=DIC)
if(sum(DIC)) {
deviance <- all$sims.array[, , dim(sims.array)[3], drop = FALSE]
dim(deviance) <- dim(deviance)[1:2]
Modified: trunk/R2WinBUGS/R/attach.all.R
===================================================================
--- trunk/R2WinBUGS/R/attach.all.R 2006-12-29 16:10:15 UTC (rev 8)
+++ trunk/R2WinBUGS/R/attach.all.R 2007-04-07 18:04:11 UTC (rev 9)
@@ -1,11 +1,12 @@
attach.all <- function(x, overwrite = NA, name = "attach.all"){
+ if(is.R()){
rem <- names(x) %in% ls(.GlobalEnv)
if(!any(rem)) overwrite <- FALSE
rem <- names(x)[rem]
if(is.na(overwrite)){
question <- paste("The following objects in .GlobalEnv will mask\nobjects in the attached database:\n",
- paste(rem, collapse=", "),
- "\nRemove these objects from .GlobalEnv?", sep="")
+ paste(rem, collapse=", "),
+ "\nRemove these objects from .GlobalEnv?", sep="")
if(interactive()){
if(.Platform$OS.type == "windows")
overwrite <- "YES" == winDialog(type = "yesno", question)
@@ -16,6 +17,9 @@
}
if(overwrite) remove(list=rem, envir=.GlobalEnv)
attach(x, name=name)
+ } else {
+ attach.default(x, name = name)
+ }
}
attach.bugs <- function (x, overwrite = NA){
@@ -25,12 +29,24 @@
detach("bugs.sims")}
x$sims.list$n.sims <- x$n.sims # put n.sims into sims.list for convenience
r2 <- attach.all(x$sims.list, overwrite = overwrite, name = "bugs.sims")
- invisible (bugs.sims = r2)
+ if (is.R())
+ invisible (bugs.sims = r2)
+ else
+ invisible (r2)
}
-detach.all <- function(name = "attach.all")
+detach.all <- function(name = "attach.all"){
+ if (is.R()){
do.call("detach", list(name=name))
+ } else {
+ do.call("detach", list(what=name))
+ }
+}
detach.bugs <- function(){
+ if (is.R()){
detach.all("bugs.sims")
+ } else {
+ invisible(detach.all("bugs.sims"))
+ }
}
Modified: trunk/R2WinBUGS/R/bugs.R
===================================================================
--- trunk/R2WinBUGS/R/bugs.R 2006-12-29 16:10:15 UTC (rev 8)
+++ trunk/R2WinBUGS/R/bugs.R 2007-04-07 18:04:11 UTC (rev 9)
@@ -10,17 +10,23 @@
clearWD = FALSE, useWINE = .Platform$OS.type != "windows", WINE = Sys.getenv("WINE"),
newWINE = FALSE, WINEPATH = NULL){
- ## If OpenBUGS, we only call openbugs() and exit...
program <- match.arg(program)
if (program %in% c("openbugs", "OpenBugs"))
- return(openbugs(data, inits, parameters.to.save, model.file,
- n.chains, n.iter, n.burnin, n.thin, DIC, bugs.directory,
- working.directory, digits))
-
+ if (is.R()){
+ ## If OpenBUGS, we only call openbugs() and exit...
+ return(openbugs(data, inits, parameters.to.save, model.file,
+ n.chains, n.iter, n.burnin, n.thin, DIC, bugs.directory,
+ working.directory, digits))
+ } else {
+ stop ("OpenBUGS is not yet available in S-PLUS")
+ }
## Checking number of inits, which is NOT save here:
if(!missing(inits) && !is.function(inits) && !is.null(inits) && (length(inits) != n.chains))
stop("Number of initialized chains (length(inits)) != n.chains")
- if (useWINE) { # attempt to find wine and winepath
+ if(useWINE) {
+ if (!is.R())
+ stop ("Non-Windows platforms not yet supported in R2WinBUGS for S-PLUS")
+ ## attempt to find wine and winepath
if (!nchar(WINE)) {
WINE <- system("locate wine | grep bin/wine$", intern = TRUE)
WINE <- WINE[length(WINE)]
@@ -31,7 +37,7 @@
WINEPATH <- WINEPATH[length(WINEPATH)]
}
if (!length(WINEPATH)) stop("couldn't locate WINEPATH binary")
- }
+ }
if(!is.null(working.directory)){
savedWD <- getwd()
setwd(working.directory)
@@ -59,8 +65,13 @@
if(codaPkg)
return(file.path(getwd(), paste("coda", 1:n.chains, ".txt", sep="")))
- sims <- c(bugs.sims(parameters.to.save, n.chains, n.iter, n.burnin, n.thin, DIC),
- model.file = model.file, is.DIC = !is.null(DIC), program = program)
+ if (is.R()){
+ sims <- c(bugs.sims(parameters.to.save, n.chains, n.iter, n.burnin, n.thin, DIC),
+ model.file = model.file, is.DIC = !is.null(DIC), program = program)
+ } else {
+ sims <- c(bugs.sims(parameters.to.save, n.chains, n.iter, n.burnin, n.thin, DIC),
+ model.file = model.file, is.DIC = DIC, program = program)
+ }
if(clearWD)
file.remove(c("data.txt", "log.odc", "log.txt", "codaIndex.txt",
paste("inits", 1:n.chains, ".txt", sep=""),
Modified: trunk/R2WinBUGS/R/bugs.data.R
===================================================================
--- trunk/R2WinBUGS/R/bugs.data.R 2006-12-29 16:10:15 UTC (rev 8)
+++ trunk/R2WinBUGS/R/bugs.data.R 2007-04-07 18:04:11 UTC (rev 9)
@@ -1,12 +1,222 @@
-"bugs.data" <-
+"bugs.data" <-
function(data, dir = getwd(), digits = 5){
if(is.numeric(unlist(data)))
- write.datafile(lapply(data, formatC, digits = digits, format = "E"),
- file.path(dir, "data.txt"))
+ if(is.R()) {
+ write.datafile(lapply(data, formatC, digits = digits, format = "E"),
+ file.path(dir, "data.txt"))
+ }
+ else {
+ writeDatafileS4(data, towhere = "data.txt")
+ }
else {
- data.list <- lapply(as.list(data), get, pos = parent.frame(2))
- names(data.list) <- as.list(data)
- write.datafile(lapply(data.list, formatC, digits = digits, format = "E"),
- file.path(dir, "data.txt"))
- }
+ if(is.R()) {
+ data.list <- lapply(as.list(data), get, pos = parent.frame(2))
+ names(data.list) <- as.list(data)
+ write.datafile(lapply(data.list, formatC, digits = digits, format = "E"),
+ file.path(dir, "data.txt"))
+ }
+ else {
+ data.list <- lapply(as.list(data), get, where = parent.frame(2))
+ names(data.list) <- unlist(data)
+ writeDatafileS4(data.list, towhere = "data.txt")
+ }
+ }
}
+
+if (!is.R()) {
+
+"writeDatafileS4" <-
+#
+# Writes to file "towhere" text defining a list containing "DATA" in a form compatable with WinBUGS.
+# Required arguments:
+# DATA - either a data frame or else a list consisting of any combination of scalars, vectors, arrays or data frames (but not lists).
+# If a list, all list elements that are not data.frames must be named. Names of data.frames in DATA are ignored.
+# Optional arguments:
+# towhere - file to receive output. Is clipboard by default, which is convenient for pasting into a WinBUTS ODC file.
+# fill - If numeric, number of columns for output. If FALSE, output will be on one line. If TRUE (default), number of
+# columns is given by .Options$width.
+# Value:
+# Text defining a list is output to file "towhere".
+# Details:
+# The function performs considerable checking of DATA argument. Since WinBUGS requires numeric input, no factors or character vectors
+# are allowed. All data must be named, either as named elements of DATA (if it is a list) or else using the names given in data frames.
+# Data frames may contain matrices.
+# Arrays of any dimension are rearranged to be in row-major order, as required by WinBUGS. Scientific notation is also handled properly.
+# In particular, the number will consist of a mantissa _containing a decimal point_ followed by "E", then either "+" or "-", and finally
+# a _two-digit_ number. S-Plus does not always provide a decimal point in the mantissa, uses "e" instead of "E", followed by
+# either a "+" or "-" and then _three_ digits.
+# Written by Terry Elrod. Disclaimer: This function is used at the user's own risk.
+# Please send comments to Ter...@UA....
+# Revision history: 2002-11-19. Fixed to handle missing values properly.
+function(DATA, towhere = "clipboard", fill = TRUE)
+{
+ formatDataS4 =
+ #
+ # Prepared DATA for input to WinBUGS.
+ function(DATA)
+ {
+ toSingleS4 =
+ #
+ # Takes numeric vector and removes digit of exponent in scientific notation (if any)
+ function(x)
+ {
+ xdim <- dim(x)
+ x <- as.character(as.single(x))
+ # First to look for positives:
+ pplus <- regMatchPos(x, "e\\+0")
+ pplusind <- apply(pplus, 1, function(y)
+ (!any(is.na(y))))
+ if(any(pplusind)) {
+ # Making sure that periods are in mantissa...
+ init <- substring(x[pplusind], 1, pplus[
+ pplusind, 1] - 1)
+ #...preceeding exponent
+ pper <- regMatchPos(init, "\\.")
+ pperind <- apply(pper, 1, function(y)
+ (all(is.na(y))))
+ if(any(pperind))
+ init[pperind] <- paste(init[pperind],
+ ".0", sep = "")
+ # Changing the format of the exponent...
+ x[pplusind] <- paste(init, "E+", substring(
+ x[pplusind], pplus[pplusind, 2] + 1),
+ sep = "")
+ }
+ # Then to look for negatives:
+ pminus <- regMatchPos(x, "e\\-0")
+ pminusind <- apply(pminus, 1, function(y)
+ (!any(is.na(y))))
+ if(any(pminusind)) {
+ # Making sure that periods are in mantissa...
+ init <- substring(x[pminusind], 1, pminus[
+ pminusind, 1] - 1)
+ #...preceeding exponent
+ pper <- regMatchPos(init, "\\.")
