[R] new to repeated measures anova in R

[John Fox]

Dear Peter,

On Mon, 5 Mar 2012 17:28:32 +0100
 peter dalgaard <pdalgd at gmail.com> wrote:
> 
> On Mar 5, 2012, at 16:05 , Tamre Cardoso wrote:
> 
> > Thank you.
> > 
> > I have attached the data:
> 
> The list software seems to have scrubbed it though...
> 
> > The error message from Anova is:  
> > 
> >> pressure.aov = Anova(multmodel, idata=fact.idata, idesign = ~Shoe * Region, type="III")
> > Error in linearHypothesis.mlm(mod, hyp.matrix, SSPE = SSPE, idata = idata,  : 
> >  The error SSP matrix is apparently of deficient rank = 9 < 14
> 
> Oho. Yes that can be a problem. I it is not actually required to have a full rank SSP to do the F tests, but the design of Anova() is such that it tries to do multivariate analyses somewhere along the way, and I don't think there's a way to tell it not to (John?). 
> 

Yes, that's right: Anova() starts with the multivariate repeated-measures analysis and derives the univariate tests from that. When I have a chance, I'll take a look to see whether I can change that, reporting the error only when the MANOVA is requested.

Best,
 John

> I don't think plain anova.mlm has this particular restriction. It's basically the same issue as this:
> 
> > X <- matrix(rnorm(12),3,4)
> > idata <- data.frame(gg = factor(1:4))
> > anova(m,idata=idata, X=~1, test="Spherical")
> Analysis of Variance Table
> 
> 
> Contrasts orthogonal to
> ~1
> 
> Greenhouse-Geisser epsilon: 0.4312
> Huynh-Feldt epsilon:        0.8876
> 
>             Df      F num Df den Df  Pr(>F)  G-G Pr  H-F Pr
> (Intercept)  1 0.3376      3      6 0.79935 0.66045 0.77968
> Residuals    2                                             
> > Anova(m,idata=idata, idesign=~gg, type="III")
> Error in linearHypothesis.mlm(mod, hyp.matrix, SSPE = SSPE, idata = idata,  : 
>   The error SSP matrix is apparently of deficient rank = 2 < 3
> > anova(m,idata=idata, X=~1) # Full MV test fails here too
> Error in anova.mlm(m, idata = idata, X = ~1) : residuals have rank 2 < 3
> 
> 
> -- 
> Peter Dalgaard, Professor
> Center for Statistics, Copenhagen Business School
> Solbjerg Plads 3, 2000 Frederiksberg, Denmark
> Phone: (+45)38153501
> Email: pd.mes at cbs.dk  Priv: PDalgd at gmail.com
> 
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