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From: Gregor G. <gre...@bf...> - 2007-09-17 08:52:00
|
Sparapani, Rodney wrote: > I replied again last night, but it never got to the list. I HATE OUTLOOK WEB ACCESS!!!! > Ok, 2.1-6 does work. Here's what I tested: > >> Sys.setenv(WINE="/Applications/Darwine/Wine.bundle/Contents/bin/wine") >> Sys.setenv(WINEPATH="/Applications/Darwine/Wine.bundle/Contents/bin/winepath") >> schools.sim <- bugs (data=data, > inits=inits, > parameters.to.save=parameters, > model.file="schools.txt", > n.chains=3, > n.iter=1000, > bugs.directory="/Applications/WinBUGS14", > debug=FALSE) > > However, fitbugs() does not work. Since bugs() no longer needs WINE/WINEPATH/etc., > that should not be the issue. It seems like fitbugs does not know about bugs.directory!?! > Here's what it looks like: As stated before, fitbugs() is not part of R2WinBUGS and you are right that fitbugs() does not obey bugs.directory. I do not know what should be fixed. Gregor |
|
From: Gregor G. <gre...@bf...> - 2007-09-17 08:29:34
|
Hi Rodney. Sorry for late response. Rodney Sparapani wrote: > Gorjanc Gregor wrote: >>> DarWINE 0.9.43 and 0.9.44 have some problems as well. >>> >> Any meaningful error message? >> > Not really. And, it's very surprising. OpenBUGS had a pretty > good track record with DarWINE. v. 2.2.0 started working > with DarWINE 0.9.12 and worked for every version that I tried after > that. WinBUGS was far more tempermental. v. 1.4.3 > is the first that I have ever been able to run with DarWINE. Can not help here. But it is good to have some feedback on which versions are happy with each other. >>> Now, how do I install the latest trunk to do the same test? >>> I've downloaded it, but there does not appear to be a .tgz file. >>> >> Just build it. I guess mac side should not be much different from >> >> R CMD build R2WinBUGS >> > Ah, didn't think of that. I'll give it a try. But, it would > probably be easier to just include the .tgz in the repository. Tarball is available from CRAN for published packages. If we would provide tarball in the repository for each commit, the the size of SVN databse would probably blow up. I think that R CMD build is not that hard to do. > In any case, I was looking around in R2WinBUGS and I noticed that > fitbugs is not included. Is there any reason for this? I'd like to see > a version of fitbugs that returns the object and also allows WINE to be > used. The version of fitbugs that I found doesn't appear to have either > of these. But, maybe there is a later version somewhere? Here's the > one I've been looking at http://www.stat.columbia.edu/~kerman/td/fitbugs.R > Of course, I'm willing to work on this. But, I didn't want to > re-invent the wheel. fitbugs() was written by Jouni Kerman and Uwe has implemented part of it as write.model(). Maybe he can comment on why only writing a model from an R function was implemented. > Lastly, one thing that I forgot to mention. When I ran the > BUGS-L example, a new WinBUGS window opens, performs the > analysis, creates some graphics, and then closes, before you > have a chance to actually look at the graphics. The posterior/summary > is returned, but I'm wondering why the window closes. Is this supposed > to happen? Or is this a problem only on Mac? |
|
From: Gorjanc G. <Gre...@bf...> - 2007-09-17 06:53:33
|
OK. I agree with you. Gregor ________________________________________ From: Uwe Ligges [li...@st...] Sent: Sunday, September 16, 2007 7:08 PM To: Gorjanc Gregor Cc: bug...@li... Subject: Re: [Bugs-r-devel] BRugs 0.4-1 with OpenBUGS 3.0.2 ready for relea= se Gorjanc Gregor wrote: > Hi, > > ... >> Note that >> - you need to include OpenBUGS 3.0.2. > > Does this mean that user will have to install OpenBUGS by himself or will > new version of OpenBUGS also be included in BRugs package? Will be included! This README file is only in the svn repository, but not in the tarball, as you can see from file .Rbuildignore I will put OpenBUGS into the tarball before the release. It does not make sense to check OpenBUGS' xxxxMB into the repository, because nobody touches OpenBUGS itself, I guess. Uwe > Gregor > > ------------------------------------------------------------------------- > This SF.net email is sponsored by: Microsoft > Defy all challenges. Microsoft(R) Visual Studio 2005. > http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ > _______________________________________________ > Bugs-r-devel mailing list > Bug...@li... > https://lists.sourceforge.net/lists/listinfo/bugs-r-devel |
|
From: <li...@us...> - 2007-09-16 17:33:14
|
Revision: 62
http://bugs-r.svn.sourceforge.net/bugs-r/?rev=62&view=rev
Author: ligges
Date: 2007-09-16 10:33:18 -0700 (Sun, 16 Sep 2007)
Log Message:
-----------
clean up
Modified Paths:
--------------
trunk/BRugs/R/zzz.R
Modified: trunk/BRugs/R/zzz.R
===================================================================
--- trunk/BRugs/R/zzz.R 2007-09-16 17:33:07 UTC (rev 61)
+++ trunk/BRugs/R/zzz.R 2007-09-16 17:33:18 UTC (rev 62)
@@ -1,8 +1,6 @@
if (is.R()){
".onLoad" <- function(lib, pkg){
- ## Don't know whether we have to do this before useDynLib()???
- #Sys.putenv("LD_ASSUME_KERNEL"="2.4.1")
## sets path / file variables and initializes subsystems
root <- file.path(system.file("OpenBUGS", package=pkg))
## we do have a NAMESPACE now: library.dynam("BRugs", pkg, lib)
@@ -12,8 +10,6 @@
.C("SetTempDir", as.character(tempDir), nchar(tempDir), PACKAGE="BRugs")
command <- "BugsMappers.SetDest(2)"
.C("CmdInterpreter", as.character(command), nchar(command), integer(1), PACKAGE="BRugs")
- #.C("Initialize", as.character(root), as.character(tempDir),
- # as.integer(len), nchar(tempDir), PACKAGE="BRugs")
if(is.null(getOption("BRugsVerbose")))
options("BRugsVerbose" = TRUE)
}
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|
|
From: <li...@us...> - 2007-09-16 17:33:05
|
Revision: 61
http://bugs-r.svn.sourceforge.net/bugs-r/?rev=61&view=rev
Author: ligges
Date: 2007-09-16 10:33:07 -0700 (Sun, 16 Sep 2007)
Log Message:
-----------
forgot to update...
