How to get Greenhouse-Geisser epsilons from anova?

Dear Nils,

-----Original Message-----
From: Skotara [mailto:nils.skotara at uni-hamburg.de]
Sent: December-09-08 12:21 PM
To: John Fox
Cc: 'Peter Dalgaard'; r-help at 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.