[R] (no subject)

C. Maranto cmaranto at u.washington.edu
Sat Oct 3 00:13:57 CEST 2009


Dear R Community,

I am running GLM's within the "MASS" library.  My data are overdispersed and 
I am accounting for the overdispersion by using an ANOVA 'F' test instead of 
ANOVA 'Chisq'.  You will have to forgive me because I am new at this, but I 
am not sure if R is conducting an ANOVA 'F' test appropriately.  I was 
hoping to explain this using my data results below:

>anova(glm.model,test="F")
Analysis of Deviance Table
Model:binomial,link:logit
Response: ytrips

Terms added squentially (first to last)

                                                    DF            Deviance 
Resid. Df                    Resid. Dev.             F                Pr(>F)
NULL 
125                        1008.55
WaterLevel                                    1                0.14 
124                        1008.42            0.1365        0.7118
RiverFlowObserved                       1                13.34 
123                        995.07              13.3427      0.0002594
WSBacklog                                   1                12.47 
122                        982.61              12.4675      0.0004141
factor(WDEW)                              1                83.13 
121                        899.48              83.1258      <2.2e-16
ChickDays                                     1               157.22 
120                        742.26             157.2225     <2.2e-16
Salmon                                          1                6.91 
119                        735.34              6.9143        0.0085509
factor(Year)                                   3                370.31 
116                        365.03              123.4375    <2.2e-16
WSBacklog:factor(WDEW)          1                9.06 
115                        355.97              9.0644         0.0026063


I think the F-values in the results are over-inflated for an F-test.

For an F-test,

F-observed = (Deviance/Df numerator)/("MSE"=Residual Deviance/Residual Df)

When I calculate F-observed for one of my main effects, such as 
'WSBacklogfactor(WDEW)' above I get:

F-observed = (9.06/1)/(355.97/115)=2.92  NOT 9.0644(as shown in the results 
above)

It seems that the F-test in 'R' is not dividing by the "MSE".

Does anyone have any thoughts on this? Or can let me know where I am going 
wrong?

Thank you!


~Christina




Christina J. Maranto
University of Washington
Department of Zoology
Box 351800
Seattle, WA 98195
(206) 618-2956




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