
I don't know if this is what you're looking for but it describes how to do a 2 way repeated measures with R.  You problem may be different and I lack the stats knowledge to know that.  If that's the case I apoligize:

http://rtutorialseries.blogspot.com/2011/02/r-tutorial-series-two-way-repeated.html
 
Tyler
 
From: tintin_jb@hotmail.com
To: r-help@r-project.org
Date: Tue, 22 Mar 2011 15:56:27 +0100
Subject: [R] Looking for a repeated measure two groups comparison and a two factor ANOVA in Circular distribution

 
Hi,
I am looking for a way to study some phase data with a circular distribution measured in rad.I would like to do a two way ANOVA (if possible mixed, with inter and intrasubject).I haven´t found a package that does that in R?Does sombeody know if there is one or how to do the analysis.Thanks in advance
J ToledoCNDR UPenn 		 	   		  
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