[R] glm.nb, anova.negbin

[juli g. pausas]

That's solve the problem. Thank you very much.
I think that there is still a minor problem, in the display of the results only.
When ommiting the intercept, the dispaly in the anova do not show the P(>|Chi|) of
the first var. This is very minor problem but you may like to know it.

t.tax <- rnbinom(200,mu=1,size=1)
t.var1 <- rnorm(200, t.tax, 5)
t.var2 <- runif(200)
t <- glm.nb(t.tax ~ t.var1)
t2 <- update(t, .~ .+t.var2)
t3 <- update(t3, .~ . -1 )
anova(t3)

Analysis of Deviance Table

Model: Negative Binomial(1.3652), link: log

Response: t.tax

Terms added sequentially (first to last)


        Df Deviance Resid. Df Resid. Dev P(>|Chi|)
NULL                      199    205.098
t.var1   0    4.597       199    200.501
t.var2   1    1.534       198    198.967     0.215
t.var3   1    0.055       197    198.912     0.815
Warning messages:
1: tests made without re-estimating theta in: anova.negbin(t3)
2: NaNs produced in: pchisq(q, df, lower.tail, log.p)



Prof Brian Ripley escribió:

> 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

--
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


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