Modified Paths:
--------------
trunk/BRugs/man/help.WinBUGS.Rd
Modified: trunk/BRugs/man/help.WinBUGS.Rd
===================================================================
--- trunk/BRugs/man/help.WinBUGS.Rd 2007-09-16 17:16:36 UTC (rev 60)
+++ trunk/BRugs/man/help.WinBUGS.Rd 2007-09-16 17:33:07 UTC (rev 61)
@@ -1,7 +1,7 @@
\name{help.WinBUGS}
\alias{help.WinBUGS}
\title{WinBUGS documentation}
-\description{Function that open the html version of the WinBUGS manual}
+\description{Function that open the html version of the OpenBUGS manual}
\usage{
help.WinBUGS(browser = getOption("browser"))
}
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|
|
From: <li...@us...> - 2007-09-16 17:16:41
|
Revision: 60
http://bugs-r.svn.sourceforge.net/bugs-r/?rev=60&view=rev
Author: ligges
Date: 2007-09-16 10:16:36 -0700 (Sun, 16 Sep 2007)
Log Message:
-----------
libtaucs.dll is no longer required (I got a not yet published BRugs.dll/so from Andrew)
Modified Paths:
--------------
trunk/BRugs/configure.win
Modified: trunk/BRugs/configure.win
===================================================================
--- trunk/BRugs/configure.win 2007-09-16 17:15:45 UTC (rev 59)
+++ trunk/BRugs/configure.win 2007-09-16 17:16:36 UTC (rev 60)
@@ -1,4 +1,4 @@
#!/bin/sh
mkdir $DPKG/libs
cp ./inst/OpenBUGS/brugs.dll $DPKG/libs/BRugs.dll
-cp ./inst/OpenBUGS/libtaucs.dll $DPKG/libs/libtaucs.dll
+
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|
|
From: <li...@us...> - 2007-09-16 17:15:46
|
Revision: 59
http://bugs-r.svn.sourceforge.net/bugs-r/?rev=59&view=rev
Author: ligges
Date: 2007-09-16 10:15:45 -0700 (Sun, 16 Sep 2007)
Log Message:
-----------
also include developer documentation and remove statement on distributing everything.
Modified Paths:
--------------
trunk/BRugs/inst/README-inst_OpenBUGS
Modified: trunk/BRugs/inst/README-inst_OpenBUGS
===================================================================
--- trunk/BRugs/inst/README-inst_OpenBUGS 2007-09-16 17:15:08 UTC (rev 58)
+++ trunk/BRugs/inst/README-inst_OpenBUGS 2007-09-16 17:15:45 UTC (rev 59)
@@ -7,9 +7,7 @@
OpenBUGS/Examples/*.bmp
OpenBUGS/Examples/*.html
OpenBUGS/Examples/*.txt
+OpenBUGS/Developer/*.bmp
+OpenBUGS/Developer/*.html
OpenBUGS/Manuals/*.bmp
OpenBUGS/Manuals/*.html
-
-
-Hmmm, but we maybe should ship all OpenBUGS,
-because we may need to ship sources according to GPL.
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|
|
From: <li...@us...> - 2007-09-16 17:15:14
|
Revision: 58
http://bugs-r.svn.sourceforge.net/bugs-r/?rev=58&view=rev
Author: ligges
Date: 2007-09-16 10:15:08 -0700 (Sun, 16 Sep 2007)
Log Message:
-----------
Name of the manual page has changed again ....
Modified Paths:
--------------
trunk/BRugs/R/unix/help.R
trunk/BRugs/R/windows/help.R
Modified: trunk/BRugs/R/unix/help.R
===================================================================
--- trunk/BRugs/R/unix/help.R 2007-09-14 14:14:03 UTC (rev 57)
+++ trunk/BRugs/R/unix/help.R 2007-09-16 17:15:08 UTC (rev 58)
@@ -24,6 +24,6 @@
"switch to its window."),
exdent = 4))
writeLines("Otherwise, be patient ...")
- browseURL(system.file("OpenBUGS", "docu", "WinBUGS Manual.html", package="BRugs"))
+ browseURL(system.file("OpenBUGS", "Manuals", "Contents.html", package="BRugs"))
invisible("")
}
Modified: trunk/BRugs/R/windows/help.R
===================================================================
--- trunk/BRugs/R/windows/help.R 2007-09-14 14:14:03 UTC (rev 57)
+++ trunk/BRugs/R/windows/help.R 2007-09-16 17:15:08 UTC (rev 58)
@@ -15,7 +15,7 @@
help.WinBUGS <- function(browser = getOption("browser"))
{
# stolen from help.start()
- a <- system.file("OpenBUGS", "Manuals", "WinBUGS Manual.html", package="BRugs")
+ a <- system.file("OpenBUGS", "Manuals", "Contents.html", package="BRugs")
if (!file.exists(a))
stop("I can't find the html help")
if (is.R())
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|
|
From: Uwe L. <li...@st...> - 2007-09-16 17:08:35
|
Gorjanc Gregor wrote: > Hi, > > ... >> Note that >> - you need to include OpenBUGS 3.0.2. > > Does this mean that user will have to install OpenBUGS by himself or will > new version of OpenBUGS also be included in BRugs package? Will be included! This README file is only in the svn repository, but not in the tarball, as you can see from file .Rbuildignore I will put OpenBUGS into the tarball before the release. It does not make sense to check OpenBUGS' xxxxMB into the repository, because nobody touches OpenBUGS itself, I guess. Uwe > Gregor > > ------------------------------------------------------------------------- > This SF.net email is sponsored by: Microsoft > Defy all challenges. Microsoft(R) Visual Studio 2005. > http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ > _______________________________________________ > Bugs-r-devel mailing list > Bug...@li... > https://lists.sourceforge.net/lists/listinfo/bugs-r-devel |
|
From: Gorjanc G. <Gre...@bf...> - 2007-09-16 16:15:14
|
Hi, ... > Note that > - you need to include OpenBUGS 3.0.2. Does this mean that user will have to install OpenBUGS by himself or will new version of OpenBUGS also be included in BRugs package? Gregor |
|
From: Gorjanc G. <Gre...@bf...> - 2007-09-16 08:51:17
|
As far as I know, URL is enough. Gregor ________________________________________ From: bug...@li... [bugs-r-devel-bounces@list= s.sourceforge.net] On Behalf Of Uwe Ligges [ligges@statistik.uni-dortmund.d= e] Sent: Friday, September 14, 2007 4:29 PM To: bug...@li...; Dawn Woodard Cc: Andrew Thomas Subject: [Bugs-r-devel] BRugs 0.4-1 with OpenBUGS 3.0.2 ready for release Hi, I think we have BRugs_0.4-1 with OpenBUGS 3.0.2 ready for release now, except that Andrew is going to remove libtaucs.* and make new dll / so files available. I'll wait until that happens and release shortly thereafter, given there are no objections. Note that - you need to include OpenBUGS 3.0.2. - I will omit the sources as stated in BRugs/inst/README-inst_OpenBUGS unless anybody shouts. Does anybody know if we are really violating GPL? The URL of OpenBUGS is given in the DESCRIPTION file, hence the pointer to the sources is there. Dawn, is this also fine for S-PLUS now? Best, Uwe ------------------------------------------------------------------------- This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2005. http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ _______________________________________________ Bugs-r-devel mailing list Bug...@li... https://lists.sourceforge.net/lists/listinfo/bugs-r-devel |
|
From: Dawn W. <dwo...@in...> - 2007-09-14 18:00:33
|
BRugs looks good on the S-PLUS side!