+ pperind <- apply(pper, 1, function(y)
+ (all(is.na(y))))
+ if(any(pperind))
+ init[pperind] <- paste(init[pperind],
+ ".0", sep = "")
+ # Changing the format of the exponent...
+ x[pminusind] <- paste(init, "E-", substring(
+ x[pminusind], pminus[pminusind, 2] +
+ 1), sep = "")
+ }
+ x
+ }
+ if(!is.list(DATA))
+ stop("DATA must be a named list or data frame.")
+ dlnames <- names(DATA)
+ if(is.data.frame(DATA))
+ DATA <- as.list(DATA)
+ #
+ # Checking for lists in DATA....
+ lind <- sapply(DATA, is.list)
+ # Checking for data frames in DATA....
+ dfind <- sapply(DATA, is.data.frame)
+ # Any lists that are not data frames?...
+ if(any(lind & !dfind)) stop("DATA may not contain lists.")
+ # Checking for unnamed elements of list that are not data frames....
+ if(any(dlnames[!dfind] == "")) stop(
+ "When DATA is a list, all its elements that are not data frames must be named."
+ )
+ # Checking for duplicate names....
+ dupnames <- unique(dlnames[duplicated(dlnames)])
+ if(length(dupnames) > 0)
+ stop(paste(
+ "The following names are used more than once in DATA:",
+ paste(dupnames, collapse = ", ")))
+ if(any(dfind)) {
+ dataold <- DATA
+ DATA <- vector("list", 0)
+ for(i in seq(along = dataold)) {
+ if(dfind[i])
+ DATA <- c(DATA, as.list(dataold[[i]]))
+ else DATA <- c(DATA, dataold[i])
+ }
+ dataold <- NULL
+ }
+ dlnames <- names(DATA)
+ dupnames <- unique(dlnames[duplicated(dlnames)])
+ # Checking for duplicated names again (now that columns of data frames are included)....
+ if(length(dupnames) > 0) stop(paste(
+ "The following names are used more than once in DATA (at least once within a data frame):",
+ paste(dupnames, collapse = ", ")))
+ # Checking for factors....
+ factorind <- sapply(DATA, is.factor)
+ if(any(factorind))
+ stop(paste(
+ "DATA may not include factors. One or more factor variables were detected:",
+ paste(dlnames[factorind], collapse = ", ")))
+ # Checking for character vectors....
+ charind <- sapply(DATA, is.character)
+ if(any(charind))
+ stop(paste(
+ "WinBUGS does not handle character data. One or more character variables were detected:",
+ paste(dlnames[charind], collapse = ", ")))
+ # Checking for complex vectors....
+ complexind <- sapply(DATA, is.complex)
+ if(any(complexind))
+ stop(paste(
+ "WinBUGS does not handle complex data. One or more complex variables were detected:",
+ paste(dlnames[complexind], collapse = ", ")))
+ # Checking for values farther from zero than 1E+38 (which is limit of single precision)....
+ toobigind <- sapply(DATA, function(x)
+ {
+ y <- abs(x[!is.na(x)])
+ any(y[y > 0] > 9.9999999999999998e+37)
+ }
+ )
+ if(any(toobigind))
+ stop(paste(
+ "WinBUGS works in single precision. The following variables contain data outside the range +/-1.0E+38: ",
+ paste(dlnames[toobigind], collapse = ", "),
+ ".\n", sep = ""))
+ # Checking for values in range +/-1.0E-38 (which is limit of single precision)....
+ toosmallind <- sapply(DATA, function(x)
+ {
+ y <- abs(x[!is.na(x)])
+ any(y[y > 0] < 9.9999999999999996e-39)
+ }
+ )
+ n <- length(dlnames)
+ data.string <- as.list(rep(NA, n))
+ for(i in 1:n) {
+ if(length(DATA[[i]]) == 1) {
+ ac <- toSingleS4(DATA[[i]])
+ data.string[[i]] <- paste(names(DATA)[i], "=",
+ ac, sep = "")
+ next
+ }
+ if(is.vector(DATA[[i]]) & length(DATA[[i]]) > 1) {
+ ac <- toSingleS4(DATA[[i]])
+ data.string[[i]] <- paste(names(DATA)[i], "=c(",
+ paste(ac, collapse = ", "), ")", sep =
+ "")
+ next
+ }
+ if(is.array(DATA[[i]])) {
+ ac <- toSingleS4(aperm(DATA[[i]]))
+ data.string[[i]] <- paste(names(DATA)[i],
+ "= structure(.Data= c(", paste(ac,
+ collapse = ", "), "), \n .Dim=c(",
+ paste(as.character(dim(DATA[[i]])),
+ collapse = ", "), "))", sep = "")
+ }
+ }
+ data.tofile <- paste("list(", paste(unlist(data.string),
+ collapse = ", "), ")", sep = "")
+ if(any(toosmallind))
+ warning(paste(
+ "WinBUGS works in single precision. The following variables contained nonzero data",
+ "\ninside the range +/-1.0E-38 that were set to zero: ",
+ paste(dlnames[toosmallind], collapse = ", "),
+ ".\n", sep = ""))
+ return(data.tofile)
+ }
+ rslt <- formatDataS4(DATA)
+ cat(rslt, file = towhere, fill = fill)
+ invisible(0)
+}
+
+} # ends if (!is.R())
Modified: trunk/R2WinBUGS/R/bugs.inits.R
===================================================================
--- trunk/R2WinBUGS/R/bugs.inits.R 2006-12-29 16:10:15 UTC (rev 8)
+++ trunk/R2WinBUGS/R/bugs.inits.R 2007-04-07 18:04:11 UTC (rev 9)
@@ -1,13 +1,22 @@
-"bugs.inits" <-
+"bugs.inits" <-
function (inits, n.chains, digits){
- if(!is.null(inits)){
- for (i in 1:n.chains){
- if (is.function(inits))
- write.datafile(lapply(inits(), formatC, digits = digits, format = "E"),
- paste ("inits", i, ".txt", sep=""))
- else
- write.datafile(lapply(inits[[i]], formatC, digits = digits, format = "E"),
- paste ("inits", i, ".txt", sep=""))
- }
- }
+ if(!is.null(inits)) {
+ for(i in 1:n.chains) {
+ if(is.function(inits))
+ if(is.R()) {
+ write.datafile(lapply(inits(), formatC, digits = digits, format = "E"),
+ paste("inits", i, ".txt", sep = ""))
+ } else {
+ writeDatafileS4(inits(), towhere =
+ paste("inits", i, ".txt", sep = ""))
+ }
+ else if(is.R()) {
+ write.datafile(lapply(inits[[i]], formatC, digits = digits, format = "E"),
+ paste("inits", i, ".txt", sep = ""))
+ } else {
+ writeDatafileS4(inits[[i]], towhere = paste(
+ "inits", i, ".txt", sep = ""))
+ }
+ }
+ }
}
Modified: trunk/R2WinBUGS/R/bugs.plot.inferences.R
===================================================================
--- trunk/R2WinBUGS/R/bugs.plot.inferences.R 2006-12-29 16:10:15 UTC (rev 8)
+++ trunk/R2WinBUGS/R/bugs.plot.inferences.R 2007-04-07 18:04:11 UTC (rev 9)
@@ -28,8 +28,18 @@
long.short <- sims$long.short
height <- .6
par (mar=c(0,0,1,0))
+
+ ## if in Splus, suppress printing of warnings during the plotting.
+ ## otherwise a warning is generated
+ if (!is.R()){
+ warn.settings <- options("warn")[[1]]
+ options (warn = -1)
+ }
plot (c(0,1), c(-n.roots-.5,-.4),
ann=FALSE, bty="n", xaxt="n", yaxt="n", type="n")
+ if (!is.R())
+ options(warn = warn.settings)
+
W <- max(strwidth(rootnames, cex=cex.names))
B <- (1-W)/3.8
A <- 1-3.5*B
Modified: trunk/R2WinBUGS/R/bugs.plot.summary.R
===================================================================
--- trunk/R2WinBUGS/R/bugs.plot.summary.R 2006-12-29 16:10:15 UTC (rev 8)
+++ trunk/R2WinBUGS/R/bugs.plot.summary.R 2007-04-07 18:04:11 UTC (rev 9)
@@ -1,6 +1,7 @@
"bugs.plot.summary" <-
function (sims, ...){
DIC <- sims$is.DIC
+
if (.Device=="windows" ||
(.Device=="null device" && options("device")=="windows")){
cex.names <- .7
@@ -29,7 +30,11 @@
J[J==max(J)] <- max(J)-1
total <- ceiling(sum(J+.5))
}
- pos <- -1
+ if (is.R()){
+ pos <- -1
+ } else {
+ pos <- -1.5
+ }
ypos <- NULL
id <- NULL
ystart <- NULL
@@ -39,13 +44,25 @@
ystart <- numeric(n.roots)
for (k in 1:n.roots){
ystart[k] <- pos
- ypos <- c(ypos, pos - seq(0, J[k]-1))
+ if (is.R()) {
+ ypos <- c(ypos, pos - seq(0, J[k]-1))
+ } else {
+ # In S-PLUS, increase the vertical spacing
+ ypos <- c(ypos, pos - 1.5*seq(0, J[k]-1))
+ }
id <- c(id, 1:J[k])
- pos <- pos - J[k] -.5
+ if (is.R()) {
+ pos <- pos - J[k] -.5
+ } else {
+ pos <- pos - 1.5*J[k] -0.75
+ }
if (k>1) jj <- c(jj, sum(J0[1:(k-1)]) + (1:J[k]))
}
- bottom <- min(ypos)-1
-
+ if (is.R()){
+ bottom <- min(ypos)-1
+ } else {
+ bottom <- min(ypos)-1.5
+ }
med <- numeric(sum(J))
i80 <- matrix( , sum(J), 2)
i80.chains <- array (NA, c(sum(J), n.chains, 2))
@@ -61,8 +78,17 @@
a <- -b * p.rng[1]
par (mar=c(0,0,1,3))
+ # if in Splus, suppress printing of warnings during the plotting.
