[R] 2 way ANOVA with possible pseudoreplication

[nat_h]

Hi,

I have an experiment with 2 independant factors which I have been trying to
analyse in R. The problem is that there are several data points recorded on
the same animal. However, no combination of treatments  is repeated on the
same animal. All possible combinations of treatments are done in a random
order with as many points as possible being done on 1 animal before moving
onto the next.

The suggested way to remove pseudoreplication is to average the points from
the same animal. However, as my measures on the same animal are of different
treatment combinations so this makes no sense. It is also suggested that as
I have random and fixed effects I should use a mixed effects model. However,
given that my independant variables are factorial I am not sure how to
incorporate this. I would be very grateful for any advice on methods of
getting round this problem or whether I have sufficiently accounted from my
none independant measures experimentally. 

Many thanks,

Natalie
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