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

[Douglas Bates]

Christoph Scherber wrote:
> 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.

I think you should include it as a covariate but not in the way you have 
written it.  I would include it as a separate term, not in an interaction

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

I recommend that you look carefully at the number of coefficients that 
you need to estimate in the model as you have specified it and perhaps 
change to an initial model that had more additive effects and fewer 
interactions.