=20
Thank you!
Dawn
-----Original Message-----
From: Uwe Ligges [mailto:li...@st...]=20
Sent: Friday, September 14, 2007 10:29 AM
To: bug...@li...; Dawn Woodard
Cc: Sibylle Sturtz; Andrew Thomas; Anon.
Subject: BRugs 0.4-1 with OpenBUGS 3.0.2 ready for release
Hi,
I think we have BRugs_0.4-1 with OpenBUGS 3.0.2 ready for release now,=20
except that Andrew is going to remove libtaucs.* and make new dll / so=20
files available. I'll wait until that happens and release shortly=20
thereafter, given there are no objections.
Note that
- you need to include OpenBUGS 3.0.2.
- I will omit the sources as stated in
BRugs/inst/README-inst_OpenBUGS
unless anybody shouts. Does anybody know if we are really
violating GPL? The URL of OpenBUGS is given in the
DESCRIPTION file, hence the pointer to the sources is there.
Dawn, is this also fine for S-PLUS now?
Best,
Uwe
|
|
From: Uwe L. <li...@st...> - 2007-09-14 14:29:19
|
Hi,
I think we have BRugs_0.4-1 with OpenBUGS 3.0.2 ready for release now,
except that Andrew is going to remove libtaucs.* and make new dll / so
files available. I'll wait until that happens and release shortly
thereafter, given there are no objections.
Note that
- you need to include OpenBUGS 3.0.2.
- I will omit the sources as stated in
BRugs/inst/README-inst_OpenBUGS
unless anybody shouts. Does anybody know if we are really
violating GPL? The URL of OpenBUGS is given in the
DESCRIPTION file, hence the pointer to the sources is there.
Dawn, is this also fine for S-PLUS now?
Best,
Uwe
|
|
From: <li...@us...> - 2007-09-14 14:14:04
|
Revision: 57
http://bugs-r.svn.sourceforge.net/bugs-r/?rev=57&view=rev
Author: ligges
Date: 2007-09-14 07:14:03 -0700 (Fri, 14 Sep 2007)
Log Message:
-----------
Andrew renamed API:
SamplesEmbed.Sample -> SamplesEmbed.SampleValues
Modified Paths:
--------------
trunk/BRugs/R/bgr.point.R
trunk/BRugs/R/buildMCMC.R
trunk/BRugs/R/plot.autoC.R
trunk/BRugs/R/plot.density.R
trunk/BRugs/R/plot.history.R
trunk/BRugs/R/samples.sample.R
Modified: trunk/BRugs/R/bgr.point.R
===================================================================
--- trunk/BRugs/R/bgr.point.R 2007-09-14 12:32:46 UTC (rev 56)
+++ trunk/BRugs/R/bgr.point.R 2007-09-14 14:14:03 UTC (rev 57)
@@ -11,7 +11,7 @@
command <- "SamplesEmbed.SampleSize"
sampleSize <- as.integer(.C("Integer", command, nchar(command),
integer(1), integer(1), PACKAGE="BRugs")[[3]])
- command <- "SamplesEmbed.Sample"
+ command <- "SamplesEmbed.SampleValues"
if (is.R())
sample <- .C("RealArray", command, nchar(command), real(sampleSize),
as.integer(sampleSize), integer(1), PACKAGE="BRugs")[[3]]
Modified: trunk/BRugs/R/buildMCMC.R
===================================================================
--- trunk/BRugs/R/buildMCMC.R 2007-09-14 12:32:46 UTC (rev 56)
+++ trunk/BRugs/R/buildMCMC.R 2007-09-14 14:14:03 UTC (rev 57)
@@ -37,7 +37,7 @@
command <- "SamplesEmbed.SampleSize"
sampleSize <- as.integer(.C("Integer", command, nchar(command),
integer(1), integer(1), PACKAGE = "BRugs")[[3]])
- command <- "SamplesEmbed.Sample"
+ command <- "SamplesEmbed.SampleValues"
if (is.R())
sample <- .C("RealArray", command, nchar(command), real(sampleSize),
sampleSize, integer(1), PACKAGE = "BRugs")[[3]]
Modified: trunk/BRugs/R/plot.autoC.R
===================================================================
--- trunk/BRugs/R/plot.autoC.R 2007-09-14 12:32:46 UTC (rev 56)
+++ trunk/BRugs/R/plot.autoC.R 2007-09-14 14:14:03 UTC (rev 57)
@@ -16,7 +16,7 @@
else
sampleSize <- as.integer(.C("Integer", command, nchar(command),
integer(1), integer(1), PACKAGE="BRugs")[[3]])
- command <- "SamplesEmbed.Sample"
+ command <- "SamplesEmbed.SampleValues"
if (is.R())
sample <- .C("RealArray", command, nchar(command), real(sampleSize),
as.integer(sampleSize), integer(1), PACKAGE="BRugs")[[3]]
Modified: trunk/BRugs/R/plot.density.R
===================================================================
--- trunk/BRugs/R/plot.density.R 2007-09-14 12:32:46 UTC (rev 56)
