A poisson family has dispersion 1 by definition of 'Poisson'. You need a quasipoisson family to use a moment estimate of dispersion.
This difference is described on the help page for anova.glm. Note the estimated dispersion *is* used and *is* one:
summary(glm.D93)$dispersion
[1] 1
as it ought to be (and is in S-PLUS too). That it is not used in S-PLUS is not documented (and it is not used in summary.glm either) and is at least an inconsistency.
Your assumption that R is wrong and S-PLUS (sic) is correct is not appreciated. Why did you file this as an R bug and not an S-PLUS one?
On Wed, 2 Feb 2005 [EMAIL PROTECTED] wrote:
There may be a bug in the anova.glm function.
But not in the one in R!
deathstar[32] R
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counts <- c(18,17,15,20,10,20,25,13,12) outcome <- gl(3,1,9) treatment <- gl(3,3) glm.D93 <- glm(counts ~ outcome + treatment, family=poisson()) anova(glm.D93,test="Chisq")Analysis of Deviance Table
Model: poisson, link: log
Response: counts
Terms added sequentially (first to last)
Df Deviance Resid. Df Resid. Dev P(>|Chi|) NULL 8 10.5814 outcome 2 5.4523 6 5.1291 0.0655 treatment 2 0.0000 4 5.1291 1.0000
anova(glm.D93,test="F")Analysis of Deviance Table
Model: poisson, link: log
Response: counts
Terms added sequentially (first to last)
Df Deviance Resid. Df Resid. Dev F Pr(>F) NULL 8 10.5814 outcome 2 5.4523 6 5.1291 2.7262 0.06547 . treatment 2 0.0000 4 5.1291 0.0000 1.00000 --- Signif. codes: 0 `***' 0.001 `**' 0.01 `*' 0.05 `.' 0.1 ` ' 1
---------------------------------------------------------------------- The F test should use the estimated dispersion parameter, so should be different from the Chisq test. The following is what I got from Splus:
deathstar[31] Splus S-PLUS : Copyright (c) 1988, 2000 MathSoft, Inc. S : Copyright Lucent Technologies, Inc. Version 6.0 Release 1 for Linux 2.2.12 : 2000 Working data will be in /data/home/faculty/yuedong/MySworkcounts <- c(18,17,15,20,10,20,25,13,12) outcome <- factor(rep(1:3,3)) treatment <- factor(rep(1:3,c(3,3,3))) glm.D93 <- glm(counts ~ outcome + treatment, family=poisson()) anova(glm.D93, test="Chisq")Analysis of Deviance Table
Poisson model
Response: counts
Terms added sequentially (first to last) Df Deviance Resid. Df Resid. Dev Pr(Chi) NULL 8 10.58145 outcome 2 5.452305 6 5.12914 0.0654707 treatment 2 0.000000 4 5.12914 1.0000000anova(glm.D93, test="F")Analysis of Deviance Table
Poisson model
Response: counts
Terms added sequentially (first to last) Df Deviance Resid. Df Resid. Dev F Value Pr(F) NULL 8 10.58145 outcome 2 5.452305 6 5.12914 2.108359 0.2369863 treatment 2 0.000000 4 5.12914 0.000000 1.0000000
-------------------------------------------------------------------- Yuedong Wang Phone: (805) 893-4870 Dept of Statistics & Applied Probability Fax: (805) 893-2334 Univ of California [EMAIL PROTECTED] Santa Barbara, CA 93106 http://www.pstat.ucsb.edu/faculty/yuedong
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