[R-sig-ME] Odd ANOVA degrees of freedom with ZI component of glmmTMB model

[John Fox]

Dear Elliot and Ben,

Yes, something definitely seems wrong here, and as usual a reproducible 
example would help. Given that, and as soon as I have some time, I'll 
try to see what went wrong, but I won't be able to do that this week.

My apologies for the problem,
  John

John Fox, Professor Emeritus
McMaster University
Hamilton, Ontario, Canada
web: https://socialsciences.mcmaster.ca/jfox/

On 2023-01-11 1:12 p.m., Ben Bolker wrote:
>       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
>>
>>     [[alternative HTML version deleted]]
>>
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