[R] R to winbugs interface
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PRAGYA SUR
Jul 9, 2012, 1:20:46 AM7/9/12
to r-h...@r-project.org
Hello everyone,
I need some help regarding calling WinBUGS from R. I
have a model for WinBUGS and an R code which calls WinBUGS. On running the
code I am being shown the 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
Files/WinBUGS14//System/Rsrc/Registry_Rsave.odc', reason 'Permission denied'
2: In file(con, "wb") :
cannot open file 'c:/Program Files/WinBUGS14//System/Rsrc/Registry.odc':
Permission denied
In addition in WinBUGS a window crops up which is named black box. and says
trap #060 and then gives some details. I am not being able to understand
what all hese error messages mean. I am also giving the R code and the code
for the model here :
R code :
regpractwo=function(Ytilde,D,Xtilde,a,b,n,FEV,Age,Smoke)
{
Xtildeinv=solve(Xtilde)
beta0=c(t(Xtildeinv%*%Ytilde))
C0=Xtildeinv%*%D%*%t(Xtildeinv)
C0inv=solve(C0)
r=dim(Xtildeinv)[1]
FEVdataBUGS=list("n","r","beta0","C0inv","a","b","FEV","Age","Smoke")
#creates list of imputs for winbugs code
parameters=c("beta","tau","meanFEVs","meanFEVns","FEV20s","FEV20ns")
#parameters to be monitored by winbugs
inits=list(list(tau=1,beta=c(0,0,0,0),FEV20s=2,FEV20ns=2)) # giving initial
values
FEV.fit=bugs(FEVdataBUGS,inits,parameters,"FEVWBModel.txt",n.chains=1,n.iter=60000,n.thin=1,n.burnin=10000)
print(FEV.fit,digits=3)
attach.bugs(FEV.fit)
}
The model :
model
{
for (i in 1:n)
{
FEV[i]~dnorm(mu[i],tau)
mu[i]<-beta[1]+beta[2]*Age[i]+beta[3]*Smoke[i]+beta[4]*Age[i]*Smoke[i]
}
beta[1:r]~dmnorm(beta0[1:r],C0inv[1:r,1:r])
tau~dgamma(a,b)
for (i in 1:10)
{
meanFEVs[i] <- beta[1] + (beta[2]+beta[4])*(i+9) + beta[3]
meanFEVns[i] <- beta[1] + beta[2]*(i+9)
}
FEV20s ~ dnorm(mu20s,tau)
FEV20ns ~ dnorm(mu20ns,tau)
mu20s <- beta[1] + (beta[2]+beta[4])*20 + beta[3]
mu20ns <- beta[1] + beta[2]*20
}
Please help me with this problem.
[[alternative HTML version deleted]]
______________________________________________
R-h...@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
I need some help regarding calling WinBUGS from R. I
have a model for WinBUGS and an R code which calls WinBUGS. On running the
code I am being shown the 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
Files/WinBUGS14//System/Rsrc/Registry_Rsave.odc', reason 'Permission denied'
2: In file(con, "wb") :
cannot open file 'c:/Program Files/WinBUGS14//System/Rsrc/Registry.odc':
Permission denied
In addition in WinBUGS a window crops up which is named black box. and says
trap #060 and then gives some details. I am not being able to understand
what all hese error messages mean. I am also giving the R code and the code
for the model here :
R code :
regpractwo=function(Ytilde,D,Xtilde,a,b,n,FEV,Age,Smoke)
{
Xtildeinv=solve(Xtilde)
beta0=c(t(Xtildeinv%*%Ytilde))
C0=Xtildeinv%*%D%*%t(Xtildeinv)
C0inv=solve(C0)
r=dim(Xtildeinv)[1]
FEVdataBUGS=list("n","r","beta0","C0inv","a","b","FEV","Age","Smoke")
#creates list of imputs for winbugs code
parameters=c("beta","tau","meanFEVs","meanFEVns","FEV20s","FEV20ns")
#parameters to be monitored by winbugs
inits=list(list(tau=1,beta=c(0,0,0,0),FEV20s=2,FEV20ns=2)) # giving initial
values
FEV.fit=bugs(FEVdataBUGS,inits,parameters,"FEVWBModel.txt",n.chains=1,n.iter=60000,n.thin=1,n.burnin=10000)
print(FEV.fit,digits=3)
attach.bugs(FEV.fit)
}
The model :
model
{
for (i in 1:n)
{
FEV[i]~dnorm(mu[i],tau)
mu[i]<-beta[1]+beta[2]*Age[i]+beta[3]*Smoke[i]+beta[4]*Age[i]*Smoke[i]
}
beta[1:r]~dmnorm(beta0[1:r],C0inv[1:r,1:r])
tau~dgamma(a,b)
for (i in 1:10)
{
meanFEVs[i] <- beta[1] + (beta[2]+beta[4])*(i+9) + beta[3]
meanFEVns[i] <- beta[1] + beta[2]*(i+9)
}
FEV20s ~ dnorm(mu20s,tau)
FEV20ns ~ dnorm(mu20ns,tau)
mu20s <- beta[1] + (beta[2]+beta[4])*20 + beta[3]
mu20ns <- beta[1] + beta[2]*20
}
Please help me with this problem.
