Hi,
I'm trying to run R2WinBUGS using the R code below (Thinkpad Yoga 260,
Win8, system x86_64, mingw32, R version 3.3.1). It worked fine for several
times but then one error began to pop up in every run: command #Bugs:set
cannot be executed (is greyed out). I've been trying for more than one
On 17.07.2016 05:33, Christopher Kelvin via R-help wrote:
Dear R-User,
I have written a simple code to analyze some data using Bayesian logistic
regression via the R2WinBUGS package. The code when run in WinBUGS stops
WinBUGS from running it and using the package returns no results also.
Dear R-User,
I have written a simple code to analyze some data using Bayesian logistic
regression via the R2WinBUGS package. The code when run in WinBUGS stops
WinBUGS from running it and using the package returns no results also.
I attach herewith, the code and a sample of the dataset.
Any
Hi Mariana,
Not sure if my post was accepted. Try running R from your desktop but right
clicking on the icon and selecting "Run as Administrator", rather than opening
R in the normal manner.
Good luck,
Mark
Date: Fri, 18 Sep 2015 08:43:53 -0700
From: ml-node+s789695n4712456...@n4.nabble.com
Hi Mariana,
I was not able to solve this issue entirely satisfactorily, but after
speaking to IT personnel, they advised that I try running R from my desktop
by right clicking on the R icon and selecting "Run as Administrator", rather
than opening in the normal manner. Remarkably this avoided the
I am facing the same problem. I have been able to run my code in another
computer with Windows 8 but not in my computer at work, which also runs
Windowns 8.
I am looking forward for solving this problem.
Mariana.
--
View this message in context:
On 23.12.2014 08:46, thanoon younis wrote:
Dear all R-members
I have a problem with R when i wanted to call WinBUGS from R as following:
#Call WinBUGS
model-bugs(data,inits,parameters,model.file=D:/Run/model.txt,
n.chains=2,n.iter=5000,n.burnin=1000,n.thin=1,'DIC=True',
???
You
Dear all R-members
I have a problem with R when i wanted to call WinBUGS from R as following:
#Call WinBUGS
model-bugs(data,inits,parameters,model.file=D:/Run/model.txt,
n.chains=2,n.iter=5000,n.burnin=1000,n.thin=1,'DIC=True',
bugs.directory=c:/Program Files/WinBUGS14/,
On 18.09.2014 08:22, Hanze Zhang wrote:
Hi, guys,
I am a new user for package R2winbugs. When I run the code a=bugs(...), an
error message always comes out, see below:
Error in file(con, wb) : cannot open the connection
In addition: Warning messages:
1: In file.create(to[okay]) :
cannot
Hi, guys,
I am a new user for package R2winbugs. When I run the code a=bugs(...), an
error message always comes out, see below:
Error in file(con, wb) : cannot open the connection
In addition: Warning messages:
1: In file.create(to[okay]) :
cannot create file 'c:/Program
Hi all,
I am currently in a Bayesian Modeling course and am trying to implement an
analog representation model using R, WinBUGS, and R2WinBUGS. I'm currently
stuck banging my head against an expected collection operator c error. I
am working off of a template code, and I swear I haven't moved
This is probably a BUGS rather than an R problem, hence better for a
BUGS mailing list. But if we should help, then we need at least the
modelfile.
Best,
Uwe Ligges
On 02.04.2014 19:10, zumacrume wrote:
Hi all,
I am currently in a Bayesian Modeling course and am trying to implement an
Dear R users,
Can anyone tell me why I might get the error message
the array index is greater than the upper bound for t in WinBUGS ? t is a
vector I have defined. I have checked repeatedly that the array index for t
does match with the upper bound till which the loop is run. I
Reproducible code? The error seems to be rather clear.
Also, this seems more of a BUGS question than an R question.
Michael
On Jul 17, 2012, at 11:06 AM, PRAGYA SUR pragya1...@gmail.com wrote:
Dear R users,
Can anyone tell me why I might get the error message
the array
On 17.07.2012 19:58, Michael Weylandt wrote:
Reproducible code? The error seems to be rather clear.
Also, this seems more of a BUGS question than an R question.
Indeed, the reproducible code is somthing for a BUGS mailing list. just
a guess: The typical row vs. column confusion in BUGS.
On 07.02.2012 15:23, anaraster wrote:
Hi!
I am new to BUGS and running BUGS from R. I am trying to run a regression
model from R, however I have this error message:
Error in file(con, wb) : cannot open the connection In addition: Warning
messages:
1: In file.create(to[okay]) : cannot
Hi!
