[R] Error when using polr() in MASS

[Tord Snall]

Dear Prof. Ripley,

Thanks for your replies! 

I just want to add this below, which might be helpful to others who get a
similar problem in the future.

Tord


> skuggor<- dat[!is.na(dat$skugg), ] 
> skugg.cpy1<- subset(skuggor, cpy==1)
> skugg.cpy1.dat<- as.data.frame(table(skugg.cpy1$skugg, skugg.cpy1$grupp))
> names(skugg.cpy1.dat)<- c("skugg", "grupp", "frekv")
> skugg.cpy1.dat<- subset(skugg.cpy1.dat, grupp == "gr3" | grupp == "gr5")
> skugg.cpy1.dat
   skugg grupp frekv
4      1   gr3     0
5      2   gr3     3
6      3   gr3     6
10     1   gr5     1
11     2   gr5    12
12     3   gr5     1
> summary(polr(as.ordered(skugg) ~ as.factor(grupp),
weights=as.numeric(frekv), data= as.data.frame(skugg.cpy1.dat)))
Error in optim(start, fmin, gmin, method = "BFGS", hessian = Hess, ...) : 
        non-finite value supplied by optim

I guess it is a matter of data format It seem to be, because the following
works:

> 
> s<- skugg.cpy1.dat[,1]
> g<- skugg.cpy1.dat[,2]
> f<- skugg.cpy1.dat[,3]
> sgf<- as.data.frame(cbind(s,g,f))
> sgf
  s g  f
1 1 2  0
2 2 2  3
3 3 2  6
4 1 4  1
5 2 4 12
6 3 4  1
> summary(polr(as.ordered(s) ~ as.factor(g), weights=as.numeric(f), data=
sgf))

Re-fitting to get Hessian

Call:
polr(formula = as.ordered(s) ~ as.factor(g), data = sgf, weights =
as.numeric(f))

Coefficients:
     Value Std. Error    t value 
 -3.287802   1.252344  -2.625318 

Intercepts:
    Value   Std. Error t value
1|2 -5.8783  1.5565    -3.7765
2|3 -0.6973  0.7062    -0.9875

Residual Deviance: 25.76504 
AIC: 31.76504 




>
>That example works here (once I make skugg an ordered factor):
>
>Call:
>polr(formula = skugg ~ grupp, data = dat, weights = frekv)
>
>Coefficients:
>     Value Std. Error    t value 
> -3.287802   1.252344  -2.625318 
>
>Intercepts:
>    Value   Std. Error t value
>1|2 -5.8783  1.5565    -3.7765
>2|3 -0.6973  0.7062    -0.9875
>
>Residual Deviance: 25.76504 
>AIC: 31.76504 
>
>BTW, there is no point in including points with zero weight.
>
>
>On Wed, 22 Jan 2003, Tord Snall wrote:
>
>> Dear all,
>> 
>> I get an error message when I use polr() in MASS. These are my data:
>> 
>>    skugg grupp frekv
>> 4      1   gr3     0
>> 5      2   gr3     3
>> 6      3   gr3     6
>> 10     1   gr5     1
>> 11     2   gr5    12
>> 12     3   gr5     1
>> > 
>> > summary(polr(skugg ~ grupp, weights=frekv, data= skugg.cpy1.dat))
>> Error in optim(start, fmin, gmin, method = "BFGS", hessian = Hess, ...) : 
>>         non-finite value supplied by optim
>> 
>> Does this depend on the very few observations in skugg 1 - the
>> proportional-odds assumption doesn't hold (p 231, MASS 3ed)? If so, I would
>> be happy for a recommendation on another approach.
>> 
>> And I also have a similar data set where only the skugg classes 2 and 3 are
>> observed. Would you recommend glm, family= binomial for that analysis?
>> 
>> I use R 1.6.2, MASS 7.0-10, Win 2000. 
>> 
>> 
>> Thanks in advance!
>> 
>> Please reply also to me because I'm on the once a day-list
>> 
>> 
>> Sincerely,
>> Tord
>> 
>> -----------------------------------------------------------------------
>> Tord Snäll
>> Avd. f växtekologi, Evolutionsbiologiskt centrum, Uppsala universitet
>> Dept. of Plant Ecology, Evolutionary Biology Centre, Uppsala University
>> Villavägen 14			
>> SE-752 36 Uppsala, Sweden
>> Tel: 018-471 28 82 (int +46 18 471 28 82) (work)
>> Tel: 018-25 71 33 (int +46 18 25 71 33) (home)
>> Fax: 018-55 34 19 (int +46 18 55 34 19) (work)
>> E-mail: Tord.Snall at ebc.uu.se
>> Check this: http://www.vaxtbio.uu.se/resfold/snall.htm!
>> ------------------------------------------------------------------------
>> 
>> ______________________________________________
>> R-help at stat.math.ethz.ch mailing list
>> http://www.stat.math.ethz.ch/mailman/listinfo/r-help
>> 
>
>-- 
>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
>
>

-----------------------------------------------------------------------
Tord Snäll
Avd. f växtekologi, Evolutionsbiologiskt centrum, Uppsala universitet
Dept. of Plant Ecology, Evolutionary Biology Centre, Uppsala University
Villavägen 14			
SE-752 36 Uppsala, Sweden
Tel: 018-471 28 82 (int +46 18 471 28 82) (work)
Tel: 018-25 71 33 (int +46 18 25 71 33) (home)
Fax: 018-55 34 19 (int +46 18 55 34 19) (work)
E-mail: Tord.Snall at ebc.uu.se
Check this: http://www.vaxtbio.uu.se/resfold/snall.htm!
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