+++ trunk/BRugs/R/plot.density.R 2007-09-14 14:14:03 UTC (rev 57)
@@ -11,7 +11,7 @@
command <- "SamplesEmbed.SampleSize"
sampleSize <- as.integer(.C("Integer", command, nchar(command),
integer(1), integer(1), PACKAGE="BRugs")[[3]])
- command <- "SamplesEmbed.Sample"
+ command <- "SamplesEmbed.SampleValues"
if (is.R())
sample <- .C("RealArray", command, nchar(command), real(sampleSize),
as.integer(sampleSize), integer(1), PACKAGE="BRugs")[[3]]
Modified: trunk/BRugs/R/plot.history.R
===================================================================
--- trunk/BRugs/R/plot.history.R 2007-09-14 12:32:46 UTC (rev 56)
+++ trunk/BRugs/R/plot.history.R 2007-09-14 14:14:03 UTC (rev 57)
@@ -17,7 +17,7 @@
sampleSize <- as.integer(.C("Integer", command, nchar(command),
integer(1), integer(1), PACKAGE="BRugs")[3][[1]])
}
- command <- "SamplesEmbed.Sample"
+ command <- "SamplesEmbed.SampleValues"
if (is.R())
sample <- .C("RealArray", command, nchar(command), real(sampleSize),
sampleSize, integer(1), PACKAGE="BRugs")[[3]]
Modified: trunk/BRugs/R/samples.sample.R
===================================================================
--- trunk/BRugs/R/samples.sample.R 2007-09-14 12:32:46 UTC (rev 56)
+++ trunk/BRugs/R/samples.sample.R 2007-09-14 14:14:03 UTC (rev 57)
@@ -9,7 +9,7 @@
command <- "SamplesEmbed.SampleSize"
sampleSize <- as.integer(.C("Integer", command, nchar(command),
integer(1), integer(1), PACKAGE="BRugs")[[3]])
- command <- "SamplesEmbed.Sample"
+ command <- "SamplesEmbed.SampleValues"
.C("RealArray", command, nchar(command),
double(sampleSize), sampleSize, integer(1), PACKAGE="BRugs")[[3]]
}
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|
|
From: <li...@us...> - 2007-09-14 12:32:42
|
Revision: 56
http://bugs-r.svn.sourceforge.net/bugs-r/?rev=56&view=rev
Author: ligges
Date: 2007-09-14 05:32:46 -0700 (Fri, 14 Sep 2007)
Log Message:
-----------
This function is currently BROKEN with OpenBUGS 3.0.2 (waiting for a comment from Andrew),
for the meantime just a simplification for both S-PLUS and R.
Modified Paths:
--------------
trunk/BRugs/R/samples.sample.R
Modified: trunk/BRugs/R/samples.sample.R
===================================================================
--- trunk/BRugs/R/samples.sample.R 2007-09-14 11:21:12 UTC (rev 55)
+++ trunk/BRugs/R/samples.sample.R 2007-09-14 12:32:46 UTC (rev 56)
@@ -10,10 +10,6 @@
sampleSize <- as.integer(.C("Integer", command, nchar(command),
integer(1), integer(1), PACKAGE="BRugs")[[3]])
command <- "SamplesEmbed.Sample"
- if (is.R())
- .C("RealArray", command, nchar(command),
- real(sampleSize), sampleSize, integer(1), PACKAGE="BRugs")[[3]]
- else
- .C("RealArray", command, nchar(command),
- double(sampleSize), sampleSize, integer(1), PACKAGE="BRugs")[[3]]
+ .C("RealArray", command, nchar(command),
+ double(sampleSize), sampleSize, integer(1), PACKAGE="BRugs")[[3]]
}
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|
|
From: <li...@us...> - 2007-09-14 11:21:59
|
Revision: 55
http://bugs-r.svn.sourceforge.net/bugs-r/?rev=55&view=rev
Author: ligges
Date: 2007-09-14 04:21:12 -0700 (Fri, 14 Sep 2007)
Log Message:
-----------
some more deleted functions (get*Obj) - API has gone, NAMESPACE adapted
Modified Paths:
--------------
trunk/BRugs/NAMESPACE
Removed Paths:
-------------
trunk/BRugs/R/get.graphObj.R
trunk/BRugs/R/get.updaterObj.R
trunk/BRugs/man/get.Obj.Rd
Modified: trunk/BRugs/NAMESPACE
===================================================================
--- trunk/BRugs/NAMESPACE 2007-09-14 10:13:36 UTC (rev 54)
+++ trunk/BRugs/NAMESPACE 2007-09-14 11:21:12 UTC (rev 55)
@@ -2,8 +2,7 @@
importFrom(coda, mcmc)
export(BRugsFit, bugsData, bugsInits, buildMCMC, currentValues,
dicClear, dicSet, dicStats,
-getGraphObj, getNumChains,
-getUpdaterObj, help.BRugs, help.WinBUGS, loadModule,
+getNumChains, help.BRugs, help.WinBUGS,
modelAdaptivePhase, modelCheck, modelCompile, modelData,
modelGenInits, modelGetSeed, modelInits, modelIteration,