I am new to BUGS and running BUGS from R. I am trying to run a regression
model from R, however I have this error message:
Error in file(con, wb) : cannot open the connection In addition: Warning
messages:
1: In file.create(to[okay]) : cannot create file 'c:/Program
I have successfully used R2WinBUGS in the past and an trying to use basically
the same code with some different data but I'm getting the following error:
out - bugs(data=win.data, inits=inits, parameters.to.save=params,
model.file = PoissonGLMM.txt, n.chains=nc, n.iter=ni, n.burn=nb,
I have successfully used R2WinBUGS in the past and an trying to use basically
the same code with some different data but I'm getting the following error:
out - bugs(data=win.data, inits=inits, parameters.to.save=params,
model.file = PoissonGLMM.txt, n.chains=nc, n.iter=ni, n.burn=nb,
Sorry for the additional post - I received the suggestion to include the
following additional information:
* traceback()*
5: FUN(X[[12L]], ...)
4: lapply(data, formatC, digits = digits, format = E)
3: write.datafile(lapply(data, formatC, digits = digits, format = E),
file.path(dir,
Sorry for continuing to reply to myself. I believe that my problem was
putting a factor (plot) in my data for the bugs(data,...) call. I still
have stuff to work out in the code but I don't get the error if I exclude
plot from the win.data - list(...) assignment. I have to think if that will
now
Dear all,
I'm having a slight issue with R2WinBugs it cannot detect where WinBUGS is
located.
Q: How can I change the default path?
Any advice is greatly appreciated. Thanks.
Regards
Erica
I'm using R2WinBUGs (R version 2.21.1) on windows platform (Windows 7).
I have downloaded
Would you please mind to read ?bugs and see that the argument called
bugs.directory may be relevant?
Uwe Ligges
On 14.01.2011 15:53, Erica Donnelly-Swift wrote:
Dear all,
I'm having a slight issue with R2WinBugs it cannot detect where WinBUGS is
located.
Q: How can I change the
Yes, I just realised this
Apologies for the inconvenience
Thanks
From: Uwe Ligges [lig...@statistik.tu-dortmund.de]
Sent: 14 January 2011 15:20
To: Erica Donnelly-Swift
Cc: r-help@R-project.org
Subject: Re: [R] R2WinBUGS-Windows 7
Would you please
For some purpose, I need to transfer a NAs array to WinBugs through
R2WinBugs, But I constantly got an error message:'type' must be real for
this format. Here is my data to transfer:
x = matrix(data=NA,nrow=3,ncol=3)
x = as.array(x)
data - list (x)
if I add a line to above setting, then I can
On Dec 26, 2010, at 12:44 AM, unsown wrote:
For some purpose, I need to transfer a NAs array to WinBugs through
R2WinBugs, But I constantly got an error message:'type' must be
real for
this format. Here is my data to transfer:
x = matrix(data=NA,nrow=3,ncol=3)
str(x)
It is of mode
You solved my problem, thank you.
As you said it's the type of the content in the matrix that caused the
problem.
I needed to put variable x along with other variables to the list, somehow
it turned out that x must be used in form of character in the statement:
dat - list(x,otherVariables)
When I use the 'bugs' function from R, WinBUGS runs correctly, but R freezes.
The only way to use R after this is to stop calculations (without my file
that documents the calculation). However, I want to save the output in R so
I can use it in further models. Does anyone know how to fix this
On 22.11.2010 21:41, bmiddle wrote:
When I use the 'bugs' function from R, WinBUGS runs correctly, but R freezes.
The only way to use R after this is to stop calculations (without my file
that documents the calculation).
R freezes as long as the WinBUGS process is opened. AFter closing it,
When I use the 'bugs' function from R, WinBUGS runs correctly, but R
freezes.
The only way to use R after this is to stop calculations (without my file
that documents the calculation).
R freezes as long as the WinBUGS process is opened. AFter closing it,
R should respond again.
If you
I found the problem which is a scoping issue in BRugs::bugsData() and
will fix it for the next release.
For now, you can workaround by calling your parameters (in this case
particularly beta) with a names that are different from R function names
(e.g. call it beta1).
Best wishes,
Uwe
On 13.11.2010 18:05, Uwe Ligges wrote:
I found the problem which is a scoping issue in BRugs::bugsData() and
will fix it for the next release.
For now, you can workaround by calling your parameters (in this case
particularly beta) with a names that are different from R function names
(e.g.