+ # otherwise a warning is generated
+ if (!is.R()){
+ warn.settings <- options("warn")[[1]]
+ options (warn = -1)
+ }
plot (c(0,1), c(min(bottom, -max.length)-3,2.5),
ann=FALSE, bty="n", xaxt="n", yaxt="n", type="n")
+ if (!is.R())
+ options(warn = warn.settings)
+
W <- max(strwidth(unlist(dimnames(summ)[[1]]), cex=cex.names))
B <- (1-W)/3.6
A <- 1-3.5*B
@@ -100,7 +126,16 @@
for (j in 1:sum(J)){
name <- dimnames(summ)[[1]][jj[j]]
if (id[j]==1)
- text (0, ypos[j], name, adj=0, cex=cex.names)
+ if (is.R()) {
+ text (0, ypos[j], name, adj=0, cex=cex.names)
+ } else {
+ # in S-PLUS, strwidth is an upper bound on the length of the string,
+ # so we must align the brackets differently than in R
+ pos <- as.vector(regexpr("[[]", name))
+ text (0, ypos[j], substring(name, 1, pos-1), adj=0, cex=cex.names)
+ text (strwidth(substring(name,1,pos-1),cex=cex.names),
+ ypos[j], substring(name, pos, nchar(name)), adj=0, cex=cex.names)
+ }
else {
pos <- as.vector(regexpr("[[]", name))
text (strwidth(substring(name,1,pos-1),cex=cex.names),
Modified: trunk/R2WinBUGS/R/bugs.run.R
===================================================================
--- trunk/R2WinBUGS/R/bugs.run.R 2006-12-29 16:10:15 UTC (rev 8)
+++ trunk/R2WinBUGS/R/bugs.run.R 2007-04-07 18:04:11 UTC (rev 9)
@@ -1,15 +1,24 @@
"bugs.run" <-
function(n.burnin, bugs.directory, WINE = "",
useWINE = .Platform$OS.type != "windows", newWINE = TRUE){
-
+
+if(useWINE && !is.R())
+ stop ("Non-Windows platforms not yet supported in R2WinBUGS for S-PLUS")
if(useWINE && !newWINE) bugs.directory <- win2native(bugs.directory)
## Update the lengths of the adaptive phases in the Bugs updaters
try(bugs.update.settings(n.burnin, bugs.directory))
## Return the lengths of the adaptive phases to their original settings
- on.exit(try(file.copy(file.path(bugs.directory, "System/Rsrc/Registry_Rsave.odc"),
- file.path(bugs.directory, "System/Rsrc/Registry.odc"),
- overwrite = TRUE)))
+ if (is.R()){
+ on.exit(try(file.copy(file.path(bugs.directory, "System/Rsrc/Registry_Rsave.odc"),
+ file.path(bugs.directory, "System/Rsrc/Registry.odc"),
+ overwrite = TRUE)))
+ } else {
+ on.exit(try(splus.file.copy(file.path(bugs.directory, "System/Rsrc/Registry_Rsave.odc"),
+ file.path(bugs.directory, "System/Rsrc/Registry.odc"),
+ overwrite = TRUE)))
+ }
+
## Search Win*.exe (WinBUGS executable) within bugs.directory
dos.location <- file.path(bugs.directory,
grep("^Win[[:alnum:]]*[.]exe$", list.files(bugs.directory), value = TRUE)[1])
@@ -26,9 +35,15 @@
if(temp == -1)
stop("Error in bugs.run().\nCheck that WinBUGS is in the specified directory.")
## Stop and print an error message if Bugs did not run correctly
- if (length(grep("Bugs did not run correctly",
- scan("coda1.txt", character(), quiet=TRUE, sep="\n"))) > 0)
- stop("Look at the log file and\ntry again with debug=TRUE and figure out what went wrong within Bugs.")
+ if(is.R()) {
+ if(length(grep("Bugs did not run correctly",
+ scan("coda1.txt", character(), quiet=TRUE, sep="\n"))) > 0)
+ stop("Look at the log file and\ntry again with debug=TRUE and figure out what went wrong within Bugs.")
+ } else {
+ if (length(grep("Bugs did not run correctly",
+ scan("coda1.txt", character(), sep="\n"))) > 0)
+ stop("Look at the log file and\ntry again with debug=TRUE and figure out what went wrong within Bugs.")
+ }
}
Modified: trunk/R2WinBUGS/R/bugs.sims.R
===================================================================
--- trunk/R2WinBUGS/R/bugs.sims.R 2006-12-29 16:10:15 UTC (rev 8)
+++ trunk/R2WinBUGS/R/bugs.sims.R 2007-04-07 18:04:11 UTC (rev 9)
@@ -1,10 +1,18 @@
"bugs.sims" <-
function (parameters.to.save, n.chains, n.iter, n.burnin, n.thin, DIC = TRUE){
-# Read the simulations from Bugs into R, format them, and monitor convergence
+## Read the simulations from Bugs into R, format them, and monitor convergence
sims.files <- paste ("coda", 1:n.chains, ".txt", sep="")
- index <- read.table ("codaIndex.txt", header=FALSE, sep="\t")
- parameter.names <- as.vector(index[,1])
- n.keep <- index[1,3] - index[1,2] + 1
+ index <- read.table("codaIndex.txt", header = FALSE, sep = "\t") # read in the names of the parameters and the indices of their samples
+ ## in Splus, read.table interprets the first row of the file as row names,
+ ## while in R it does not
+ if(is.R()) {
+ parameter.names <- as.vector(index[, 1])
+ n.keep <- index[1, 3] - index[1, 2] + 1
+ }
+ else {
+ parameter.names <- row.names(index)
+ n.keep <- index[1, 2] - index[1, 1] + 1
+ }
n.parameters <- length(parameter.names)
n.sims <- n.keep*n.chains
sims <- matrix( , n.sims, n.parameters)
@@ -50,7 +58,9 @@
rank.long <- unlist(long.short)
for (i in 1:n.chains){
- sims.i <- scan (sims.files[i], quiet=TRUE) [2*(1:(n.keep*n.parameters))]
+ if(is.R())
+ sims.i <- scan(sims.files[i], quiet = TRUE)[2 * (1:(n.keep * n.parameters))]
+ else sims.i <- scan(sims.files[i])[2 * (1:(n.keep * n.parameters))]
sims[(n.keep*(i-1)+1):(n.keep*i), ] <- sims.i
sims.array[,i,] <- sims.i
}
@@ -112,6 +122,8 @@
LOG <- bugs.log("log.txt")$DIC
if(any(is.na(LOG))){
deviance <- all$sims.array[, , dim(sims.array)[3], drop = FALSE]
+ if(!is.R())
+ dimnames(deviance) <- NULL
dim(deviance) <- dim(deviance)[1:2]
pD <- numeric(n.chains)
DIC <- numeric(n.chains)
@@ -128,3 +140,9 @@
}
return(all)
}
+
+if (!is.R()){
+ .subset <- function(x, index){
+ return (x[index])
+ }
+}
Modified: trunk/R2WinBUGS/R/bugs.update.settings.R
===================================================================
--- trunk/R2WinBUGS/R/bugs.update.settings.R 2006-12-29 16:10:15 UTC (rev 8)
+++ trunk/R2WinBUGS/R/bugs.update.settings.R 2007-04-07 18:04:11 UTC (rev 9)
@@ -1,20 +1,36 @@
"bugs.update.settings" <-
function (n.burnin, bugs.directory){
+ if (!is.R())
+ if (!require(rwBin)) stop ("The rwBin package is required")
+
char.burnin <- as.character(n.burnin - 1)
- file.copy(file.path(bugs.directory, "System/Rsrc/Registry.odc"),
+ if (is.R()){
+ file.copy(file.path(bugs.directory, "System/Rsrc/Registry.odc"),
file.path(bugs.directory, "System/Rsrc/Registry_Rsave.odc"),
- overwrite = TRUE)
+ overwrite = TRUE)
+ } else {
+ splus.file.copy(file.path(bugs.directory, "System/Rsrc/Registry.odc"),
+ file.path(bugs.directory, "System/Rsrc/Registry_Rsave.odc"),
+ overwrite = TRUE)
+ }
registry <- readBin(file.path(bugs.directory, "System/Rsrc/Registry.odc"),
"character", 400, size = 1, endian = "little")
locale <- Sys.getlocale("LC_CTYPE")
Sys.setlocale("LC_CTYPE", "C")
- info <- registry[regexpr("Int", registry, fixed = TRUE, useBytes = TRUE) > 0]
+ if (is.R())
+ info <- registry[regexpr("Int", registry, fixed = TRUE, useBytes = TRUE) > 0]
+ else
+ info <- registry[regexpr("Int", registry, fixed = TRUE) > 0]
while(regexpr("\r", info) > 0){
newline <- regexpr("\r", info)
info <- substring(info, newline + 1)
line <- substring(info, 1, regexpr("\r", info) - 1)
if(regexpr("AdaptivePhase", line) > 0){
- numpos <- regexpr("Int", line, fixed = TRUE, useBytes = TRUE) + 4
+ if (is.R())
+ numpos <- regexpr("Int", line, fixed = TRUE, useBytes = TRUE) + 4
+ else
+ numpos <- regexpr("Int", line, fixed = TRUE) + 4
+
num <- substring(line, numpos)
if (as.numeric(num) > n.burnin){
blanks <- rep(" ", nchar(num, type = "chars") - nchar(char.burnin, type = "chars"))
@@ -28,3 +44,21 @@
writeBin (registry,
file.path(bugs.directory, "System/Rsrc/Registry.odc"), endian = "little")
}
+
+if (!is.R()){
+
+"splus.file.copy"<-
+function(from, to, overwrite = FALSE)
+{
+ require(rwBin)
+ if(!file.exists(from))
+ stop("File: ", from, " does not exist")
+ if(!overwrite && file.exists(to))
+ stop("File: ", to, " already exists and overwrite is FALSE")
+ n <- file.info(from)$size
+ z <- writeBin(readBin(from, what = "integer", size = 1, n = n), to,
+ size = 1)
+ invisible(z)
+}
+
+} #ends if (!is.R())
Modified: trunk/R2WinBUGS/R/conv.par.R
===================================================================
--- trunk/R2WinBUGS/R/conv.par.R 2006-12-29 16:10:15 UTC (rev 8)
+++ trunk/R2WinBUGS/R/conv.par.R 2007-04-07 18:04:11 UTC (rev 9)
@@ -29,7 +29,7 @@
B <- n*var(xdot)
varW <- var(s2)/m
varB <- B^2 * 2/(m-1)
- covWB <- (n/m)*(cov(s2,xdot^2) - 2*muhat*cov(s2,xdot))
+ covWB <- (n/m)*(var(s2, xdot^2) - 2*muhat*var(s2, xdot))
sig2hat <- ((n-1)*W + B)/n
# Posterior interval post.range combines all uncertainties
Modified: trunk/R2WinBUGS/R/monitor.R
===================================================================
--- trunk/R2WinBUGS/R/monitor.R 2006-12-29 16:10:15 UTC (rev 8)
+++ trunk/R2WinBUGS/R/monitor.R 2007-04-07 18:04:11 UTC (rev 9)
@@ -30,6 +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)) }
+ }
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$n.eff)
Modified: trunk/R2WinBUGS/R/openbugs.R
===================================================================
--- trunk/R2WinBUGS/R/openbugs.R 2006-12-29 16:10:15 UTC (rev 8)
+++ trunk/R2WinBUGS/R/openbugs.R 2007-04-07 18:04:11 UTC (rev 9)
@@ -1,3 +1,5 @@
+if (is.R()){
+
openbugs <- function(data, inits, parameters.to.save, model.file="model.txt",
n.chains = 3, n.iter = 2000, n.burnin = floor(n.iter/2),
n.thin = max(1, floor(n.chains *(n.iter - n.burnin)/1000)),
@@ -83,3 +85,5 @@
a.stem <- substr(a, 1, ifelse(bracket.pos>0, bracket.pos-1, nchar(a)))
return(a[order(match(a.stem, b))])
}
+
+}
Modified: trunk/R2WinBUGS/R/plot.bugs.R
===================================================================
--- trunk/R2WinBUGS/R/plot.bugs.R 2006-12-29 16:10:15 UTC (rev 8)
+++ trunk/R2WinBUGS/R/plot.bugs.R 2007-04-07 18:04:11 UTC (rev 9)
@@ -1,7 +1,11 @@
plot.bugs <- function (x, display.parallel = FALSE, ...){
mar.old <- par("mar")
pty.old <- par(pty = "m")
- layout(matrix(c(1,2),1,2))
+ if (is.R())
+ layout(matrix(c(1,2),1,2))
+ else
+ par(mfrow = c(1,2))
+
bugs.plot.summary (x, ...)
