[Rd] summary for negative binomial GLMs (PR#13640)
Ben Bolker
bolker at ufl.edu
Fri Apr 10 15:04:10 CEST 2009
Bump? Does anyone else have an opinion on this one?
cheers
Ben Bolker
Ben Bolker wrote:
>
> <kushler <at> oakland.edu> writes:
>
>>
>> Full_Name: Robert Kushler
>> Version: 2.7.2
>> OS: Windows XP
>> Submission from: (NULL) (69.246.102.98)
>>
>> I believe that the negative binomial family (from MASS) should be
>> added to the
>> list for which dispersion is set to 1.
>
> Could you please clarify? In what procedures, under what
> circumstances? Sounds like you mean l. 573 of glm.R:
>
> if(object$family$family %in% c("poisson", "binomial")) 1
>
> The use case here is using negative.binomial with a fixed
> theta parameter, right? Using glm.nb takes care of this problem
> (it produces an object of class "negbin": MASS:::summary.negbin
> shows that the dispersion gets set to 1 here).
>
> I guess there's a little bit of a jurisdictional
> argument here, since the negative.binomial family is
> in MASS, and summary.glm is in base R ... also, there's
> a bit of a challenge in figuring out the test, because
> object$family$family is not a fixed string for negative
> binomial-family objects (e.g. "Negative Binomial(0.4)"
> in the example below) -- I'm not sure of the cleanest
> way to detect this case.
>
> I think I agree with you, but it would help to present
> your case in more detail ...
>
> Ben Bolker
>
> ====================
> Example:
>
> x <- rep(seq(0,23,by=1),50)
> s <- rep(seq(1,2,length=50*24),1)
>
> tmp2 <- data.frame(y=rnbinom(length(s),
> mu=8*(sin(2*pi*x/24)+2),size = 0.4),x=factor(x),s=s)
>
> library(MASS)
> tmp.glm.nb2 <- glm.nb(y~factor(x)-1 +offset(log(s)),data = tmp2)
> summary(tmp.glm.nb2)
> ## summary.negbin takes care of this case
>
> tmp.glm.nb3 <- glm(y~factor(x)-1 +offset(log(s)),data = tmp2,
> family=negative.binomial(theta=0.4))
>
> summary(tmp.glm.nb3)
>
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>
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