modelModules, modelNames, modelPrecision, modelSaveState,
Deleted: trunk/BRugs/R/get.graphObj.R
===================================================================
--- trunk/BRugs/R/get.graphObj.R 2007-09-14 10:13:36 UTC (rev 54)
+++ trunk/BRugs/R/get.graphObj.R 2007-09-14 11:21:12 UTC (rev 55)
@@ -1,9 +0,0 @@
-"getGraphObj" <-
-function(node)
-# Get type of GraphNode objects
-{
- command <- paste("BugsEmbed.SetVariable(", sQuote(node), "); BugsEmbed.Nodes")
- .C("CmdInterpreter", command, nchar(command), integer(1), PACKAGE="BRugs")
- buffer <- file.path(tempdir(), "buffer.txt")
- read.table(buffer)
-}
Deleted: trunk/BRugs/R/get.updaterObj.R
===================================================================
--- trunk/BRugs/R/get.updaterObj.R 2007-09-14 10:13:36 UTC (rev 54)
+++ trunk/BRugs/R/get.updaterObj.R 2007-09-14 11:21:12 UTC (rev 55)
@@ -1,9 +0,0 @@
-"getUpdaterObj" <-
-function(node)
-# Get type of UpdaterUpdaters objects
-{
- command <- paste("BugsEmbed.SetVariable(", sQuote(node), "); BugsEmbed.Methods")
- .C("CmdInterpreter", command, nchar(command), integer(1), PACKAGE="BRugs")
- buffer <- file.path(tempdir(), "buffer.txt")
- read.table(buffer)
-}
Deleted: trunk/BRugs/man/get.Obj.Rd
===================================================================
--- trunk/BRugs/man/get.Obj.Rd 2007-09-14 10:13:36 UTC (rev 54)
+++ trunk/BRugs/man/get.Obj.Rd 2007-09-14 11:21:12 UTC (rev 55)
@@ -1,30 +0,0 @@
-\name{getObj}
-\alias{getGraphObj}
-\alias{getUpdaterObj}
-\title{Expert functions}
-\description{Getting class names of Component Pascal object}
-\usage{
-getGraphObj(node)
-getUpdaterObj(node)
-}
-\arguments{
- \item{node}{Character vector of length 1, name of a variable in the model.}
-}
-\details{
-OpenBUGS creates Component Pascal objects to represent each component of a name in the graphial model.
-}
-\value{
-\code{getGraphObj} returns a data frame of the class names of the Component Pascal object associated with each component.
-
-\code{getUpdaterObj} returns a data frame of the class names of the Component Pascal object
-for each component of a variable that needs updating.
-}
-\seealso{\code{\link{BRugs}}, \code{\link{help.WinBUGS}}}
-\keyword{interface}
-
-
-
-
-
-
-
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From: <li...@us...> - 2007-09-14 10:13:33
|
Revision: 54
http://bugs-r.svn.sourceforge.net/bugs-r/?rev=54&view=rev
Author: ligges
Date: 2007-09-14 03:13:36 -0700 (Fri, 14 Sep 2007)
Log Message:
-----------
load module no longer in OpenBUGS API...
Removed Paths:
-------------
trunk/BRugs/R/loadModule.R
trunk/BRugs/man/loadModule.Rd
Deleted: trunk/BRugs/R/loadModule.R
===================================================================
--- trunk/BRugs/R/loadModule.R 2007-09-14 10:12:29 UTC (rev 53)
+++ trunk/BRugs/R/loadModule.R 2007-09-14 10:13:36 UTC (rev 54)
@@ -1,9 +0,0 @@
-"loadModule" <-
-function(module)
-# Load module
-{
- command <- as.character(module)
- .C("Load", command, nchar(command), integer(1), PACKAGE="BRugs")
- if(getOption("BRugsVerbose"))
- buffer()
-}
Deleted: trunk/BRugs/man/loadModule.Rd
===================================================================
--- trunk/BRugs/man/loadModule.Rd 2007-09-14 10:12:29 UTC (rev 53)
+++ trunk/BRugs/man/loadModule.Rd 2007-09-14 10:13:36 UTC (rev 54)
@@ -1,12 +0,0 @@
-\name{loadModule}
-\alias{loadModule}
-\title{Load a module}
-\description{This function loads a module.}
-\usage{
-loadModule(module)
-}
-\arguments{
- \item{module}{character, name of the module.}
-}
-\seealso{See \code{\link{modelModules}} for currently loaded modules. \code{\link{BRugs}}, \code{\link{help.WinBUGS}}}
-\keyword{interface}
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From: <li...@us...> - 2007-09-14 10:12:29
|
Revision: 53
http://bugs-r.svn.sourceforge.net/bugs-r/?rev=53&view=rev
Author: ligges
Date: 2007-09-14 03:12:29 -0700 (Fri, 14 Sep 2007)
Log Message:
-----------
bugfix: we have to read the buffer as fixed width format now, unfortunately ...