bugs.plot.inferences (x, display.parallel, ...)
header <- ""
@@ -12,5 +16,42 @@
header <- paste(header, x$n.chains, " chains, each with ",
x$n.iter, " iterations (first ", x$n.burnin, " discarded)", sep = "")
mtext(header, outer = TRUE, line = -1, cex = 0.7)
- par(pty = pty.old[[1]], mar = mar.old)
+ if (is.R()) par(pty = pty.old[[1]], mar = mar.old)
+ else invisible(par(pty = pty.old[[1]], mar = mar.old))
}
+
+if (!is.R()) {
+
+strwidth <-function(s, units = c("user", "inches", "figure"), cex = NULL) {
+ s<-as.character(s)
+ if (!missing(cex)) {
+ oldcex <- par(cex=cex)
+ on.exit(par(oldcex))
+ }
+ units <- match.arg(units)
+ if (units == "user") {
+ nchar(s) * par("cxy")[1]
+ } else if (units == "inches") {
+ nchar(s) * par("cin")[1]
+ } else if (units == "figure") {
+ nchar(s) * par("cin")[1] / par("fin")[1]
+ }
+}
+
+strheight <- function(s, units = "user", cex = NULL) {
+ s<-as.character(s)
+ if (!missing(cex)) {
+ oldcex <- par(cex=cex)
+ on.exit(par(oldcex))
+ }
+ units <- match.arg(units)
+ if (units == "user") {
+ par("cxy")[2]
+ } else if (units == "inches") {
+ par("cin")[2]
+ } else if (units == "figure") {
+ par("cin")[2] / par("fin")[2]
+ }
+}
+
+} #ends if (!is.R())
Modified: trunk/R2WinBUGS/R/wineutils.R
===================================================================
--- trunk/R2WinBUGS/R/wineutils.R 2006-12-29 16:10:15 UTC (rev 8)
+++ trunk/R2WinBUGS/R/wineutils.R 2007-04-07 18:04:11 UTC (rev 9)
@@ -1,5 +1,7 @@
## from Jun Yan's rbugs package, extended
+if (is.R()){
+
## get drive mapping table from ~/.wine/config
winedriveMap <- function(config="~/.wine/config") {
if (!file.exists(config)) return (NULL);
@@ -48,10 +50,16 @@
else x
}
+} # end if (is.R())
+
native2win <- function(x, useWINE=.Platform$OS.type != "windows", newWINE=TRUE) { # native -> win
- if (useWINE && !newWINE) return(winedriveRTr(x))
- if (useWINE && newWINE) {
- x <- system(paste(WINEPATH, "-w", x), intern = TRUE)
- return(gsub("\\\\", "/", x)) ## under wine BUGS cannot use \ or \\
- } else x
+ if(is.R()){
+ if (useWINE && !newWINE) return(winedriveRTr(x))
+ if (useWINE && newWINE) {
+ x <- system(paste(WINEPATH, "-w", x), intern = TRUE)
+ return(gsub("\\\\", "/", x)) ## under wine BUGS cannot use \ or \\
+ } else x
+ } else { #S-PLUS
+ gsub("\\\\", "/", x)
+ }
}
Modified: trunk/R2WinBUGS/R/write.model.R
===================================================================
--- trunk/R2WinBUGS/R/write.model.R 2006-12-29 16:10:15 UTC (rev 8)
+++ trunk/R2WinBUGS/R/write.model.R 2007-04-07 18:04:11 UTC (rev 9)
@@ -1,7 +1,14 @@
write.model <- function(model, con = "model.bug")
{
- model.text <- attr(model, "source")
- model.text <- sub("^\\s*function\\s*\\(\\s*\\)", "model", model.text)
+ if (is.R()){
+ model.text <- attr(model, "source")
+ model.text <- sub("^\\s*function\\s*\\(\\s*\\)", "model", model.text)
+ } else {
+ ## In S-PLUS the source code of a function can be obtained with
+ ## as.character(function_name). This omits the "function_name <- function()" piece
+ model.text <- as.character(model)
+ model.text <- paste("model", model.text)
+ }
model.text <- gsub("%_%", "", model.text)
writeLines(model.text, con = con)
}
Modified: trunk/R2WinBUGS/man/bugs.Rd
===================================================================
--- trunk/R2WinBUGS/man/bugs.Rd 2006-12-29 16:10:15 UTC (rev 8)
+++ trunk/R2WinBUGS/man/bugs.Rd 2007-04-07 18:04:11 UTC (rev 9)
@@ -1,9 +1,9 @@
\name{bugs}
\alias{bugs}
-\title{Run WinBUGS and OpenBUGS from R}
+\title{Run WinBUGS and OpenBUGS from R or S-PLUS}
\description{The \code{bugs} function takes data and starting values as input.
It automatically writes a WinBUGS script, calls the model,
-and saves the simulations for easy access in R.}
+and saves the simulations for easy access in R or S-PLUS.}
\usage{
bugs(data, inits, parameters.to.save, model.file = "model.bug",
n.chains = 3, n.iter = 2000, n.burnin = floor(n.iter/2),
@@ -57,7 +57,8 @@
through function \code{\link{read.bugs}}. (not used if \code{program = "openbugs"})}
\item{bugs.directory}{directory that contains the WinBUGS executable}
\item{program}{the program to use, either \code{winbugs}/\code{WinBugs} or \code{openbugs}/\code{OpenBugs},
- the latter makes use of function \code{\link{openbugs}} and requires the CRAN package \pkg{BRugs}.}
+ the latter makes use of function \code{\link{openbugs}} and requires the CRAN package \pkg{BRugs}.
+ The \code{openbugs}/\code{OpenBugs} choice is not available in S-PLUS.}
\item{working.directory}{sets working directory during execution of this function;
WinBUGS' in- and output will be stored in this directory;
if \code{NULL}, the current working directory is chosen.}
@@ -69,7 +70,8 @@
\item{useWINE}{logical; attempt to use the WINE emulator to run WinBUGS,
defaults to \code{TRUE} on Windows, and \code{FALSE} otherwise.
If WINE is used, the arguments \code{bugs.directory} and \code{working.directory} must be given in form of Linux paths
- rather than Windows paths (if not \code{NULL}).}
+ rather than Windows paths (if not \code{NULL}).
+ The \code{useWINE = TRUE} option is not available in S-PLUS.}
\item{WINE}{character; name of WINE binary file}
\item{newWINE}{Set this one to \code{TRUE} for new versions of WINE.}
\item{WINEPATH}{Path the WINE, it is tried hard to get the information automatically if not given.}
@@ -78,12 +80,12 @@
To run:
\enumerate{
\item Write a WinBUGS model in a ASCII file.
-\item Go into R.
+\item Go into R / S-PLUS.
\item Prepare the inputs to the \code{bugs} function and run it (see Example).
-\item A WinBUGS window will pop up amd R will freeze up. The model
+\item A WinBUGS window will pop up and R / S-PLUS will freeze up. The model
will now run in WinBUGS. It might take awhile. You will see
things happening in the Log window within WinBUGS. When WinBugs
- is done, its window will close and R will work again.
+ is done, its window will close and R / S-PLUS will work again.
\item If an error message appears, re-run with \code{debug = TRUE}.
