[R] glm.nb, anova.negbin

[Prof Brian Ripley]

That's an error in anova.glm: try it with glm rather than glm.nb.

The line in anova.glm like

            fit <- method(x = x[, varseq <= i], y = object$y,

should be

            fit <- method(x = x[, varseq <= i, drop = FALSE], y = object$y,

You are really good at finding long-standing bugs!


On Wed, 26 Sep 2001, juli g. pausas wrote:

> > > I looked quickly, and it seems that this error comes actually from
> > > `anova.glm'  and from the following `get':
> > >
> > >         if (!is.function(method))
> > >             method <- get(method, mode = "function")
> > >
> > > `anova.negbin' sends the  `negbin' `object' to `anova.glm', but the
> > > negbin object does not have a method (`glm' objects have method
> > > "glm.fit"). There seem to be some other differences in `negbin' and
> > > `glm' objects, so that `anova.glm' can't handle them (e.g., glm.control
> > > object is missing in `negbin' object).
> > >
> > > I would like to help, but I don't have time now (got to mark exams).
> >
> > Yes, that's it: R is incompatible with S.  Although the information
> > is in the saved call, R uses a duplicate copy.  In glm.nb() adding
> >     fit$method <- method
> >     fit$control <- control
> > at the end seems to fix it, but without an example I can reproduce,
> > I cannot of course be sure.
> >
>
> Thank you very much. This fix the problem on my own dataset.
> I have tried to test in other reproducible exemples, following the example by
> Ben Bolker (many thanks!), and it works well. I've only got problems when
> trying to fit -1. I'm not sure if this is because it doen't make sense with
> this dataset or because there is still a bug there (see below). Anyway, my
> main problem is solved now. Many thanks.
>
> t.tax <- rnbinom(200,mu=1,size=1)
> t.var1 <- runif(200)
> t.var2 <- runif(200)
> t.var3 <- runif(200)
> t.var4 <- runif(200)
> t.var5 <- runif(200)
>
> ## ignore warning messages about convergence
> t <- glm.nb(t.tax ~ t.var1)
> t2 <- update(t, .~ .+t.var2)
> t3 <- update(t2, .~ .+t.var3)
> t4 <- update(t3, .~ .+t.var4)
> t5 <- update(t4, .~ .+t.var5)
> t6 <- update(t5, .~ . -1 )
>
>
> anova(t, t2, t3, t4, t5, t6) ## OK
> anova(t5)   ## OK
> summary(t6) ## OK
> anova(t6)   ## error
>
> Error in "names<-.default"(*tmp*, value = c("", "", "", "", "", "", "",  :
>         names attribute must be the same length as the vector
> In addition: Warning message:
> tests made without re-estimating theta in: anova.negbin(t6)
>
>
>
>
> > And that was my main point: if reporting problems *please* report the
> > results of traceback(), and if possible a small reproducible example.
> >
> > --
> > 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 272860 (secr)
> > Oxford OX1 3TG, UK                Fax:  +44 1865 272595
>
> --
> Juli G. Pausas   (Mr)
> Centro de Estudios Ambientales del Mediterraneo (CEAM)
> C/ C.R. Darwin 14, Parc Tecnologic,
> 46980 Paterna, Valencia, SPAIN
> Tel: (+ 34) 96 131 8227; Fax: (+ 34) 96 131 8190
> mailto:juli at ceam.es
> http://www.gva.es/ceam
>
> GCTE Fire Network - http://www.gva.es/ceam/FireNetwork
>
>
>

-- 
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 272860 (secr)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595

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