Odd ANOVA degrees of freedom with ZI component of glmmTMB model
???? The difference in 'Df' between the two components, which appear to have the same fixed-effect model specification, is definitely surprising. ???? It's not surprising that chisq=9.46 with 2 df could have a lower p-value than chisq=9.89 with 3 df; the larger the df (i.e. the larger the difference in the number of parameters/complexity between the two models implicitly being compared), the more dispersed the null distribution of the deviance difference (=='chisq'). ?? To troubleshoot I would look at the guts of glmmTMB:::Anova.glmmTMB and see what's going on. I'm not claiming that will be obvious: if you can post a *reproducible* example to the glmmTMB issues list I'd be happy to take a look.
On 2023-01-11 12:14 PM, Elliot Johnston wrote:
Hi all,
I am using the car package to run ANOVAs (type II Wald chi square tests) on
the following model:
m1 <- glmmTMB(Count ~ Time_Period*Assignment + (1|Region/Site_ID),
ziformula = ~ Time_Period*Assignment + (1|Region/Site_ID),
data = allbirds, family = poisson)
Time Period has three levels and Assignment has two levels. When running
the ANOVA on the conditional component -- car::Anova(m1, component =
"cond") -- the degrees of freedom in the output is as I would expected
(n-1):
Chisq Df Pr(>Chisq)
Time_Period 0.9105 2 0.63429
Assignment 2.1043 1 0.14689
Time_Period:Assignment 6.8486 2 0.03257 *
But when I run the ANOVA for the zero-inflated component -- car::Anova(m1,
component = "zi") -- the output looks strange:
Chisq Df Pr(>Chisq)
Time_Period 9.8876 3 0.019546 *
Assignment 9.4648 2 0.008805 **
Time_Period:Assignment 7.9605 2 0.018681 *
Why would the degrees of freedom change? FWIW this df discrepancy between
the conditional and ZI ANOVAs does *not* happen when running the above
glmmTMB model with subsetted data frames based on different bird guilds. It
also seems strange that between the Time Period and Assignment terms the
smaller chi square value leads to greater statistical significance. Do you
agree that something seems wrong here or am I misunderstanding what is
going on under the hood? Any ideas on how to troubleshoot?
Thank you!
-Elliot
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