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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