Modified Paths:
--------------
trunk/BRugs/R/model.modules.R
Modified: trunk/BRugs/R/model.modules.R
===================================================================
--- trunk/BRugs/R/model.modules.R 2007-09-14 10:11:39 UTC (rev 52)
+++ trunk/BRugs/R/model.modules.R 2007-09-14 10:12:29 UTC (rev 53)
@@ -5,5 +5,9 @@
command <- "BugsEmbed.Modules"
.C("CmdInterpreter", command, nchar(command), integer(1), PACKAGE="BRugs")
buffer <- file.path(tempdir(), "buffer.txt")
- read.table(buffer)
+ result <- read.fwf(buffer, c(50, 12, 12, 12, 12, 10), skip = 1, as.is=TRUE)
+ for(i in c(1,4,5,6))
+ result[,i] <- gsub(" ", "", result[,i])
+ names(result) <- c("Module", "Clients", "Version", "Maintainer", "Compiled", "Loaded")
+ return(result)
}
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From: <li...@us...> - 2007-09-14 10:11:35
|
Revision: 52
http://bugs-r.svn.sourceforge.net/bugs-r/?rev=52&view=rev
Author: ligges
Date: 2007-09-14 03:11:39 -0700 (Fri, 14 Sep 2007)
Log Message:
-----------
bugfix
Modified Paths:
--------------
trunk/BRugs/R/model.dynamic.R
Modified: trunk/BRugs/R/model.dynamic.R
===================================================================
--- trunk/BRugs/R/model.dynamic.R 2007-09-14 09:44:27 UTC (rev 51)
+++ trunk/BRugs/R/model.dynamic.R 2007-09-14 10:11:39 UTC (rev 52)
@@ -3,7 +3,7 @@
# Enable Dynamic Compilation
{
command <- "BugsEmbed.CompiledGuard; BugsEmbed.EnableDynamic"
- invisible(.C("Integer", command, nchar(command), integer(1), integer(1), PACKAGE="BRugs")[[3]])
+ invisible(.C("CmdInterpreter", command, nchar(command), integer(1), PACKAGE="BRugs")[[3]])
}
"modelDisableDynamic" <-
@@ -11,5 +11,5 @@
# Disable Dynamic Compilation
{
command <- "BugsEmbed.CompiledGuard; BugsEmbed.DisableDynamic"
- invisible(.C("Integer", command, nchar(command), integer(1), integer(1), PACKAGE="BRugs")[[3]])
+ invisible(.C("CmdInterpreter", command, nchar(command), integer(1), PACKAGE="BRugs")[[3]])
}
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From: <li...@us...> - 2007-09-14 09:44:39
|
Revision: 50
http://bugs-r.svn.sourceforge.net/bugs-r/?rev=50&view=rev
Author: ligges
Date: 2007-09-14 02:43:56 -0700 (Fri, 14 Sep 2007)
Log Message:
-----------
We need to copy libtaucs.dll now
Modified Paths:
--------------
trunk/BRugs/configure.win
Modified: trunk/BRugs/configure.win
===================================================================
--- trunk/BRugs/configure.win 2007-09-14 08:07:09 UTC (rev 49)
+++ trunk/BRugs/configure.win 2007-09-14 09:43:56 UTC (rev 50)
@@ -1,3 +1,4 @@
#!/bin/sh
mkdir $DPKG/libs
-cp ./inst/OpenBUGS/brugs.dll $DPKG/libs/BRugs.dll
\ No newline at end of file
+cp ./inst/OpenBUGS/brugs.dll $DPKG/libs/BRugs.dll
+cp ./inst/OpenBUGS/libtaucs.dll $DPKG/libs/libtaucs.dll
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From: <li...@us...> - 2007-09-14 09:44:25
|
Revision: 51
http://bugs-r.svn.sourceforge.net/bugs-r/?rev=51&view=rev
Author: ligges
Date: 2007-09-14 02:44:27 -0700 (Fri, 14 Sep 2007)
Log Message:
-----------
modelNames rewritten to work with OpenBUGS 3.x.y
Modified Paths:
--------------
trunk/BRugs/R/model.names.R
Modified: trunk/BRugs/R/model.names.R
===================================================================
--- trunk/BRugs/R/model.names.R 2007-09-14 09:43:56 UTC (rev 50)
+++ trunk/BRugs/R/model.names.R 2007-09-14 09:44:27 UTC (rev 51)
@@ -2,8 +2,19 @@
function()
{
# gets names in OpenBUGS model
- command <- "BugsRobjects.Names"
- .C("CmdInterpreter", command, nchar(command), integer(1), PACKAGE="BRugs")
- buffer <- file.path(tempdir(), "buffer.txt")
- readLines(buffer)
+ command <- "BugsRobjects.GetNumberNames"
+ number <- .C("Integer", command, nchar(command), integer(1), integer(1), PACKAGE="BRugs")[[3]]
+ name <- character(number)
+ if(length(number)){
+ for(i in 1:number){
+ command <- paste("BugsRobjects.SetIndex(", i-1, ")", sep="")
+ .C("CmdInterpreter", command, nchar(command), integer(1), PACKAGE="BRugs")
+ command <- "BugsRobjects.GetStringLength"
+ numchar <- .C("Integer", command, nchar(command), integer(1), integer(1), PACKAGE="BRugs")[[3]]
+ command <- "BugsRobjects.GetVariable"
+ char <- paste(rep(" ", numchar), collapse="")
+ name[i] <- .C("CharArray", command, nchar(command), char, numchar, integer(1), PACKAGE="BRugs")[[3]]
+ }
+ }
+ return(name)
}
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From: <li...@us...> - 2007-09-14 08:07:05
|
Revision: 49
http://bugs-r.svn.sourceforge.net/bugs-r/?rev=49&view=rev
Author: ligges
Date: 2007-09-14 01:07:09 -0700 (Fri, 14 Sep 2007)
Log Message:
-----------
switching to OpenBUGS 3.0.2
Modified Paths:
--------------
trunk/BRugs/DESCRIPTION
trunk/BRugs/R/zzz.R
Modified: trunk/BRugs/DESCRIPTION
===================================================================
--- trunk/BRugs/DESCRIPTION 2007-09-13 16:53:03 UTC (rev 48)
+++ trunk/BRugs/DESCRIPTION 2007-09-14 08:07:09 UTC (rev 49)
@@ -1,7 +1,7 @@
Package: BRugs
Title: OpenBUGS and its R / S-PLUS interface BRugs
-Version: 0.4-0
-Date: 2007-07-24
+Version: 0.4-1
+Date: 2007-09-14
Author: The Chief Software Bug is Andrew Thomas, with web assistance from Real Bug Bob O'Hara. Other members of the BUGS team are statisticians David Spiegelhalter, Nicky Best, Dave Lunn and Ken Rice. Dave Lunn has also made major contributions to the software development. R Code modified, extended and packaged for R by Uwe Ligges and Sibylle Sturtz. Some ideas taken from the R2WinBUGS package based on code by Andrew Gelman.
Description: An R / S-PLUS package containing OpenBUGS and its R / S-PLUS interface BRugs.