}}
\value{
Modified: trunk/R2WinBUGS/man/bugs.log.Rd
===================================================================
--- trunk/R2WinBUGS/man/bugs.log.Rd 2006-12-29 16:10:15 UTC (rev 8)
+++ trunk/R2WinBUGS/man/bugs.log.Rd 2007-04-07 18:04:11 UTC (rev 9)
@@ -17,7 +17,7 @@
}
\details{
In later releases of R2WiNBUGS, this function is considered to read the relevant data from the log file rather than
-analysing and calculating the relevant data in R again.
+analysing and calculating the relevant data in R / S-PLUS again.
}
\seealso{The main function that generates the log file is \code{\link{bugs}}.}
\keyword{IO}
Modified: trunk/R2WinBUGS/man/bugs.run.Rd
===================================================================
--- trunk/R2WinBUGS/man/bugs.run.Rd 2006-12-29 16:10:15 UTC (rev 8)
+++ trunk/R2WinBUGS/man/bugs.run.Rd 2007-04-07 18:04:11 UTC (rev 9)
@@ -13,7 +13,8 @@
\item{bugs.directory}{directory that contains the WinBUGS executable}
\item{WINE}{name of WINE binary, for Windows emulation}
\item{useWINE}{logical; attempt to use the WINE emulator to run WinBUGS,
- defaults to \code{TRUE} on Windows, and \code{FALSE} otherwise.}
+ defaults to \code{TRUE} on Windows, and \code{FALSE} otherwise.
+ The \code{useWINE = TRUE} option is not available in S-PLUS.}
\item{newWINE}{set this one to \code{TRUE} for new versions of WINE.}
}
\value{
Modified: trunk/R2WinBUGS/man/bugs.script.Rd
===================================================================
--- trunk/R2WinBUGS/man/bugs.script.Rd 2006-12-29 16:10:15 UTC (rev 8)
+++ trunk/R2WinBUGS/man/bugs.script.Rd 2007-04-07 18:04:11 UTC (rev 9)
@@ -20,7 +20,8 @@
or have to be generated by WinBUGS}
\item{bin}{number of iterations between saving of results}
\item{DIC}{logical; if \code{TRUE}, compute deviance, pD, and DIC automatically in WinBUGS}
- \item{useWINE}{logical; use WINE to run WinBUGS under Linux}
+ \item{useWINE}{logical; use WINE to run WinBUGS under Linux.
+ The \code{useWINE = TRUE} option is not available in S-PLUS.}
\item{newWINE}{set this one to \code{TRUE} for new versions of WINE.}
\item{WINEPATH}{Path the WINE, \code{bugs} tries hard to get the information automatically and
pass it to this function, if not given.}
Modified: trunk/R2WinBUGS/man/bugs.sims.Rd
===================================================================
--- trunk/R2WinBUGS/man/bugs.sims.Rd 2006-12-29 16:10:15 UTC (rev 8)
+++ trunk/R2WinBUGS/man/bugs.sims.Rd 2007-04-07 18:04:11 UTC (rev 9)
@@ -2,7 +2,7 @@
\alias{bugs.sims}
\title{WinBUGS output reader - intended for internal use only}
\description{
-Reads simulations from WinBUGS into R, formats them, monitors convergence,
+Reads simulations from WinBUGS into R/ S-PLUS, formats them, monitors convergence,
performs convergence checks, and computes medians and quantiles. Intended for internal use only.}
\usage{
bugs.sims(parameters.to.save, n.chains, n.iter, n.burnin, n.thin,
Modified: trunk/R2WinBUGS/man/openbugs.Rd
===================================================================
--- trunk/R2WinBUGS/man/openbugs.Rd 2006-12-29 16:10:15 UTC (rev 8)
+++ trunk/R2WinBUGS/man/openbugs.Rd 2007-04-07 18:04:11 UTC (rev 9)
@@ -2,7 +2,8 @@
\alias{openbugs}
\title{Wrapper to run OpenBUGS}
\description{The \code{openbugs} function takes data and starting values as input.
-It automatically calls the package \pkg{BRugs} and runs something similar to \code{\link[BRugs]{BRugsFit}}.}
+It automatically calls the package \pkg{BRugs} and runs something similar to \code{\link[BRugs]{BRugsFit}}.
+Not available in S-PLUS.}
\usage{
openbugs(data, inits, parameters.to.save,
model.file = "model.txt", n.chains = 3, n.iter = 2000,
Modified: trunk/R2WinBUGS/man/write.model.Rd
===================================================================
--- trunk/R2WinBUGS/man/write.model.Rd 2006-12-29 16:10:15 UTC (rev 8)
+++ trunk/R2WinBUGS/man/write.model.Rd 2007-04-07 18:04:11 UTC (rev 9)
@@ -1,12 +1,12 @@
\name{write.model}
\alias{write.model}
\title{Creating a WinBUGS model file}
-\description{Convert R function to a WinBUGS model file}
+\description{Convert R / S-PLUS function to a WinBUGS model file}
\usage{
write.model(model, con = "model.bug")
}
\arguments{
- \item{model}{R function containg the BUGS model in the BUGS model language, for minor differences see Section Details.}
+ \item{model}{R / S-PLUS function containing the BUGS model in the BUGS model language, for minor differences see Section Details.}
\item{con}{passed to \code{link{writeLines}} which actually writes the model file}
}
\value{
@@ -18,7 +18,7 @@
As a difference, BUGS syntax allows truncation specification like this:
\code{dnorm(...) I(...)}
-but this is illegal in R. To overcome this incompatibility, use \code{\%_\%} before \code{I(...)}:
+but this is illegal in R / S-PLUS. To overcome this incompatibility, use \code{\%_\%} before \code{I(...)}:
\code{dnorm(...) \%_\% I(...)}.
The dummy operator \code{\%_\%} will be removed before the BUGS code is saved.
}
@@ -36,8 +36,14 @@
sigma.theta ~ dunif (0, 1000)
}
-## some temporary filename:
-filename <- file.path(tempdir(), "schoolsmodel.bug")
+if (is.R()){ # for R
+ ## some temporary filename:
+ filename <- file.path(tempdir(), "schoolsmodel.bug")
+} else{ # for S-PLUS
+ ## put the file in the working directory:
+ filename <- "schoolsmodel.bug"
+}
+
## write model file:
write.model(schoolsmodel, filename)
## and let's take a look:
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <st...@us...> - 2006-12-29 16:11:05
|
Revision: 8
http://svn.sourceforge.net/bugs-r/?rev=8&view=rev
Author: sturtz
Date: 2006-12-29 08:10:15 -0800 (Fri, 29 Dec 2006)
Log Message:
-----------
bugfix if thinning != 1
Modified Paths:
--------------
trunk/BRugs/R/bgr.grid.R
Modified: trunk/BRugs/R/bgr.grid.R
===================================================================
--- trunk/BRugs/R/bgr.grid.R 2006-11-30 22:26:24 UTC (rev 7)
+++ trunk/BRugs/R/bgr.grid.R 2006-12-29 16:10:15 UTC (rev 8)
@@ -11,7 +11,7 @@
end <- min(c(samplesGetEnd(), modelIteration()))
numChains <- samplesGetLastChain() - samplesGetFirstChain() + 1
sampleSize <- sampleSize %/% numChains
- beg <- end - (sampleSize - 1)
+ beg <- end - (sampleSize * samplesGetThin() - 1)
delta <- sampleSize %/% bins
grid <- ((1 : (bins - 1)) * delta) + beg
grid <- c(grid, end)
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: Gregor G. <gre...@bf...> - 2006-12-21 18:04:40
|
Welcome! Uwe Ligges wrote: > Hi, > > I have added Sibylle Sturtz, maintainer of R2WinBUGS, to the list of > developers of bugs-r-devel. > Sibylle, welcome as maintainer of the package you are maintaining! ;-) Gregor |
|
From: Uwe L. <li...@st...> - 2006-12-21 17:57:02
|
Hi, I have added Sibylle Sturtz, maintainer of R2WinBUGS, to the list of developers of bugs-r-devel. Sibylle, welcome as maintainer of the package you are maintaining! ;-) Best, Uwe |
|
From: Kenneth B. <kb...@tc...> - 2006-12-13 15:35:48
|
I think Rodney is right, the problem is that we (especially I) are clueless as to how Mac OS handles the application bundles. Mac OS/X is certainly capable of command-line executables as any unix is, and this is how (most) all of the fink packages ported from linux/unix work. But Crossover is a "proper" application and hence works in the mac.app way. I will e-mail Crossover and see if they can suggest anything. ken Rodney Sparapani wrote: > Kenneth Benoit wrote: >> OK - the plot thickens... >> >> open Applications/CrossOver/WinBUGS14.app /par script.txt >> >> does *not* work because Apple did not program its magical "open" >> command (which is designed to be the command-line equivalent of >> double-clicking an icon) to allow command-line arguments following the >> name of the program. >> >> There is an open-x11 equivalent for opening X11 apps, and the lack of >> a command line seems to have made this almost unusable for many >> people. I found therefore that someone had written a version which >> allowed arguments: >> >> http://xanana.ucsc.edu/Library/init/zsh/man/html/open-x11.html >> >> but I could not find any equivalent for the plain "open". >> >> A workaround would be to hard-wire the excecution of script.txt into >> WinBUGS14.app itself, either through Mac OS/X or something in WinBUGS... >> >> Ken > Hi Gang: > > I don't see an obvious solution. First of all, if you want to run a script > in OpenBUGS, then the command is: > open bugs.exe > > What happens here is, LaunchServices looks at the file and determines which > application is necessary to run it; in this case DarWINE. > > But, you still run into the problem that no command line arguments are > allowed. Also, open-x11 doesn't actually do anything. open-x11 > is a part of OS X and this ZSH variant just works around some bugs. But, > basically, X11 applications are already built with a command line interface > to begin with, so there isn't any magic super-glue necessary. The main guts > of the function are towards the end: > "$@" & > > The problem that we are seeing is a little bit different. Mac applications > were never launched from the command-line because the Mac never had a > command > line. So, all open does is launch the application. But, some applications, > R for example, can be launched from the command-line with arguments. I took > a quick look at the R script that manages this, but I couldn't figure > out how > it does it. I'm guessing that when it was ported from Linux it had all the > necessary command-line stuff so the transition was easy. > > Perhaps this is a question for the DarWINE or R-SIG-Mac lists as we are all > clueless. > > Rodney > > ------------------------------------------------------------------------- > Take Surveys. Earn Cash. Influence the Future of IT > Join SourceForge.net's Techsay panel and you'll get the chance to share your > opinions on IT & business topics through brief surveys - and earn cash > http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV > _______________________________________________ > Bugs-r-devel mailing list > Bug...@li... > https://lists.sourceforge.net/lists/listinfo/bugs-r-devel > |
