[R] mixed effects model:how to include initial conditions

[Christoph Scherber]

Dear R users,

I am analyzing a dataset on growth of plants in response to several 
factors. I am using a mixed-effects model of the following structure:

model<-lme(growth~block*treatment*factor1*factor2,
random=~1|plot/treatment/initialsize)

I have measured the initial size of the plants (in 2003) and thought it 
might be sensible to include this (random) variation into the random 
effects term of the model.

Is that correct? Or should "initialsize" rather be included as a 
covariate into the fixed effects term, as in:

alternative<-lme(growth~block*initialsize*treatment*factor1*factor2,
random=~1|plot/treatment)

I would very much appreciate any suggestions on how to analyze these 
data correctly.

Best regards
Chris.