Maintainer: Uwe Ligges <li...@st...>
Modified: trunk/BRugs/R/zzz.R
===================================================================
--- trunk/BRugs/R/zzz.R 2007-09-13 16:53:03 UTC (rev 48)
+++ trunk/BRugs/R/zzz.R 2007-09-14 08:07:09 UTC (rev 49)
@@ -19,7 +19,7 @@
}
".onAttach" <- function(lib, pkg){
- message("Welcome to BRugs running on OpenBUGS version 3.0.1")
+ message("Welcome to BRugs running on OpenBUGS version 3.0.2")
}
".onUnload" <- function(libpath){
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From: <li...@us...> - 2007-09-13 16:53:07
|
Revision: 48
http://bugs-r.svn.sourceforge.net/bugs-r/?rev=48&view=rev
Author: ligges
Date: 2007-09-13 09:53:03 -0700 (Thu, 13 Sep 2007)
Log Message:
-----------
We need to overwrite sQuote within the Namespace:
R-alpha has a fancy sQuote intended for human readable fancy quoting only. We do NOT export this version of sQuote!!!
Modified Paths:
--------------
trunk/BRugs/R/zzz.R
Modified: trunk/BRugs/R/zzz.R
===================================================================
--- trunk/BRugs/R/zzz.R 2007-09-13 16:47:55 UTC (rev 47)
+++ trunk/BRugs/R/zzz.R 2007-09-13 16:53:03 UTC (rev 48)
@@ -1,51 +1,56 @@
if (is.R()){
-".onLoad" <- function(lib, pkg){
- ## Don't know whether we have to do this before useDynLib()???
- #Sys.putenv("LD_ASSUME_KERNEL"="2.4.1")
- ## sets path / file variables and initializes subsystems
- root <- file.path(system.file("OpenBUGS", package=pkg))
- ## we do have a NAMESPACE now: library.dynam("BRugs", pkg, lib)
- len <- nchar(root)
- tempDir <- gsub("\\\\", "/", tempdir())
- .C("SetRoot", as.character(root), len, PACKAGE="BRugs")
- .C("SetTempDir", as.character(tempDir), nchar(tempDir), PACKAGE="BRugs")
- command <- "BugsMappers.SetDest(2)"
- .C("CmdInterpreter", as.character(command), nchar(command), integer(1), PACKAGE="BRugs")
- #.C("Initialize", as.character(root), as.character(tempDir),
- # as.integer(len), nchar(tempDir), PACKAGE="BRugs")
- if(is.null(getOption("BRugsVerbose")))
- options("BRugsVerbose" = TRUE)
-}
+ ".onLoad" <- function(lib, pkg){
+ ## Don't know whether we have to do this before useDynLib()???
+ #Sys.putenv("LD_ASSUME_KERNEL"="2.4.1")
+ ## sets path / file variables and initializes subsystems
+ root <- file.path(system.file("OpenBUGS", package=pkg))
+ ## we do have a NAMESPACE now: library.dynam("BRugs", pkg, lib)
+ len <- nchar(root)
+ tempDir <- gsub("\\\\", "/", tempdir())
+ .C("SetRoot", as.character(root), len, PACKAGE="BRugs")
+ .C("SetTempDir", as.character(tempDir), nchar(tempDir), PACKAGE="BRugs")
+ command <- "BugsMappers.SetDest(2)"
+ .C("CmdInterpreter", as.character(command), nchar(command), integer(1), PACKAGE="BRugs")
+ #.C("Initialize", as.character(root), as.character(tempDir),
+ # as.integer(len), nchar(tempDir), PACKAGE="BRugs")
+ if(is.null(getOption("BRugsVerbose")))
+ options("BRugsVerbose" = TRUE)
+ }
+
+ ".onAttach" <- function(lib, pkg){
+ message("Welcome to BRugs running on OpenBUGS version 3.0.1")
+ }
+
+ ".onUnload" <- function(libpath){
+ library.dynam.unload("BRugs", libpath)
+ }
-".onAttach" <- function(lib, pkg){
- message("Welcome to BRugs running on OpenBUGS version 3.0.1")
-}
+ ## Overwriting new (from R-2.6.0) sQuote (for typing human readable text) in R within the BRugs Namespace!
+ ## we cannot use sQuote that uses fancy quotes!
+ sQuote <- function(x) paste("'", x, "'", sep="")
+
-".onUnload" <- function(libpath){
- library.dynam.unload("BRugs", libpath)
-}
-
} else { # ends if (is.R())
-".First.lib" <- function(lib.loc, section)
-{
- dyn.open(system.file("OpenBUGS", "brugs.dll", package="BRugs"))
- ## sets path / file variables and initializes subsystems
- root <- file.path(system.file("OpenBUGS", package="BRugs"))
- len <- nchar(root)
- tempDir <- gsub("\\\\", "/", tempdir())
- .C("SetRoot", as.character(root), len)
- .C("SetTempDir", as.character(tempDir), nchar(tempDir))
- command <- "BugsMappers.SetDest(2)"
- .C("CmdInterpreter", as.character(command), nchar(command), integer(1))
- if(is.null(getOption("BRugsVerbose")))
- options("BRugsVerbose" = TRUE)
- invisible()
-}
+ ".First.lib" <- function(lib.loc, section)
+ {
+ dyn.open(system.file("OpenBUGS", "brugs.dll", package="BRugs"))
+ ## sets path / file variables and initializes subsystems
+ root <- file.path(system.file("OpenBUGS", package="BRugs"))
+ len <- nchar(root)
+ tempDir <- gsub("\\\\", "/", tempdir())
+ .C("SetRoot", as.character(root), len)
+ .C("SetTempDir", as.character(tempDir), nchar(tempDir))
+ command <- "BugsMappers.SetDest(2)"
+ .C("CmdInterpreter", as.character(command), nchar(command), integer(1))
+ if(is.null(getOption("BRugsVerbose")))
+ options("BRugsVerbose" = TRUE)
+ invisible()
+ }
+
+ .tempDir <- getwd()
+
+ tempdir <- function(){ .tempDir }
-.tempDir <- getwd()
-
-tempdir <- function(){ .tempDir }
-
} # ends else
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From: <li...@us...> - 2007-09-13 16:47:52
|
Revision: 47
http://bugs-r.svn.sourceforge.net/bugs-r/?rev=47&view=rev
Author: ligges
Date: 2007-09-13 09:47:55 -0700 (Thu, 13 Sep 2007)
Log Message:
-----------
too many braces!