|
From: Rodney S. <rsp...@mc...> - 2006-12-13 15:12:07
|
Kenneth Benoit wrote: > OK - the plot thickens... > > open Applications/CrossOver/WinBUGS14.app /par script.txt > > does *not* work because Apple did not program its magical "open" > command (which is designed to be the command-line equivalent of > double-clicking an icon) to allow command-line arguments following the > name of the program. > > There is an open-x11 equivalent for opening X11 apps, and the lack of > a command line seems to have made this almost unusable for many > people. I found therefore that someone had written a version which > allowed arguments: > > http://xanana.ucsc.edu/Library/init/zsh/man/html/open-x11.html > > but I could not find any equivalent for the plain "open". > > A workaround would be to hard-wire the excecution of script.txt into > WinBUGS14.app itself, either through Mac OS/X or something in WinBUGS... > > Ken Hi Gang: I don't see an obvious solution. First of all, if you want to run a script in OpenBUGS, then the command is: open bugs.exe What happens here is, LaunchServices looks at the file and determines which application is necessary to run it; in this case DarWINE. But, you still run into the problem that no command line arguments are allowed. Also, open-x11 doesn't actually do anything. open-x11 is a part of OS X and this ZSH variant just works around some bugs. But, basically, X11 applications are already built with a command line interface to begin with, so there isn't any magic super-glue necessary. The main guts of the function are towards the end: "$@" & The problem that we are seeing is a little bit different. Mac applications were never launched from the command-line because the Mac never had a command line. So, all open does is launch the application. But, some applications, R for example, can be launched from the command-line with arguments. I took a quick look at the R script that manages this, but I couldn't figure out how it does it. I'm guessing that when it was ported from Linux it had all the necessary command-line stuff so the transition was easy. Perhaps this is a question for the DarWINE or R-SIG-Mac lists as we are all clueless. Rodney |
|
From: Gregor G. <gre...@bf...> - 2006-12-13 11:56:23
|
Hi, Kenneth Benoit wrote: > OK - the plot thickens... > > open Applications/CrossOver/WinBUGS14.app /par script.txt > > does *not* work because Apple did not program its magical "open" command > (which is designed to be the command-line equivalent of double-clicking > an icon) to allow command-line arguments following the name of the program. > > There is an open-x11 equivalent for opening X11 apps, and the lack of a > command line seems to have made this almost unusable for many people. I > found therefore that someone had written a version which allowed > arguments: > > http://xanana.ucsc.edu/Library/init/zsh/man/html/open-x11.html > > but I could not find any equivalent for the plain "open". > > A workaround would be to hard-wire the excecution of script.txt into > WinBUGS14.app itself, either through Mac OS/X or something in WinBUGS... According to WinBUGS14 documentation BackBUGS does this, but I think it assumes that script is in the same place as BackBUGS or WinBUGS binary is located. This can be a bit strict as one might not have write acces in that map. I did not find any equivalent in OpenBUGS. Anyone with skills to write Mac OS X specific script? Any comments on my previous questions about figuring out why DarWINE and CrossOver start automagically? Gregor |
|
From: Kenneth B. <kb...@tc...> - 2006-12-13 11:09:57
|
OK - the plot thickens... open Applications/CrossOver/WinBUGS14.app /par script.txt does *not* work because Apple did not program its magical "open" command (which is designed to be the command-line equivalent of double-clicking an icon) to allow command-line arguments following the name of the program. There is an open-x11 equivalent for opening X11 apps, and the lack of a command line seems to have made this almost unusable for many people. I found therefore that someone had written a version which allowed arguments: http://xanana.ucsc.edu/Library/init/zsh/man/html/open-x11.html but I could not find any equivalent for the plain "open". A workaround would be to hard-wire the excecution of script.txt into WinBUGS14.app itself, either through Mac OS/X or something in WinBUGS... Ken Gorjanc Gregor wrote: > Rodney talked about wine - DarWINE, you talk about CrossOver. So, Mac > "just knows" which emulator needs to be started. Sounds a bit magical. How > is this done? We need to know, if we want to enable this in R2WinBUGS. > Additionally, what happens, if there are both DarWINE and CrossOver installed. > > Kenneth & Rodney, can you also try to start {Win,Open}BUGS with script option > i.e. > > open Applications/CrossOver/WinBUGS14.app /par script.txt > > Thanks, Gregor > > -----Original Message----- > From: Kenneth Benoit [mailto:kb...@tc...] > Sent: Wed 2006-12-13 07:09 > To: Rodney Sparapani > Cc: Rodney Sparapani; Gorjanc Gregor; Ben Bolker; bug...@li... > Subject: Re: [R] R2WinBUGS and calling WinBUGS in Crossover MAC BETA > > Thanks Rodney, that so simple "mac" solution worked: > > open Applications/CrossOver/WinBUGS14.app > > starts Crossover and opens WinBUGS. So if I can pass that argument to > R2WinBUGS then it seems like it should work! > > Ken > > > Rodney Sparapani wrote: >> Ahha... >> Finally, something that I can answer. If I'm at the terminal command >> prompt, and type: >> open /Applications/OpenBUGS\ 2.2.0/winbugs.exe >> then, first DarWINE starts, then XDarwin or whatever it is called, and then >> OpenBUGS!!! >> >> The Fonz gives Richie motorcycle riding advice >> Fonzie: ... where a helmet and never smile! >> Richie: Why not? >> Fonzie: You get bugs in your teeth >> >> >> >> -----Original Message----- >> From: Kenneth Benoit [mailto:kb...@tc...] >> Sent: Tue 12/12/2006 4:42 PM >> To: Rodney Sparapani >> Cc: gre...@bf...; Ben Bolker; >> bug...@li... >> Subject: Re: [R] R2WinBUGS and calling WinBUGS in Crossover MAC BETA >> >> Hi - That, plus the difficulty I encountered in getting Darwine to work >> at all, led me to remove it and to install Crossover Mac Beta instead. >> It works just great with WinBUGS 1.4, running it quickly and completely >> *except* that first I have to start Crossover and then choose the >> installed WinBUGS from the programs menu to start it. (and then it pops >> right up and runs fine!) >> >> So the only question seems to be: how to get it started from the command >> line which R2WinBUGS can call?? >> >> Ken >> >> >> Rodney Sparapani wrote: >> > >> >> Rodney (can you please join to bugs-r development list) reported that he >> >> was able to start OpenBUGS under Intel Mac, but not WinBUGS. Maybe he >> >> can say more. >> > Hi Guys: >> > >> > Couldn't really follow the discussion. But, WinBUGS does not work with >> > DarWINE, although, OpenBUGS does. I'm using v. 0.9.21 DP, but this >> hasn't >> > changed going back to about v. 0.9.10 DP. And, before >> > that OpenBUGS doesn't work either. >> > I've spent a lot of time trying to >> > figure it out, but it's madness. WINE and R are written, more or less, >> > from the Linux standpoint. Compiling R even on industry-standard >> > Solaris can be tricky and WINE on Solaris is virtually impossible. >> > Mac OS X adds its own wrinkles. Many of the infrastucture that R >> requires >> > are already there, but often R chooses to install a slightly different >> > compiler and/or library and you are pulling out your hair trying to >> > figure out >> > what you are supposed to do and why. Of course, a professional Mac >> > developer would figure this out in a couple of minutes, but we >> > statisticians >> > must suffer for our art :) >> > >> > And to add insult to injury, I tried to subscribe to the mailing list >> > on sourceforge, but I couldn't figure it out. There is this obnoxious >> > adware that sourceforge employs that covers the search dialog. No >> > matter what I did in Firefox 2.0, I couldn't get past it. >> > >> > Rodney > |
|
From: Gorjanc G. <Gre...@bf...> - 2006-12-13 07:33:58
|
Rodney talked about wine - DarWINE, you talk about CrossOver. So, Mac
"just knows" which emulator needs to be started. Sounds a bit magical. =
How
is this done? We need to know, if we want to enable this in R2WinBUGS.=20
Additionally, what happens, if there are both DarWINE and CrossOver =
installed.
Kenneth & Rodney, can you also try to start {Win,Open}BUGS with script =
option=20
i.e.
open Applications/CrossOver/WinBUGS14.app /par script.txt
Thanks, Gregor
-----Original Message-----
From: Kenneth Benoit [mailto:kb...@tc...]
Sent: Wed 2006-12-13 07:09
To: Rodney Sparapani
Cc: Rodney Sparapani; Gorjanc Gregor; Ben Bolker; =
bug...@li...
Subject: Re: [R] R2WinBUGS and calling WinBUGS in Crossover MAC BETA
=20
Thanks Rodney, that so simple "mac" solution worked:
open Applications/CrossOver/WinBUGS14.app
starts Crossover and opens WinBUGS. So if I can pass that argument to=20
R2WinBUGS then it seems like it should work!
Ken
Rodney Sparapani wrote:
> Ahha...=20
> Finally, something that I can answer. If I'm at the terminal command=20
> prompt, and type:
> open /Applications/OpenBUGS\ 2.2.0/winbugs.exe
> then, first DarWINE starts, then XDarwin or whatever it is called, and =
then
> OpenBUGS!!!
>=20
> The Fonz gives Richie motorcycle riding advice
> Fonzie: ... where a helmet and never smile!
> Richie: Why not?
> Fonzie: You get bugs in your teeth
>=20
>=20
>=20
> -----Original Message-----
> From: Kenneth Benoit [mailto:kb...@tc...]
