[R] Linear mixed effects model ?

Dieter Menne dieter.menne at menne-biomed.de
Tue Oct 6 17:26:20 CEST 2009

Daniel Perkins wrote:
> Ideally we would do an ANCOVA to test for differences in slope or 
> intercepts for the different streams. However as there were repeated 
> measures and unequal n and unbalanced design, I have used a linear mixed 
> effect model (from nlme package in R) in the form:
> model <- lme (Rate ~ Temp* Stream, random = ~ Time|Replicate)

This should rather be

model <- lme (Rate ~ Temp* Stream, random = ~ 1|Time/Replicate)

Always start your model with the more parsimonious "equal slopes" assumption
denoted by 1|. When you place the Time variable as you did, it estimates
separate slopes for Time, which could be ill conditioned.


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