Modified Paths:
--------------
trunk/BRugs/man/bgr.point.Rd
trunk/BRugs/man/model.check.Rd
trunk/BRugs/man/plot.bgr.Rd
Modified: trunk/BRugs/man/bgr.point.Rd
===================================================================
--- trunk/BRugs/man/bgr.point.Rd 2007-09-12 17:46:47 UTC (rev 46)
+++ trunk/BRugs/man/bgr.point.Rd 2007-09-13 16:47:55 UTC (rev 47)
@@ -3,7 +3,7 @@
\alias{bgrPoint}
\title{Internal functions (to support plotting the Gelman-Rubin convergence statistic)}
\description{These functions are for internal use only.
- They support \code{\link{samplesBgr}} and \code{\link{plotBgr}}.}
+ They support \code{\link{samplesBgr}} and \code{\link{plotBgr}}.
}
\usage{
bgrGrid(node, bins = 50)
Modified: trunk/BRugs/man/model.check.Rd
===================================================================
--- trunk/BRugs/man/model.check.Rd 2007-09-12 17:46:47 UTC (rev 46)
+++ trunk/BRugs/man/model.check.Rd 2007-09-13 16:47:55 UTC (rev 47)
@@ -10,7 +10,7 @@
}
\value{
If a syntax error is detected the position of the error and a description of the error is printed,
-otherwise the \sQuote{model is syntaxicaly correct} message is displayed.}
+otherwise the \sQuote{model is syntaxicaly correct} message is displayed.
}
\note{
If an attempt is made to execute this function in an inappropriate context the generic error message
Modified: trunk/BRugs/man/plot.bgr.Rd
===================================================================
--- trunk/BRugs/man/plot.bgr.Rd 2007-09-12 17:46:47 UTC (rev 46)
+++ trunk/BRugs/man/plot.bgr.Rd 2007-09-13 16:47:55 UTC (rev 47)
@@ -2,7 +2,7 @@
\alias{plotBgr}
\title{Plot the Gelman-Rubin convergence statistic for a scalar variable}
\description{This function calculates and plots the Gelman-Rubin convergence statistic for a scalar variable,
- as modified by Brooks and Gelman (1998).}
+ as modified by Brooks and Gelman (1998).
}
\usage{
plotBgr(node, plot = TRUE, main = NULL, xlab = "iteration",
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From: Sparapani, R. <rsp...@mc...> - 2007-09-13 14:32:39
|
I replied again last night, but it never got to the list. I HATE =
OUTLOOK WEB ACCESS!!!! =20
Ok, 2.1-6 does work. Here's what I tested:
> =
Sys.setenv(WINE=3D"/Applications/Darwine/Wine.bundle/Contents/bin/wine")
> =
Sys.setenv(WINEPATH=3D"/Applications/Darwine/Wine.bundle/Contents/bin/win=
epath")
> schools.sim <- bugs (data=3Ddata,
inits=3Dinits,
parameters.to.save=3Dparameters,
model.file=3D"schools.txt",
n.chains=3D3,
n.iter=3D1000,
bugs.directory=3D"/Applications/WinBUGS14",
debug=3DFALSE)
However, fitbugs() does not work. Since bugs() no longer needs =
WINE/WINEPATH/etc.,
that should not be the issue. It seems like fitbugs does not know about =
bugs.directory!?!
Here's what it looks like:
> source("fitbugs.R")
> .schools.bugs.model <- function () {
# data : J, y, sigma.y
# param : theta, mu.theta, sigma.theta
# theta =3D rnorm(1)
# mu.theta =3D rnorm(1)
# sigma.theta =3D runif(1)
for (j in 1:J){
y[j] ~ dnorm (theta[j], tau.y[j])
theta[j] ~ dnorm (mu.theta, tau.theta)
tau.y[j] <- pow(sigma.y[j], -2)
}
mu.theta ~ dnorm (0, 1.0E-6)
tau.theta <- pow(sigma.theta, -2)
sigma.theta ~ dunif (0, 1000)
}
> fitbugs(.schools.bugs.model, =
bugs.directory=3D"/Applications/WinBUGS14")
Error in file(con, "rb") : unable to open connection
In addition: Warning message:
cannot open file '/Users/rsparapa/.wine/dosdevices/c:/Program =
Files/WinBUGS14/System/Rsrc/Registry.odc', reason 'No such file or =
directory' in: file(con, "rb")=20
Error in bugs.run(n.burnin, bugs.directory, WINE =3D WINE, useWINE =3D =
useWINE, :=20
WinBUGS executable does not exist in =
/Users/rsparapa/.wine/dosdevices/c:/Program Files/WinBUGS14
In addition: Warning message:
list.files: '/Users/rsparapa/.wine/dosdevices/c:/Program =
Files/WinBUGS14' is not a readable directory in: =
list.files(bugs.directory)=20
Any ideas? I tried to add bugs.directory to fitbugs.R, but I'm not =
getting the syntax right.
Rodney
-----Original Message-----
From: Gorjanc Gregor [mailto:Gre...@bf...]
Sent: Wed 9/12/2007 1:54 AM
To: Sparapani, Rodney; bug...@li...
Subject: RE: [Bugs-r-devel] Recent changes
=20
Hi Rodney
> I can now confirm that the example that recently appeared on
> BUGS-L works with R2WinBUGS 2.1-4,
> DarWINE 0.9.42 and WinBUGS 1.4.3 if I do the following first:
>
> Sys.setenv(DISPLAY=3D":0.0")
I tried to unset the DISPLAY variable on my Ubunutu box and I also was =
not
able to run the example (R2WinBUGS 2.1-6). Setting it back to :0.0 =
worked.
> However, it does not work with OpenBUGS 3.0.1 or 3.0.2. Also,
It can not work, since OpenBUGS has slightly different model syntax. =
rbugs
has implemented it and I would like to port that to R2WinBUGS - though =
we
might just go via BRugs since Bob announced that OpenBUGS should now
work also under Linux. Stay tunned ;)
> DarWINE 0.9.43 and 0.9.44 have some problems as well.
Any meaningful error message?
> Now, how do I install the latest trunk to do the same test?
> I've downloaded it, but there does not appear to be a .tgz file.
Just build it. I guess mac side should not be much different from
R CMD build R2WinBUGS
Regards, Gregor
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