> Sent: Tue 12/12/2006 4:42 PM
> To: Rodney Sparapani
> Cc: gre...@bf...; Ben Bolker;=20
> bug...@li...
> Subject: Re: [R] R2WinBUGS and calling WinBUGS in Crossover MAC BETA
>=20
> Hi - That, plus the difficulty I encountered in getting Darwine to =
work
> at all, led me to remove it and to install Crossover Mac Beta instead.
> It works just great with WinBUGS 1.4, running it quickly and =
completely
> *except* that first I have to start Crossover and then choose the
> installed WinBUGS from the programs menu to start it. (and then it =
pops
> right up and runs fine!)
>=20
> So the only question seems to be: how to get it started from the =
command
> line which R2WinBUGS can call??
>=20
> Ken
>=20
>=20
> Rodney Sparapani wrote:
> >
> >> Rodney (can you please join to bugs-r development list) reported =
that he
> >> was able to start OpenBUGS under Intel Mac, but not WinBUGS. Maybe =
he
> >> can say more.
> > Hi Guys:
> >
> > Couldn't really follow the discussion. But, WinBUGS does not work =
with
> > DarWINE, although, OpenBUGS does. I'm using v. 0.9.21 DP, but this =
> hasn't
> > changed going back to about v. 0.9.10 DP. And, before
> > that OpenBUGS doesn't work either.
> > I've spent a lot of time trying to
> > figure it out, but it's madness. WINE and R are written, more or =
less,
> > from the Linux standpoint. Compiling R even on industry-standard
> > Solaris can be tricky and WINE on Solaris is virtually impossible.
> > Mac OS X adds its own wrinkles. Many of the infrastucture that R=20
> requires
> > are already there, but often R chooses to install a slightly =
different
> > compiler and/or library and you are pulling out your hair trying to
> > figure out
> > what you are supposed to do and why. Of course, a professional Mac
> > developer would figure this out in a couple of minutes, but we
> > statisticians
> > must suffer for our art :)
> >
> > And to add insult to injury, I tried to subscribe to the mailing =
list
> > on sourceforge, but I couldn't figure it out. There is this =
obnoxious
> > adware that sourceforge employs that covers the search dialog. No
> > matter what I did in Firefox 2.0, I couldn't get past it.
> >
> > Rodney
>=20
>=20
|
|
From: Kenneth B. <kb...@tc...> - 2006-12-13 06:09:44
|
Thanks Rodney, that so simple "mac" solution worked: open Applications/CrossOver/WinBUGS14.app starts Crossover and opens WinBUGS. So if I can pass that argument to R2WinBUGS then it seems like it should work! Ken Rodney Sparapani wrote: > Ahha... > Finally, something that I can answer. If I'm at the terminal command > prompt, and type: > open /Applications/OpenBUGS\ 2.2.0/winbugs.exe > then, first DarWINE starts, then XDarwin or whatever it is called, and then > OpenBUGS!!! > > The Fonz gives Richie motorcycle riding advice > Fonzie: ... where a helmet and never smile! > Richie: Why not? > Fonzie: You get bugs in your teeth > > > > -----Original Message----- > From: Kenneth Benoit [mailto:kb...@tc...] > Sent: Tue 12/12/2006 4:42 PM > To: Rodney Sparapani > Cc: gre...@bf...; Ben Bolker; > bug...@li... > Subject: Re: [R] R2WinBUGS and calling WinBUGS in Crossover MAC BETA > > Hi - That, plus the difficulty I encountered in getting Darwine to work > at all, led me to remove it and to install Crossover Mac Beta instead. > It works just great with WinBUGS 1.4, running it quickly and completely > *except* that first I have to start Crossover and then choose the > installed WinBUGS from the programs menu to start it. (and then it pops > right up and runs fine!) > > So the only question seems to be: how to get it started from the command > line which R2WinBUGS can call?? > > Ken > > > Rodney Sparapani wrote: > > > >> Rodney (can you please join to bugs-r development list) reported that he > >> was able to start OpenBUGS under Intel Mac, but not WinBUGS. Maybe he > >> can say more. > > Hi Guys: > > > > Couldn't really follow the discussion. But, WinBUGS does not work with > > DarWINE, although, OpenBUGS does. I'm using v. 0.9.21 DP, but this > hasn't > > changed going back to about v. 0.9.10 DP. And, before > > that OpenBUGS doesn't work either. > > I've spent a lot of time trying to > > figure it out, but it's madness. WINE and R are written, more or less, > > from the Linux standpoint. Compiling R even on industry-standard > > Solaris can be tricky and WINE on Solaris is virtually impossible. > > Mac OS X adds its own wrinkles. Many of the infrastucture that R > requires > > are already there, but often R chooses to install a slightly different > > compiler and/or library and you are pulling out your hair trying to > > figure out > > what you are supposed to do and why. Of course, a professional Mac > > developer would figure this out in a couple of minutes, but we > > statisticians > > must suffer for our art :) > > > > And to add insult to injury, I tried to subscribe to the mailing list > > on sourceforge, but I couldn't figure it out. There is this obnoxious > > adware that sourceforge employs that covers the search dialog. No > > matter what I did in Firefox 2.0, I couldn't get past it. > > > > Rodney > > |
|
From: Gregor G. <gre...@bf...> - 2006-12-13 05:59:33
|
Ben Bolker wrote: > Gregor Gorjanc wrote: ... >> Aha. I get it. I have been using unix type of path to WinBUGS directory >> for bugs.directory and not windows one e.g. >> >> /usr/local/wine/drive_c/Programs/BUGS/WinBUGS14/ >> >> So there is only a need to translate it to win type. I am not sure which >> type to prefer i.e. should we stick only with windows type, support only >> system specific or ... I think that we have a lot of place for changes >> as it seems that there are not (yet) much users under unix type that >> will yell at us because of changes ;) I agree that it can be confusing. >> I would like to reach some consensus here, implement it and write an >> article in RNews about running BUGS under many platforms. Any suggestions? > > Well, my argument for doing it the way I did it is that the > location of WinBUGS on Windows is a lot more stereotyped > (C:/Program Files/WinBUGS14) than it is on Linux: my I fully agree here. > WinBUGS directory, for example, is > /home/ben/.wine/dosdevices/c:/Program Files/WinBUGS14. And there are plenty of other options. > I think the easiest way to make R2WinBUGS work out of the > box for a wide range of users is to use winepath wherever > possible ... Yup, that is the reason I want to abandon .wine/config, but I do not know which style of path should we follow for bugs.directory on Linux and say Mac OS X. Should we stick with windows style i.e. C:/Program Files/WinBUGS14 or ...? It will not be easy to write a general code that will handle all kinds of possibilities. Using native style and then convert to windows style with winepath was my first idea, but I might be wrong here. It is a bit weird as WinBUGS and possibly also OpenBUGS is under Windows "tree" in wine. ### --- Windows style on MS Windows --- ## no need for wine tweaks ### --- Unix style on Linux and Mac OS X? --- winepath --windows "/some/path/to/WinBUGS14" z:\some\path\to\WinBUGS14 Regards, Gregor |
|
From: Gregor G. <gre...@bf...> - 2006-12-13 05:57:01
|
Gregor Gorjanc wrote: > Rodney Sparapani wrote: >> Ahha... >> Finally, something that I can answer. If I'm at the terminal command prompt, and type: >> open /Applications/OpenBUGS\ 2.2.0/winbugs.exe >> then, first DarWINE starts, then XDarwin or whatever it is called, and then >> OpenBUGS!!! > > But, how does wine i.e. DarWINE knows that it has to start? And to add to the discussion I have with Ben about which style path to use for bugs.directory. If I understand in Mac OS X /Applications is similar place to Windows C:\Program Files Is this true? Gregor |
|
From: Gregor G. <gre...@bf...> - 2006-12-13 05:43:54
|
Rodney Sparapani wrote: > Ahha... > Finally, something that I can answer. If I'm at the terminal command prompt, and type: > open /Applications/OpenBUGS\ 2.2.0/winbugs.exe > then, first DarWINE starts, then XDarwin or whatever it is called, and then > OpenBUGS!!! But, how does wine i.e. DarWINE knows that it has to start? > -----Original Message----- > From: Kenneth Benoit [mailto:kb...@tc...] > Sent: Tue 12/12/2006 4:42 PM > To: Rodney Sparapani > Cc: gre...@bf...; Ben Bolker; bug...@li... > Subject: Re: [R] R2WinBUGS and calling WinBUGS in Crossover MAC BETA > > Hi - That, plus the difficulty I encountered in getting Darwine to work > at all, led me to remove it and to install Crossover Mac Beta instead. > It works just great with WinBUGS 1.4, running it quickly and completely > *except* that first I have to start Crossover and then choose the > installed WinBUGS from the programs menu to start it. (and then it pops > right up and runs fine!) > > So the only question seems to be: how to get it started from the command > line which R2WinBUGS can call?? > > Ken > > > Rodney Sparapani wrote: >>> Rodney (can you please join to bugs-r development list) reported that he >>> was able to start OpenBUGS under Intel Mac, but not WinBUGS. Maybe he >>> can say more. >> Hi Guys: >> >> Couldn't really follow the discussion. But, WinBUGS does not work with >> DarWINE, although, OpenBUGS does. I'm using v. 0.9.21 DP, but this hasn't >> changed going back to about v. 0.9.10 DP. And, before >> that OpenBUGS doesn't work either. >> I've spent a lot of time trying to >> figure it out, but it's madness. WINE and R are written, more or less, >> from the Linux standpoint. Compiling R even on industry-standard >> Solaris can be tricky and WINE on Solaris is virtually impossible. >> Mac OS X adds its own wrinkles. Many of the infrastucture that R requires >> are already there, but often R chooses to install a slightly different >> compiler and/or library and you are pulling out your hair trying to >> figure out >> what you are supposed to do and why. Of course, a professional Mac >> developer would figure this out in a couple of minutes, but we >> statisticians >> must suffer for our art :) >> >> And to add insult to injury, I tried to subscribe to the mailing list >> on sourceforge, but I couldn't figure it out. There is this obnoxious >> adware that sourceforge employs that covers the search dialog. No >> matter what I did in Firefox 2.0, I couldn't get past it. |
