R devel - Jul 2007 - Error while fitting Partial Proportional Odds model using vglm

Dear R developers:

I am trying to fit a PPO model using vglm from the library VGAM, and get an
error while executing the code. Here is the data, code, and error:

Data: first row is the column names. a = age, and 1,2,3, 4 and 5 are
condition grades.

  a  1 2 3  4 5
  1  1 0 0  0 0
  2 84 2 7 10 2
  3 16 0 6  6 2
  4 13 0 3  4 0
  5  0 0 0  1 0

Library(VGAM)

rc13<-read.table("icg_rcPivot_group2.txt",header=F)
names(rc13)<-c("a","1","2","3","4","5")

ppo<-vglm(cbind(rc13[,2],rc13[,3],rc13[,4],rc13[,5],rc13[,6])~a,family
cumulative(link = logit, parallel = F , reverse = F),na.action=na.pass,
data=rc13)
summary(ppo)

I get the following error:

Error in "[<-"(`*tmp*`, , index, value = c(1.13512932539841,
0.533057528200189,  : 
	number of items to replace is not a multiple of replacement length
In addition: Warning messages:
1: NaNs produced in: log(x)
2: fitted values close to 0 or 1 in: tfun(mu = mu, y = y, w = w, res FALSE, eta
= eta, extra)
3: 19 elements replaced by 1.819e-12 in: checkwz(wz, M = M, trace = trace,
wzeps = control$wzepsilon)


Ironically, it works ok with Proportional Odds (change parallel = T above),
but fails with PPO (parallel = F). 

I will appreciate any help to fix this problem.
Thanks

Rizwan Younis
Grad Student
University of Waterloo
Waterloo, ON Canada

Instead of repeatedly posting this message to the R lists, please contact 
the maintainer as the R posting guide asked you to do in the first 
instance.

E.g. you have already sent

https://stat.ethz.ch/pipermail/r-help/2007-July/136488.html
https://stat.ethz.ch/pipermail/r-help/2007-July/136510.html

On Mon, 16 Jul 2007, Rizwan Younis wrote:
> Dear R developers:
>
> I am trying to fit a PPO model using vglm from the library VGAM, and get an
> error while executing the code. Here is the data, code, and error:
>
> Data: first row is the column names. a = age, and 1,2,3, 4 and 5 are
> condition grades.
>
>  a  1 2 3  4 5
>  1  1 0 0  0 0
>  2 84 2 7 10 2
>  3 16 0 6  6 2
>  4 13 0 3  4 0
>  5  0 0 0  1 0
>
> Library(VGAM)
>
> rc13<-read.table("icg_rcPivot_group2.txt",header=F)
>
names(rc13)<-c("a","1","2","3","4","5")
>
> ppo<-vglm(cbind(rc13[,2],rc13[,3],rc13[,4],rc13[,5],rc13[,6])~a,family
> cumulative(link = logit, parallel = F , reverse = F),na.action=na.pass,
> data=rc13)
> summary(ppo)
>
> I get the following error:
>
> Error in "[<-"(`*tmp*`, , index, value = c(1.13512932539841,
> 0.533057528200189,  :
> 	number of items to replace is not a multiple of replacement length
> In addition: Warning messages:
> 1: NaNs produced in: log(x)
> 2: fitted values close to 0 or 1 in: tfun(mu = mu, y = y, w = w, res >
FALSE, eta = eta, extra)
> 3: 19 elements replaced by 1.819e-12 in: checkwz(wz, M = M, trace = trace,
> wzeps = control$wzepsilon)
>
>
> Ironically, it works ok with Proportional Odds (change parallel = T above),
> but fails with PPO (parallel = F).
>
> I will appreciate any help to fix this problem.
> Thanks
>
> Rizwan Younis
> Grad Student
> University of Waterloo
> Waterloo, ON Canada
>
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>
-- 
Brian D. Ripley,                  ripley at stats.ox.ac.uk
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272866 (PA)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595

On Mon, 2007-07-16 at 17:27 -0400, Rizwan Younis wrote:
> Dear R developers:
This is *not* the correct list for help with R or contributed packages
on CRAN, and please do not send your messages repeatedly to any of the
lists - this is at least the 3rd time I've received this request for
help.

If you'd read the posting guide, it would have told you that you should
email the package maintainer (in this case Thomas Yee) for help with a
contributed package. If you must email the R-help list, do so only once.
If you don't get a reply, take the hint that perhaps no-one has an
answer - repeatedly bugging them isn't going to help!

By the looks of things, there is either a problem within VGAM itself
that only Thomas will be able to fix, or you are providing an
argument/data that VGAM was not expecting - there appear to be some
fitting problems also. Check that the data you are providing are what
VGAM expects, and if the problem still persists, email Thomas with a
reproducible example.

G

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