[[alternative HTML version deleted]]
______________________________________________
R-h...@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
S Ellison
Jul 9, 2012, 7:04:09 AM7/9/12
to PRAGYA SUR, r-h...@r-project.org
> -----Original 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
> Files/WinBUGS14//System/Rsrc/Registry_Rsave.odc', reason
> 'Permission denied'
> 2: In file(con, "wb") :
> cannot open file 'c:/Program
> Files/WinBUGS14//System/Rsrc/Registry.odc':
> Permission denied
Conclusion; you're trying to write to an area you don;t have permission to write to.
Either change the permissions for that area (insecure) or use a different file location for temporary files.
*******************************************************************
This email and any attachments are confidential. Any use...{{dropped:8}}
PRAGYA SUR
Jul 9, 2012, 12:19:43 PM7/9/12
to r-h...@r-project.org
I ran the same program in a different computer where it had run proper a
week ago. This time around in the log file in WinBUGS the program stopped
at a line which said :
save(C:/DOCUME~1/ADMINI~1/LOCALS~1/Temp/RtmpU3u46p/log.odc)
save(C:/DOCUME~1/ADMINI~1/LOCALS~1/Temp/RtmpU3u46p/log.txt)
and did not proceed any further.
Can anyone tell me what migh tbe the possible error here?
On Mon, Jul 9, 2012 at 7:04 AM, S Ellison <S.El...@lgcgroup.com> wrote:
>
>
> > -----Original 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
> > Files/WinBUGS14//System/Rsrc/Registry_Rsave.odc', reason
> > 'Permission denied'
>
> This tells you that you do not have operating system permission to create
> a file in the program files area referred to.
>
> > 2: In file(con, "wb") :
> > cannot open file 'c:/Program
> > Files/WinBUGS14//System/Rsrc/Registry.odc':
> > Permission denied
>
> .. and this tells you you don't have permission to open a file for writing
> (mode 'w' in the same location
>
> Conclusion; you're trying to write to an area you don;t have permission to
> write to.
>
> Either change the permissions for that area (insecure) or use a different
> file location for temporary files.
>
> *******************************************************************
> This email and any attachments are confidential. Any u...{{dropped:11}}
week ago. This time around in the log file in WinBUGS the program stopped
at a line which said :
save(C:/DOCUME~1/ADMINI~1/LOCALS~1/Temp/RtmpU3u46p/log.odc)
save(C:/DOCUME~1/ADMINI~1/LOCALS~1/Temp/RtmpU3u46p/log.txt)
and did not proceed any further.
Can anyone tell me what migh tbe the possible error here?
On Mon, Jul 9, 2012 at 7:04 AM, S Ellison <S.El...@lgcgroup.com> wrote:
>
>
> > -----Original 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
> > Files/WinBUGS14//System/Rsrc/Registry_Rsave.odc', reason
> > 'Permission denied'
>
> This tells you that you do not have operating system permission to create
> a file in the program files area referred to.
>
> > 2: In file(con, "wb") :
> > cannot open file 'c:/Program
> > Files/WinBUGS14//System/Rsrc/Registry.odc':
> > Permission denied
>
> .. and this tells you you don't have permission to open a file for writing
> (mode 'w' in the same location
>
> Conclusion; you're trying to write to an area you don;t have permission to
> write to.
>
> Either change the permissions for that area (insecure) or use a different
> file location for temporary files.
>
> *******************************************************************
Uwe Ligges
Jul 9, 2012, 1:15:26 PM7/9/12
to PRAGYA SUR, r-h...@r-project.org
On 09.07.2012 18:19, PRAGYA SUR wrote:
> I ran the same program in a different computer where it had run proper a
> week ago. This time around in the log file in WinBUGS the program stopped
> at a line which said :
> save(C:/DOCUME~1/ADMINI~1/LOCALS~1/Temp/RtmpU3u46p/log.odc)
> save(C:/DOCUME~1/ADMINI~1/LOCALS~1/Temp/RtmpU3u46p/log.txt)
> and did not proceed any further.