|
From: Rodney S. <rsp...@hp...> - 2006-12-13 03:37:36
|
Ahha... =20 Finally, something that I can answer. If I'm at the terminal command = prompt, and type:=20 open /Applications/OpenBUGS\ 2.2.0/winbugs.exe then, first DarWINE starts, then XDarwin or whatever it is called, and = then OpenBUGS!!! The Fonz gives Richie motorcycle riding advice Fonzie: ... where a helmet and never smile!=20 Richie: Why not? Fonzie: You get bugs in your teeth -----Original Message----- From: Kenneth Benoit [mailto:kb...@tc...] Sent: Tue 12/12/2006 4:42 PM To: Rodney Sparapani Cc: gre...@bf...; Ben Bolker; = bug...@li... Subject: Re: [R] R2WinBUGS and calling WinBUGS in Crossover MAC BETA =20 Hi - That, plus the difficulty I encountered in getting Darwine to work=20 at all, led me to remove it and to install Crossover Mac Beta instead.=20 It works just great with WinBUGS 1.4, running it quickly and completely=20 *except* that first I have to start Crossover and then choose the=20 installed WinBUGS from the programs menu to start it. (and then it pops = right up and runs fine!) So the only question seems to be: how to get it started from the command = line which R2WinBUGS can call?? Ken Rodney Sparapani wrote: >=20 >> Rodney (can you please join to bugs-r development list) reported that = he >> was able to start OpenBUGS under Intel Mac, but not WinBUGS. Maybe he >> can say more.=20 > Hi Guys: >=20 > Couldn't really follow the discussion. But, WinBUGS does not work = with > DarWINE, although, OpenBUGS does. I'm using v. 0.9.21 DP, but this = hasn't > changed going back to about v. 0.9.10 DP. And, before > that OpenBUGS doesn't work either. > I've spent a lot of time trying to > figure it out, but it's madness. WINE and R are written, more or = less, > from the Linux standpoint. Compiling R even on industry-standard > Solaris can be tricky and WINE on Solaris is virtually impossible. > Mac OS X adds its own wrinkles. Many of the infrastucture that R = requires > are already there, but often R chooses to install a slightly different > compiler and/or library and you are pulling out your hair trying to=20 > figure out > what you are supposed to do and why. Of course, a professional Mac > developer would figure this out in a couple of minutes, but we=20 > statisticians > must suffer for our art :) >=20 > And to add insult to injury, I tried to subscribe to the mailing list > on sourceforge, but I couldn't figure it out. There is this obnoxious > adware that sourceforge employs that covers the search dialog. No > matter what I did in Firefox 2.0, I couldn't get past it. >=20 > Rodney |
|
From: Kenneth B. <kb...@tc...> - 2006-12-12 22:42:25
|
Hi - That, plus the difficulty I encountered in getting Darwine to work at all, led me to remove it and to install Crossover Mac Beta instead. It works just great with WinBUGS 1.4, running it quickly and completely *except* that first I have to start Crossover and then choose the installed WinBUGS from the programs menu to start it. (and then it pops right up and runs fine!) So the only question seems to be: how to get it started from the command line which R2WinBUGS can call?? Ken Rodney Sparapani wrote: > >> Rodney (can you please join to bugs-r development list) reported that he >> was able to start OpenBUGS under Intel Mac, but not WinBUGS. Maybe he >> can say more. > Hi Guys: > > Couldn't really follow the discussion. But, WinBUGS does not work with > DarWINE, although, OpenBUGS does. I'm using v. 0.9.21 DP, but this hasn't > changed going back to about v. 0.9.10 DP. And, before > that OpenBUGS doesn't work either. > I've spent a lot of time trying to > figure it out, but it's madness. WINE and R are written, more or less, > from the Linux standpoint. Compiling R even on industry-standard > Solaris can be tricky and WINE on Solaris is virtually impossible. > Mac OS X adds its own wrinkles. Many of the infrastucture that R requires > are already there, but often R chooses to install a slightly different > compiler and/or library and you are pulling out your hair trying to > figure out > what you are supposed to do and why. Of course, a professional Mac > developer would figure this out in a couple of minutes, but we > statisticians > must suffer for our art :) > > And to add insult to injury, I tried to subscribe to the mailing list > on sourceforge, but I couldn't figure it out. There is this obnoxious > adware that sourceforge employs that covers the search dialog. No > matter what I did in Firefox 2.0, I couldn't get past it. > > Rodney |
|
From: Rodney S. <rsp...@mc...> - 2006-12-12 16:12:01
|
> Rodney (can you please join to bugs-r development list) reported that he > was able to start OpenBUGS under Intel Mac, but not WinBUGS. Maybe he > can say more. Hi Guys: Couldn't really follow the discussion. But, WinBUGS does not work with DarWINE, although, OpenBUGS does. I'm using v. 0.9.21 DP, but this hasn't changed going back to about v. 0.9.10 DP. And, before that OpenBUGS doesn't work either. I've spent a lot of time trying to figure it out, but it's madness. WINE and R are written, more or less, from the Linux standpoint. Compiling R even on industry-standard Solaris can be tricky and WINE on Solaris is virtually impossible. Mac OS X adds its own wrinkles. Many of the infrastucture that R requires are already there, but often R chooses to install a slightly different compiler and/or library and you are pulling out your hair trying to figure out what you are supposed to do and why. Of course, a professional Mac developer would figure this out in a couple of minutes, but we statisticians must suffer for our art :) And to add insult to injury, I tried to subscribe to the mailing list on sourceforge, but I couldn't figure it out. There is this obnoxious adware that sourceforge employs that covers the search dialog. No matter what I did in Firefox 2.0, I couldn't get past it. Rodney |
|
From: Gregor G. <gre...@bf...> - 2006-12-12 14:31:59
|
Hi, Ben Bolker wrote: > Gregor Gorjanc wrote: >> Hi Ben, >> >> I would like to discuss about changes you propose. I will start at the >> end with wineutils. First, it is hard for me to read this diffs, since >> they are not standard i.e. lines are mostly marked with ! and not with + /-. >> > > Well, that's just what I get when I run "diff -c" ... > (GNU diffutils 2.8.1) weird >> You propose change to win2native, which is OK, but why. This function is >> used only in bugs.run.R and is needed only for old wine tweak i.e. using >> .wine/config file. It is not needed if winepath is available. My plan is >> to abandon .wine/config since winepath is around quite a long time. >> Therefore I would prefer to keep this the way it is and to migrate to >> winepath part. > > I'm not sure -- it's been a while since I made these changes. > What puzzles me is the "if (useWINE && !newWINE)" test: if newWINE > is TRUE, then bugs.directory doesn't ever seem to get translated from > Windows-native to the Linux version ... Aha. I get it. I have been using unix type of path to WinBUGS directory for bugs.directory and not windows one e.g. /usr/local/wine/drive_c/Programs/BUGS/WinBUGS14/ So there is only a need to translate it to win type. I am not sure which type to prefer i.e. should we stick only with windows type, support only system specific or ... I think that we have a lot of place for changes as it seems that there are not (yet) much users under unix type that will yell at us because of changes ;) I agree that it can be confusing. I would like to reach some consensus here, implement it and write an article in RNews about running BUGS under many platforms. Any suggestions? > in bugs() it is "c:/Program Files/WinBUGS14/" by default > this gets passed straight to bugs.run > within bugs.run it gets passed to bugs.update.settings etc., > but it also gets used in various copying/searching contexts that > would almost certainly seem to break under Linux if the directory > hasn't been translated? > I must just be missing some of the logic here ... > Gregor |
|
From: Gregor G. <gre...@bf...> - 2006-12-12 12:12:34
|
Hi Ben,
I would like to discuss about changes you propose. I will start at the
end with wineutils. First, it is hard for me to read this diffs, since
they are not standard i.e. lines are mostly marked with ! and not with + /-.
You propose change to win2native, which is OK, but why. This function is
used only in bugs.run.R and is needed only for old wine tweak i.e. using
.wine/config file. It is not needed if winepath is available. My plan is
to abandon .wine/config since winepath is around quite a long time.
Therefore I would prefer to keep this the way it is and to migrate to
winepath part.
I agree about native2win i.e. addition of
WINEPATH=Sys.getenv("WINEPATH"). But would like to discuss this in next
email.
Ben Bolker wrote:
...
> *** wineutils.R 2006-10-08 14:07:50.000000000 -0400
> --- /home/ben/bugs-r/trunk/R2WinBUGS/R/wineutils.R 2006-12-10 16:21:31.000000000 -0500
> ***************
> *** 43,58 ****
> }
>
> ! win2native <- function(x, useWINE=.Platform$OS.type != "windows", newWINE=TRUE,
> ! WINEPATH=Sys.getenv("WINEPATH")) { # win -> native
> ! if (useWINE && !newWINE) winedriveTr(x)
> ! if (useWINE && newWINE) {
> ! system(paste(WINEPATH,' \"',x,'\"',sep=""), intern=TRUE)
> ! } else x
> }
>
> ! native2win <- function(x, useWINE=.Platform$OS.type != "windows", newWINE=TRUE,
> ! WINEPATH=Sys.getenv("WINEPATH")) { # native -> win
> if (useWINE && !newWINE) return(winedriveRTr(x))
> if (useWINE && newWINE) {
> x <- system(paste(WINEPATH, "-w", x), intern = TRUE)
> --- 43,54 ----
> }
>
> ! win2native <- function(x, useWINE=.Platform$OS.type != "windows") { # win -> native
> ! if (useWINE) winedriveTr(x)
> ! else x
> }
>
> ! native2win <- function(x, useWINE=.Platform$OS.type != "windows", newWINE=TRUE) { # native -> win
> if (useWINE && !newWINE) return(winedriveRTr(x))
> if (useWINE && newWINE) {
> x <- system(paste(WINEPATH, "-w", x), intern = TRUE)
|
