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