I get an error when I call bugs(..., program=OpenBUGS,
bugs.directory=c:/Program Files/OpenBUGS/OpenBUGS312),
expecting, as suggested in help(bugs), that it would fit the
model with openbugs() via BRugs.
help(bugs)
... either winbugs/WinBUGS or openbugs/OpenBUGS, the latter
makes use of
If the exactly same code runs on one machine and not on another where R
version, script, model file, inits, data etc. are all identical, then I
suspect you have different versions of R2WinBUGS installed.
Please check is really all files and all version numbers are the same.
If you still have
I'm having difficulty running R2WinBugs on a setup that previously
worked for me (Dell Laptop, Windows XP service pack 3, R 2.11.1, WinBugs
1.43) . When I issue the following command
smds.sim - bugs (data, inits, parameters, SMDSbrandLoc2.bug,
debug = T,
n.thin = n.thin,
n.chains =
2010/1/26 Ben Bolker bol...@ufl.edu
julien martin julemartin0320 at gmail.com writes:
I am generating 1000 replicate data sets in R, each data set is then
analyzed with WinBUGS in batch mode using R2WinBUGS. Unfortunately,
occasionally some data sets lead WinBUGS to open a trap window;
I am generating 1000 replicate data sets in R, each data set is then
analyzed with WinBUGS in batch mode using R2WinBUGS. Unfortunately,
occasionally some data sets lead WinBUGS to open a trap window; and the
simulations are interrupted as result of the message. Is there any ways to
set R2WinBUGS
I am generating 1000 replicate data sets in R, each data set is then
analyzed with WinBUGS in batch mode using R2WinBUGS. Unfortunately,
occasionally some data sets lead WinBUGS to open a trap window; and
the simulations are interrupted as result of the message. Is there any
ways to set R2WinBUGS
julien martin julemartin0320 at gmail.com writes:
I am generating 1000 replicate data sets in R, each data set is then
analyzed with WinBUGS in batch mode using R2WinBUGS. Unfortunately,
occasionally some data sets lead WinBUGS to open a trap window; and the
simulations are interrupted as
I have a fix in R2WinBUGS_2.1-15 which is on its way to CRAN and will
appear there within 2 days, probably.
Best wishes,
Uwe Ligges
Luwis Tapiwa Diya wrote:
Dear R users
I have been encountering an error (in the Winbugs window: Blackbox - index
out of range . ). So to me it seems
I have a fix in R2WinBUGS_2.1-15 which is on its way to CRAN and will
appear there within 2 days, probably.
Best wishes,
Uwe Ligges
Paul Heinrich Dietrich wrote:
This weekend I noticed that my R2WinBUGS connection was no longer working on
my Windows computer at work AND my Ubuntu linux
Dear R users
I have been encountering an error (in the Winbugs window: Blackbox - index
out of range . ). So to me it seems R2WinBUGS is not linking up well
with the new R version since the same model runs well under r-2.9.2. So is
my assumption correct or am I doing something wrong. The data
Hi,
I got another report about and will investigate shortly.
uwe
Luwis Tapiwa Diya wrote:
Dear R users
I have been encountering an error (in the Winbugs window: Blackbox - index
out of range . ). So to me it seems R2WinBUGS is not linking up well
with the new R version since the same
This weekend I noticed that my R2WinBUGS connection was no longer working on
my Windows computer at work AND my Ubuntu linux computer at home. As soon
as WinBUGS opens, the message reads Index Out Of Range. I have un-installed
and re-installed R on both computers and the problem remains the
Paul Heinrich Dietrich wrote:
This weekend I noticed that my R2WinBUGS connection was no longer working on
my Windows computer at work AND my Ubuntu linux computer at home. As soon
as WinBUGS opens, the message reads Index Out Of Range. I have un-installed
Yes, thanks, problem known for
Hi R Users,
I have--what I think--is a very basic question. I'm trying to use R2WinBUGS and
am having difficulty setting up the data properly for repeated measures data in
a hierarchical model.
First, I know that it is me...not the package, as I sucessfully used R2WinBUGS
to run a basic
Harlan Harris wrote:
Hi,
I'm running wine-1.0.1, OpenBUGS 3.0.3, R 2.9.0, and R2WinBUGS on a Redhat
Enterprise Linux machine.
Following various peoples' suggestions...
This works perfectly (yay!): wine Z:/opt/OpenBUGS/winbugs.exe
Within R, however, I get this:
(setup the example from
Uwe, thanks for helping! After some poking around, I realized that the
problem was that I had installed OpenBUGS instead of WinBUGS. I did an
additional installation of WinBUGS, which also runs fine under Wine, and now
everything seems to work! Thanks!
