R help - Apr 2013 - R crash

I have a generalized linear model to solve. I used package "geepack".
When
I use the correlation structure "unstructured", I get a messeage that-
R
GUI front-end has stopped working. Why this happens? What is the solution?
The r codes are as follows:
a<-read.table("d:/bmt.txt",header=T")
cutoffs<-c(1.75,3.34,5.09,6.93,9.11,11.8,15.3,20.1,23.7,27.3,30.9,34.3,37.6,41.5,46.5,51.1,57,63,73.1,93.68)
a$icr <- REL
library(pseudo)
pseudo <- pseudoci(time=a$TIME,event=a$icr,tmax=cutoffs)

#rearranging data
b <- NULL
 for(it in 1:length(pseudo$time)){
 b <- rbind(b,cbind(a,pseudo = pseudo$pseudo[[1]][,it],
 tpseudo = pseudo$time[it],id=1:nrow(a)))
 }
 b <- b[order(b$id),]


 library(geepack)

fit3 <-  geese(pseudo ~ as.factor(AGE) + as.factor(WEIGHT) +
as.factor(HEIGHT) ,
data =b, id=id, jack = TRUE, scale.fix=TRUE,
mean.link = "logit", corstr="unstructured")

#The results using the AJ variance estimate
cbind(mean = round(fit3$beta,4), SD = round(sqrt(diag(fit3$vbeta.ajs)),4),
Z = round(fit3$beta/sqrt(diag(fit3$vbeta.ajs)),4),
PVal = round(2-2*pnorm(abs(fit3$beta/sqrt(diag(fit3$vbeta.ajs)))),4))

	[[alternative HTML version deleted]]

On 13-04-09 2:41 PM, Tasnuva Tabassum wrote:
> I have a generalized linear model to solve. I used package
"geepack". When
> I use the correlation structure "unstructured", I get a messeage
that- R
> GUI front-end has stopped working. Why this happens? What is the solution?
Presumably geepack has a bug.  You should simplify your example as much 
as you can and send it to the maintainer of that package.

Duncan Murdoch
> The r codes are as follows:
> a<-read.table("d:/bmt.txt",header=T")
>
cutoffs<-c(1.75,3.34,5.09,6.93,9.11,11.8,15.3,20.1,23.7,27.3,30.9,34.3,37.6,41.5,46.5,51.1,57,63,73.1,93.68)
> a$icr <- REL
> library(pseudo)
> pseudo <- pseudoci(time=a$TIME,event=a$icr,tmax=cutoffs)
>
> #rearranging data
> b <- NULL
>   for(it in 1:length(pseudo$time)){
>   b <- rbind(b,cbind(a,pseudo = pseudo$pseudo[[1]][,it],
>   tpseudo = pseudo$time[it],id=1:nrow(a)))
>   }
>   b <- b[order(b$id),]
>
>
>   library(geepack)
>
> fit3 <-  geese(pseudo ~ as.factor(AGE) + as.factor(WEIGHT) +
> as.factor(HEIGHT) ,
> data =b, id=id, jack = TRUE, scale.fix=TRUE,
> mean.link = "logit", corstr="unstructured")
>
> #The results using the AJ variance estimate
> cbind(mean = round(fit3$beta,4), SD = round(sqrt(diag(fit3$vbeta.ajs)),4),
> Z = round(fit3$beta/sqrt(diag(fit3$vbeta.ajs)),4),
> PVal = round(2-2*pnorm(abs(fit3$beta/sqrt(diag(fit3$vbeta.ajs)))),4))
>
> 	[[alternative HTML version deleted]]
>
> ______________________________________________
> R-help at 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.
>

Have a look at the warning in ?geepack::geeglm It should be mentioned in
?geepack::geese as well.

ir. Thierry Onkelinx
Instituut voor natuur- en bosonderzoek / Research Institute for Nature and
Forest
team Biometrie & Kwaliteitszorg / team Biometrics & Quality Assurance
Kliniekstraat 25
1070 Anderlecht
Belgium
+ 32 2 525 02 51
+ 32 54 43 61 85
Thierry.Onkelinx at inbo.be
www.inbo.be

To call in the statistician after the experiment is done may be no more than
asking him to perform a post-mortem examination: he may be able to say what the
experiment died of.
~ Sir Ronald Aylmer Fisher

The plural of anecdote is not data.
~ Roger Brinner

The combination of some data and an aching desire for an answer does not ensure
that a reasonable answer can be extracted from a given body of data.
~ John Tukey

-----Oorspronkelijk bericht-----
Van: r-help-bounces at r-project.org [mailto:r-help-bounces at r-project.org]
Namens Tasnuva Tabassum
Verzonden: dinsdag 9 april 2013 20:41
Aan: R help
Onderwerp: [R] R crash

I have a generalized linear model to solve. I used package "geepack".
When I use the correlation structure "unstructured", I get a messeage
that- R GUI front-end has stopped working. Why this happens? What is the
solution?
The r codes are as follows:
a<-read.table("d:/bmt.txt",header=T")
cutoffs<-c(1.75,3.34,5.09,6.93,9.11,11.8,15.3,20.1,23.7,27.3,30.9,34.3,37.6,41.5,46.5,51.1,57,63,73.1,93.68)
a$icr <- REL
library(pseudo)
pseudo <- pseudoci(time=a$TIME,event=a$icr,tmax=cutoffs)

#rearranging data
b <- NULL
 for(it in 1:length(pseudo$time)){
 b <- rbind(b,cbind(a,pseudo = pseudo$pseudo[[1]][,it],  tpseudo =
pseudo$time[it],id=1:nrow(a)))  }  b <- b[order(b$id),]


 library(geepack)

fit3 <-  geese(pseudo ~ as.factor(AGE) + as.factor(WEIGHT) +
as.factor(HEIGHT) ,
data =b, id=id, jack = TRUE, scale.fix=TRUE, mean.link = "logit",
corstr="unstructured")

#The results using the AJ variance estimate cbind(mean = round(fit3$beta,4), SD
= round(sqrt(diag(fit3$vbeta.ajs)),4),
Z = round(fit3$beta/sqrt(diag(fit3$vbeta.ajs)),4),
PVal = round(2-2*pnorm(abs(fit3$beta/sqrt(diag(fit3$vbeta.ajs)))),4))

        [[alternative HTML version deleted]]

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and provide commented, minimal, self-contained, reproducible code.
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