> Can anyone tell me what migh tbe the possible error here?
used bugs(....., debug=TRUE)?
Uwe Ligges
PRAGYA SUR
Jul 9, 2012, 1:27:50 PM7/9/12
to Uwe Ligges, r-h...@r-project.org
Yes that was the problem. Thank you very much. Can anyone tell me the
meaning of
The following object(s) are masked _by_ '.GlobalEnv':
beta
i was shown this notification after the results were printed.
On Mon, Jul 9, 2012 at 1:15 PM, Uwe Ligges
<lig...@statistik.tu-dortmund.de>wrote:
>
>
> On 09.07.2012 18:19, PRAGYA SUR wrote:
>
>> I ran the same program in a different computer where it had run proper a
>> week ago. This time around in the log file in WinBUGS the program stopped
>> at a line which said :
>> save(C:/DOCUME~1/ADMINI~1/**LOCALS~1/Temp/RtmpU3u46p/log.**odc)
>> save(C:/DOCUME~1/ADMINI~1/**LOCALS~1/Temp/RtmpU3u46p/log.**txt)
>> R-h...@r-project.org mailing list
>> https://stat.ethz.ch/mailman/**listinfo/r-help<https://stat.ethz.ch/mailman/listinfo/r-help>
>> PLEASE do read the posting guide http://www.R-project.org/**
>> posting-guide.html <http://www.R-project.org/posting-guide.html>
meaning of
The following object(s) are masked _by_ '.GlobalEnv':
beta
i was shown this notification after the results were printed.
On Mon, Jul 9, 2012 at 1:15 PM, Uwe Ligges
<lig...@statistik.tu-dortmund.de>wrote:
>
>
> On 09.07.2012 18:19, PRAGYA SUR wrote:
>
>> I ran the same program in a different computer where it had run proper a
>> week ago. This time around in the log file in WinBUGS the program stopped
>> at a line which said :
>> save(C:/DOCUME~1/ADMINI~1/**LOCALS~1/Temp/RtmpU3u46p/log.**txt)
>> and did not proceed any further.
>> Can anyone tell me what migh tbe the possible error here?
>>
>
> Although unstated, I guess it was finished and did not close because you
> used bugs(....., debug=TRUE)?
>
> Uwe Ligges
>
>
>> On Mon, Jul 9, 2012 at 7:04 AM, S Ellison <S.El...@lgcgroup.com> wrote:
>>
>>
>>>
>>> -----Original 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
>>>> Files/WinBUGS14//System/Rsrc/**Registry_Rsave.odc', reason
>> Can anyone tell me what migh tbe the possible error here?
>>
>
> Although unstated, I guess it was finished and did not close because you
> used bugs(....., debug=TRUE)?
>
> Uwe Ligges
>
>
>> On Mon, Jul 9, 2012 at 7:04 AM, S Ellison <S.El...@lgcgroup.com> wrote:
>>
>>
>>>
>>> -----Original 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
>>>> 'Permission denied'
>>>>
>>>
>>> This tells you that you do not have operating system permission to create
>>> a file in the program files area referred to.
>>>
>>> 2: In file(con, "wb") :
>>>> cannot open file 'c:/Program
>>>> Files/WinBUGS14//System/Rsrc/**Registry.odc':
>>>>
>>>
>>> This tells you that you do not have operating system permission to create
>>> a file in the program files area referred to.
>>>
>>> 2: In file(con, "wb") :
>>>> cannot open file 'c:/Program
>>>> Permission denied
>>>>
>>>
>>> .. and this tells you you don't have permission to open a file for
>>> writing
>>> (mode 'w' in the same location
>>>
>>> Conclusion; you're trying to write to an area you don;t have permission
>>> to
>>> write to.
>>>
>>> Either change the permissions for that area (insecure) or use a different
>>> file location for temporary files.
>>>
>>> ***********************************************************************
>>>>
>>>
>>> .. and this tells you you don't have permission to open a file for
>>> writing
>>> (mode 'w' in the same location
>>>
>>> Conclusion; you're trying to write to an area you don;t have permission
>>> to
>>> write to.
>>>
>>> Either change the permissions for that area (insecure) or use a different
>>> file location for temporary files.