To clarify: both the OpenBUGS and WinBUGS
Harlan Harris wrote:
Uwe, thanks for helping! After some poking around, I realized that the
problem was that I had installed OpenBUGS instead of WinBUGS. I did an
additional installation of WinBUGS, which also runs fine under Wine, and now
everything seems to work! Thanks!
To clarify: both
Hi,
I'm running wine-1.0.1, OpenBUGS 3.0.3, R 2.9.0, and R2WinBUGS on a Redhat
Enterprise Linux machine.
Following various peoples' suggestions...
This works perfectly (yay!): wine Z:/opt/OpenBUGS/winbugs.exe
Within R, however, I get this:
(setup the example from ?bugs, then)
R
Richard.Cotton at hsl.gov.uk writes:
I'm running OpenBUGS model via the R2WinBUGS package interface, under
Windows. Is it possible to terminate running models, short of using the
Windows Task Manager to forcibly exit the program?
If you use OpenBUGS, then I guess you can not since
Gregor Gorjanc wrote:
Richard.Cotton at hsl.gov.uk writes:
I'm running OpenBUGS model via the R2WinBUGS package interface, under
Windows. Is it possible to terminate running models, short of using the
Windows Task Manager to forcibly exit the program?
If you use OpenBUGS, then I guess
Apologies if this isn't acceptable for the general help list.
I'm running OpenBUGS model via the R2WinBUGS package interface, under
Windows. Is it possible to terminate running models, short of using the
Windows Task Manager to forcibly exit the program?
Regards,
Richie.
Mathematical
Richard.Cotton at hsl.gov.uk writes:
Apologies if this isn't acceptable for the general help list.
I'm running OpenBUGS model via the R2WinBUGS package interface, under
Windows. Is it possible to terminate running models, short of using the
Windows Task Manager to forcibly exit the
Many thanks to all responders. It turns out that there is a winbugs
update available, which defines a new version of inprod, inprod2.
Using inprod2 the vectorized code runs in about the same time as the
scalar version.
On the print problem: the issue here turns out to be that the arm
I remember having similar problem with inprod function. As far as I could
remember a sole deference in my models was that I used inprod instead of
explicit sum (exactly as you did). In my case the inprod version was faster but
result were completely aberrant. So I abandoned the inprod as
I'm new to bugs, so please bear with me. Can someone tell me if the
following two models are doing the same thing? The reason I ask is
that with the same data, the first (based on 4 separate coeffs
a1--a4) takes about 50 secs, while the second (based on a vectorized
form, a[]) takes about
Philip A. Viton wrote:
I'm new to bugs, so please bear with me. Can someone tell me if the
following two models are doing the same thing? The reason I ask is
that with the same data, the first (based on 4 separate coeffs
a1--a4) takes about 50 secs, while the second (based on a
Philip,
If you are using WinBUGS 1.4, then the poor performance of the
inprod function is a known problem. An inprod2 function
was introduced in 1.4.3 to improve performance. See
http://www.mrc-bsu.cam.ac.uk/bugs/winbugs/contents.shtml#problems
You might try using that.
For WinBUGS problems,
Dear Troels,
it is possible to start without inits if the problem to solve is
appropriate, here is the changed schools example from the help page:
model.file - system.file(package=R2WinBUGS, model, schools.txt)
data(schools)
J - nrow(schools)
y - schools$estimate
sigma.y - schools$sd
data -
Dear friends - I'm on winXP, R 2.71 - I have with some help dveloped
this multivariate normal model, which gives very plausible results in
WinBUGS even without any
initial values specified. However, when I then try to run the same model
via the bugs function in R2WinBUGS with inits specified as
Dear John,
this is a new bug caused by a side effect from a new bugs.log function
by Jouni Kerman that improves many other things. I have fixed it in the
master sources on sourceforge right now and a bugfix release will appear
on CRAN within a couple of days.
Best,
Uwe Ligges
John Smith
Dear R-users,
I am trying to use the following code to reproduce results from Prof.
Gelman's book, but have the listed error for R2WinBUGS version (the openbugs
version is good). I am using R-2.6.1 on windows XP, and all the R packages
are most current ones. schools.bug can be found at
James.Dell at csiro.au writes:
...
1) I can't seem to send variables classed as factors (Month), is there a
way do this?
You can not use factors per se in BUGS. You have to convert them to numeric
(integer) variables before.
2) Checking the Log in WinBUGS I can see that the model is
James,
the first non-regular message you got in the output was:
made use of undefined node nSeaW,
so what about defining nSeaW (or did you mean to write mSeaW)?
