Message-ID: <0216a145-f66e-7bd1-a9c2-72de328d083a@mcmaster.ca>
Date: 2023-01-11T19:51:56Z
From: John Fox
Subject: Odd ANOVA degrees of freedom with ZI component of glmmTMB model
In-Reply-To: <17081_1673460776_30BICtef023863_43865e80-2980-fb8d-4d0c-c7024638c8f6@gmail.com>
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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