Dear Nils,
> -----Original Message-----
> From: Skotara [mailto:[EMAIL PROTECTED]
> Sent: December-09-08 12:21 PM
> To: John Fox
> Cc: 'Peter Dalgaard'; r-help@r-project.org
> Subject: Re: [R] How to get Greenhouse-Geisser epsilons from anova?
>
> Dear John and Peter,
>
> thank you both very much for your help!
> Everything works fine now!
>
> John, Anova also works very fine. Thank you very much!
> However, if I had more than 2 levels for the between factor the same
> thing as mentioned occured.
> The degrees of freedom showed that Anova calculated it as if all
> subjects came from the same group, for example for main effect A the dfs
> are 1 and 35.
That is odd -- the example that I sent had a factor with 3 levels, producing
2 df; here's a simplified version with s single between-subject factor
(treatment):
> OBrienKaiser$treatment
[1] control control control control control A A A A
[10] B B B B B B B
attr(,"contrasts")
[,1] [,2]
control -2 0
A 1 -1
B 1 1
Levels: control A B
> mod.ok <- lm(cbind(pre.1, pre.2, pre.3, pre.4, pre.5,
+ post.1, post.2, post.3, post.4, post.5,
+ fup.1, fup.2, fup.3, fup.4, fup.5) ~ treatment,
+ data=OBrienKaiser)
> av.ok <- Anova(mod.ok, idata=idata, idesign=~phase*hour)
> summary(av.ok, multivariate=FALSE)
Univariate Type II Repeated-Measures ANOVA Assuming Sphericity
SS num Df Error SS den Df F Pr(>F)
treatment 186.75 2 416.58 13 2.9139 0.090041 .
phase 167.50 2 92.17 26 23.6257 1.419e-06 ***
treatment:phase 77.00 4 92.17 26 5.4304 0.002578 **
hour 106.29 4 72.81 52 18.9769 1.128e-09 ***
treatment:hour 0.89 8 72.81 52 0.0798 0.999597
phase:hour 11.08 8 116.96 104 1.2319 0.287947
treatment:phase:hour 5.96 16 116.96 104 0.3312 0.992574
---
Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
Mauchly Tests for Sphericity
Test statistic p-value
phase 0.85151 0.38119
treatment:phase 0.85151 0.38119
hour 0.09859 0.00194
treatment:hour 0.09859 0.00194
phase:hour 0.00837 0.09038
treatment:phase:hour 0.00837 0.09038
Greenhouse-Geisser and Huynh-Feldt Corrections
for Departure from Sphericity
GG eps Pr(>F[GG])
phase 0.87071 5.665e-06 ***
treatment:phase 0.87071 0.004301 **
hour 0.48867 1.016e-05 ***
treatment:hour 0.48867 0.986835
phase:hour 0.50283 0.308683
treatment:phase:hour 0.50283 0.950677
---
Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
HF eps Pr(>F[HF])
phase 0.99390 1.515e-06 ***
treatment:phase 0.99390 0.002641 **
hour 0.57413 2.190e-06 ***
treatment:hour 0.57413 0.992771
phase:hour 0.75630 0.298926
treatment:phase:hour 0.75630 0.981607
---
Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
I didn't save your earlier postings, so can't check your model and data. If
you like, please feel free to send them to me privately.
Regards,
John
> Since I can get those values using anova that causes no problem.
>
> I saw that the x$G to get the greenhouse-geisser epsilon do work for:
> x<- anova(mlmfitD, X=~C+B, M=~A+C+B, test = "Spherical")
> but does not work for y$G:
> y <- anova(mlmfit, mlmfit0, X= ~C+B, M = ~A+C+B, idata =
> dd,test="Spherical")
>
> Finally, the Greenhouse-Geisser epsilons are identical using both
> methods and to the SPSS output.
> The Huynh-Feldt are not the same as them of SPSS. I will use GG instead.
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