R help - Jun 2007 - ANOVA non-sphericity test and corrections (eg, Greenhouse-Geisser)

I'm an experimental psychologist and when I run ANOVA analysis in
SPSS, I normally ask for a test of non-sphericity (Box's M-test).  I
also ask for output of the corrections for non-sphericity, such as
Greenhouse-Geisser and Huhn-Feldt.  These tests and correction factors
are commonly used in the journals for experimental and other
psychology reports.  I have been switching from SPSS to R for over a
year now, but I realize now that I don't have the non-sphericity test
and correction factors.

The backgroud to this question is that I'm doing a psychophysics
experiment and the data analysis uses an aov model that looks like
this:

roiAOV <- aov( roi ~ (Cue*Hemisphere) + Error(Subject/
(Cue*Hemisphere)), data=roiDataframe)

where Cue is 2 levels (an arrow on a screen that points left or right)
and Hemisphere is 2 levels (brain activity in the left or right
cerebral hemisphere).  There are 8 subjects and they all have one
observation for all levels of Cue * Hemisphere (ie, a within-subjects
design).

I need some functions for calculation of Box's M and the Greenhouse-
Geisser correction factor.  Below is some code example that I have for
the latter, but I don't know how to adapt it so it can take the aov
object.

# BEGIN CODE BLOCK
# see pp. 45-47 of
# http://www.psych.upenn.edu/~baron/rpsych.pdf

# ---
# create some data

x0 <- rnorm(30)
x2 <- rnorm(30)
x4 <- rnorm(30)

data <- cbind(x0,x2,x4)

# n is the number of 'subjects' or rows; while
# k is the number of levels in the factor (columns),
# which is the number of repeated measures
n <- dim(data)[1]
k <- dim(data)[2]

# if k <= 2, the epsilon correction is not required.
# When the data are perfectly spherical, epsilon = 1.
# The minimum value possible for epsilon is

epsi = 1 / (k - 1)

# if epsi == 1 and k == 2, quit now...

# ---
# calculate variance-covariance matrix
# diagonal entries are variance,
# off-diagonal are covariance
S <- var(data)

# ---
# Now estimate Epsilon

D <- k^2 * ( mean(diag(S)) - mean(S) )^2

N1 <- sum(S^2)
N2 <- 2 * k * sum( apply(S,1,mean)^2 )
N3 <- k^2 * mean(S)^2

epsi <- D / ( (k-1) * (N1 - N2 + N3) )

# e is used to modify the degrees of freedom for the
# F test, so we have (k-1) becomes epsi(k-1) and also
# (k - 1)(n - 1) becomes epsi(k - 1)(n - 1).  The new
# p-value for the F statistic is found with the
# pf() function.  For example, if we have
# df1 =  k - 1 = 3 - 1 = 2
# df2 = (k - 1)(n - 1) = (3 - 1)(10 - 1) = 18
# F = 40.719
# then the adjusted 2-tailed p-value is given by:
#

Fvalue <- 40.719
Pepsi <- 2 * (1 - pf(Fvalue, df1=epsi*(k-1), df2=epsi*(k-1)*(n-1) ) )

# Huynh-Feldt correction
# The Greenhouse-Geisser epsilon tends to underestimate
# epsilon when epsilon is greater than 0.70 (Stevens, 1990).
# An estimated e=0.96 may be actually 1. Huynh-Feldt
# correction is less conservative. The Huynh-Feldt
# epsilon is calculated from the Greenhouse-Geisser epsilon,

epsiHF <- (n * (k-1) * epsi - 2) / ((k-1) * ((n-1) - (k-1)*epsi))

PepsiHF <- 2 * (1 - pf(Fvalue, df1=epsiHF*(k-1),
df2=epsiHF*(k-1)*(n-1) ) )

# MANOVA (and multivariate tests) may be better if the
# Greenhouse-Geisser and the Huynh-Feldt corrections do not agree,
# which may happen when epsilon drops below 0.70. When epsilon
# drops below 0.40, both the G-G and H-F corrections may indicate
# that the violation of sphericity is affecting the adjusted p-values.
# MANOVA is not always appropriate, though. MANOVA usually requires
# a larger sample size. Maxwell and Delaney (1990, p. 602) suggest
# a rough rule of thumb that the sample size n should be greater
# than k+10.
# END CODE BLOCK

DarrenWeber wrote:
> I'm an experimental psychologist and when I run ANOVA analysis in
> SPSS, I normally ask for a test of non-sphericity (Box's M-test).  I
> also ask for output of the corrections for non-sphericity, such as
> Greenhouse-Geisser and Huhn-Feldt.  These tests and correction factors
> are commonly used in the journals for experimental and other
> psychology reports.  I have been switching from SPSS to R for over a
> year now, but I realize now that I don't have the non-sphericity test
> and correction factors.
>   
This can be done using anova.mlm() and mauchly.test()  which work on 
"mlm" objects, i.e., lm() output where the response is a matrix. There
is no theory, to my knowledge, to support it for general aov() models, 
the catch being that you need to have a within-subject covariance matrix.

Darren,

Further to Peter Dalgaard's help;

Take a look at the example in ---

library(car)
?Anova  # note upper case 'A' 

The example in the Anova help page following the ---

## a multivariate linear model for repeated-measures data
## See ?OBrienKaiser for a description of the data set used in this example

gives a workings for --

## Greenhouse-Geisser and Huynh-Feldt Corrections
##  for Departure from Compound Symmetry

You might find that example helpful.

John