>>>
>>> This email and any attachments are confidential. Any u...{{dropped:11}}
>>>
>>
>> ______________________________**________________
>>>
>>
>> R-h...@r-project.org mailing list
>> https://stat.ethz.ch/mailman/**listinfo/r-help<https://stat.ethz.ch/mailman/listinfo/r-help>
>> PLEASE do read the posting guide http://www.R-project.org/**
>> posting-guide.html <http://www.R-project.org/posting-guide.html>
>> and provide commented, minimal, self-contained, reproducible code.
>>
>>
>
[[alternative HTML version deleted]]
>>
>>
>
Uwe Ligges
Jul 10, 2012, 1:40:51 PM7/10/12
to PRAGYA SUR, r-h...@r-project.org
On 09.07.2012 19:27, PRAGYA SUR wrote:
> Yes that was the problem. Thank you very much. Can anyone tell me the
> meaning of
> The following object(s) are masked _by_ '.GlobalEnv':
>
> beta
('.GlobalEnv') and one that is probably in some data.frame that was
attached to the search path.
Best,
Uwe Ligges
> i was shown this notification after the results were printed.
>
> On Mon, Jul 9, 2012 at 1:15 PM, Uwe Ligges
> <lig...@statistik.tu-dortmund.de
> <mailto:lig...@statistik.tu-dortmund.de>> wrote:
>
>
>
> On 09.07.2012 18:19, PRAGYA SUR wrote:
>
> I ran the same program in a different computer where it had run
> proper a
> week ago. This time around in the log file in WinBUGS the
> program stopped
> at a line which said :
> save(C:/DOCUME~1/ADMINI~1/__LOCALS~1/Temp/RtmpU3u46p/log.__odc)
>
>
>
> On 09.07.2012 18:19, PRAGYA SUR wrote:
>
> I ran the same program in a different computer where it had run
> proper a
> week ago. This time around in the log file in WinBUGS the
> program stopped
> at a line which said :
> save(C:/DOCUME~1/ADMINI~1/__LOCALS~1/Temp/RtmpU3u46p/log.__txt)
> and did not proceed any further.
> Can anyone tell me what migh tbe the possible error here?
>
>
> Although unstated, I guess it was finished and did not close because
> you used bugs(....., debug=TRUE)?
>
> Uwe Ligges
>
>
> On Mon, Jul 9, 2012 at 7:04 AM, S Ellison
> <S.El...@lgcgroup.com <mailto:S.El...@lgcgroup.com>> wrote:
>
>
>
> -----Original 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
> Files/WinBUGS14//System/Rsrc/__Registry_Rsave.odc', reason
> Can anyone tell me what migh tbe the possible error here?
>
>
> Although unstated, I guess it was finished and did not close because
> you used bugs(....., debug=TRUE)?
>
> Uwe Ligges
>
>
> On Mon, Jul 9, 2012 at 7:04 AM, S Ellison
> <S.El...@lgcgroup.com <mailto:S.El...@lgcgroup.com>> wrote:
>
>
>
> -----Original 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
> 'Permission denied'
>
>
> This tells you that you do not have operating system
> permission to create
> a file in the program files area referred to.
>
> 2: In file(con, "wb") :
> cannot open file 'c:/Program
> Files/WinBUGS14//System/Rsrc/__Registry.odc':
>
>
> This tells you that you do not have operating system
> permission to create
> a file in the program files area referred to.
>
> 2: In file(con, "wb") :
> cannot open file 'c:/Program
> Permission denied
>
>
> .. and this tells you you don't have permission to open a
> file for writing
> (mode 'w' in the same location
>
> Conclusion; you're trying to write to an area you don;t have
> permission to
> write to.
>
> Either change the permissions for that area (insecure) or
> use a different
> file location for temporary files.
>
> ******************************__******************************__*******
>
>
> .. and this tells you you don't have permission to open a
> file for writing
> (mode 'w' in the same location
>
> Conclusion; you're trying to write to an area you don;t have
> permission to
> write to.
>
> Either change the permissions for that area (insecure) or
> use a different
> file location for temporary files.
>
> This email and any attachments are confidential. Any
> u...{{dropped:11}}
>
>
> ________________________________________________
> u...{{dropped:11}}
>
>
> R-h...@r-project.org <mailto:R-h...@r-project.org> mailing list
> https://stat.ethz.ch/mailman/__listinfo/r-help
> http://www.R-project.org/__posting-guide.html
> <http://www.R-project.org/posting-guide.html>
> and provide commented, minimal, self-contained, reproducible code.
>
>
>
> and provide commented, minimal, self-contained, reproducible code.
>
>
>
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