HI, DOUG & JOSE:
Is there some reason that "anova.lme" should NOT accept an object of class "glmmPQL" in the example below? If you don't see one either, then I suggest you consider modifying the code as described below.
I don't think that would be appropriate. AFAIK the logLik generic applied to a glmmPQL object does not return the likelihood of the fitted model or an approximation to that likelihood.
That's why there is a difference between the values of the likelihood for the same model fit by glmmPQL and fit using the PQL method in GLMM from the lme4 package.
I will add anova methods for GLMM objects whenever I manage to dig myself out of the current rewrite of the representation of linear mixed-effects models.
HI, ANDREW:
I couldn't find your data "learning" in my Windows installation of R 2.0.0pat, which meant that I had to take the time to find another example before I could get the error message you described. I got it from modifying the example in the documentation for "glmmPQL" as follows:
fit1 <- glmmPQL(y ~ trt, random = ~ 1 | ID,
family = binomial, data = bacteria)
fit2 <- glmmPQL(y ~ trt + I(week > 2), random = ~ 1 | ID,
family = binomial, data = bacteria)
anova(fit1, fit2)
Error in anova.lme(fit1, fit2) : Objects must inherit from classes "gls", "gnls" "lm","lmList", "lme","nlme","nlsList", or "nls"
I then checked the class of fit1 and fit2: > class(fit1)
[1] "glmmPQL" "lme" > class(fit2)
[1] "glmmPQL" "lme" As an experiment, I changed the class of fit1 and fit2: > class(fit1) <- "lme"
> class(fit2) <- "lme"
> anova(fit1, fit2)
Model df AIC BIC logLik Test L.Ratio p-value
fit1 1 5 1054.623 1071.592 -522.3117 fit2 2 6 1113.622 1133.984 -550.8111 1 vs 2 56.99884 <.0001
Unless someone like Doug or Jose tells us, "Don't do that", I would use these answers.
I looked briefly at the code for "anova.lme", and it looks to me like "glmmPQL" could be added to the list of allowed options in the following test roughly half way through the code:
if (!all(match(termsClass, c("gls", "gnls", "lm", "lmList",
"lme", "nlme", "nlsList", "nls"), 0))) {
stop(paste("Objects must inherit from classes \"gls\", \"gnls\"",
"\"lm\",\"lmList\", \"lme\",\"nlme\",\"nlsList\", or \"nls\""))
}
hope this helps. spencer graves
A.J. Rossini wrote:
For better or worse, it's holidays in the states. Very amusing for me being in a non-Thanksgiving celebrating country.
In addition, it's not a problem. The complaint is valid. Probably no one has coded up the right solution yet for comparison.
I can't recall if one would want those statistics for a binomial random effects model, but I do recall some issues with model comparison in that setting, though they are a bit dated (say, 2 years or so).
On Fri, 26 Nov 2004 09:31:40 +0700, Andrew Criswell
<[EMAIL PROTECTED]> wrote:
Hello:
Will someone PLEASE help me with this problem. This is the third time I've posted it.
When I appply anova() to two equations estimated using glmmPQL, I get a complaint,
anova(fm1, fm2)
Error in anova.lme(fm1, fm2) : Objects must inherit from classes "gls", "gnls" "lm","lmList", "lme","nlme","nlsList", or "nls"
The two equations I estimated are these:
fm1 <- glmmPQL(choice ~ day + stereotypy,
+ random = ~ 1 | bear, data = learning, family = binomial)
fm2 <- glmmPQL(choice ~ day + envir + stereotypy,
+ random = ~ 1 | bear, data = learning, family = binomial)
Individually, I get results from anova():
anova(fm1)
numDF denDF F-value p-value (Intercept) 1 2032 7.95709 0.0048 day 1 2032 213.98391 <.0001 stereotypy 1 2032 0.42810 0.5130
anova(fm2)
numDF denDF F-value p-value (Intercept) 1 2031 5.70343 0.0170 day 1 2031 213.21673 <.0001 envir 1 2031 12.50388 0.0004 stereotypy 1 2031 0.27256 0.6017
I did look through the archives but didn't finding anything relevant to
my problem.
Hope someone can help.
ANDREW ____________________________ _ platform i586-mandrake-linux-gnu arch i586 os linux-gnu system i586, linux-gnu status major 2 minor 0.0 year 2004 month 10 day 04 language R
-- Andrew R. Criswell, Ph.D. Graduate School, Bangkok University
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