If this is not the problem, please provide the data so that we can try
to reproduce your error, as the psoting guide (of R-help) ask
Hello R and BUGS users,
I am writing a heirarchical model in R to send to BUGS via R2WinBUGS and
I am finding it difficult to get the model to run. I seem to be having
two problems.
1) I can't seem to send variables classed as factors (Month), is there a
way do this?
2) Checking the Log in
Evan Cooch wrote:
I am trying to figure out if it is possible to run winBUGS from within
R, using R2winBUGS, without having winBUGS spawn any windows (basically
- 'true' batch - no GUI actions at all). The reason being I have a
machine which I (and several others) ssh/telnet into, and
Same answer as the one for your other R-help question [R] R2winBUGS
WinBUGS gui (November 23).
Folks, sometimes people (like me in this case) are out of office and
then it might take more then an hour to answer your questions...
Best,
Uwe Ligges
Evan Cooch wrote:
Greetings -
I run
No. The idea is to use BRugs, i.e. OpenBUGS in such cases. If OpenBUGS
lacks some features, you are certainly welcome to implement them and
send patches to Andrew Thomas.
Thanks very much. I thought as much, but given that I have had a 0%
success rate in getting OpenBUGS to run on any
No. The idea is to use BRugs, i.e. OpenBUGS in such cases. If OpenBUGS
lacks some features, you are certainly welcome to implement them and
send patches to Andrew Thomas.
Just finished trying the install of openBUGS under linux yet again. Same
problems (more or less), which I'll list
Evan Cooch wrote:
No. The idea is to use BRugs, i.e. OpenBUGS in such cases. If OpenBUGS
lacks some features, you are certainly welcome to implement them and
send patches to Andrew Thomas.
Just finished trying the install of openBUGS under linux yet again. Same
problems (more or
Yes, sure, and indeed, it is a shame that nobody of those people who
want it to work under Linux is trying to submit patches to make it work.
I agree, but I *think* the primary reason for this is that it requires
installing Blackbox as a PASCAL compiler. For much of the Linux
community,
Evan Cooch wrote:
Yes, sure, and indeed, it is a shame that nobody of those people who
want it to work under Linux is trying to submit patches to make it work.
I agree, but I *think* the primary reason for this is that it requires
installing Blackbox as a PASCAL compiler. For much
Greetings -
I run a multi-pro server box (GNU/Linux), on which I've installed
winBUGS under wine. Works fine, and plays nice with r2WinBUGS, provided
everything is done through a graphical front-end (either by working from
console, or using a virtual desktop via VNC or equivalent).
However,
I am trying to figure out if it is possible to run winBUGS from within
R, using R2winBUGS, without having winBUGS spawn any windows (basically
- 'true' batch - no GUI actions at all). The reason being I have a
machine which I (and several others) ssh/telnet into, and would like to
run winBUGS
Just while I use R2Winbugs, the following error will be presented. Please
tell me how to cope with.
Error in file(file, r) : unable to open connection
In addition: Warning message:
cannot open file 'codaIndex.txt', reason 'No such file or directory' in:
file(file, r)
Thanks
Sam_zhz
--
View this
Just while I use R2Winbugs, the following error will be presented. Please
tell me how to cope with.
Error in file(file, r) : unable to open connection
In addition: Warning message:
cannot open file 'codaIndex.txt', reason 'No such file or directory' in:
file(file, r)
Thanks
Sam_zhz
--
View this
Just while I use R2Winbugs, the following error will be presented. Please
tell me how to cope with.
Error in file(file, r) : unable to open connection
In addition: Warning message:
cannot open file 'codaIndex.txt', reason 'No such file or directory' in:
file(file, r)
Thanks
Sam_zhz
--
View this
Just while I use R2Winbugs, the following error will be presented. Please
tell me how to cope with.
Error in file(file, r) : unable to open connection
In addition: Warning message:
cannot open file 'codaIndex.txt', reason 'No such file or directory' in:
file(file, r)
Thanks
Sam_zhz
--
View this
Just while I use R2Winbugs, the following error will be presented. Please
tell me how to cope with.
Error in file(file, r) : unable to open connection
In addition: Warning message:
cannot open file 'codaIndex.txt', reason 'No such file or directory' in:
file(file, r)
Thanks
Sam_zhz
--
View this
Just while I use R2Winbugs, the following error will be presented. Please
tell me how to cope with.
Error in file(file, r) : unable to open connection
In addition: Warning message:
cannot open file 'codaIndex.txt', reason 'No such file or directory' in:
file(file, r)
Thanks
Sam_zhz
--
View this
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