[R-sig-eco] mixed effect model: compare seed families

[Zoltan Botta-Dukat]

Hi everyone,

I'm struggling with evaluation an experiment for maternal effect and 
plasticity.

We have grown offsprings of 64 individuals (seed families) in a common 
garden experiment. There was 8 replicate plots, in each plot one 
individual from each seed family.
Seeds come from 8 different sites, and 8 seed families collected in each 
site. Sites belong to two groups according to soil type: sand and clay. 
In each site 4 large and 4 small mother plant were chosen.

We would like to test:
- difference between soil types
- difference between mother size categories
- interaction between soil type and mother size
- difference between sites within a soil type (In fact we are interested 
in differences between sites in sand only, because the common garden was 
on sand, and one site is situated in its neighbour).

It is clear that soil_type and mother_size are fix factors.
I suspect that both plot and seed_family should be random factor, but 
I'm not sure what is the correct specification. Maybe 
random=~1|plot/seed_family. It's OK?
Can I include the comparison between sites into this model? Or would be 
better to make a separate analysis using seed families from sand only?

Thanks for the suggestions

Zoltan