I am constructing a model matrix for a repeated meassurments experiment with three individuals per group and three treatments per individual.
Gps <- factor(c(1,1,1,2,2,2,3,3,3)) # Groups Tts <- factor(c("A","B","C","B","A","C","C","B","A")) # Treatments
This model matrix makes sense to me, since it estimates the variance within each individual, using the per individual mean of treatment A as the intercept.
However, I often see a matrix like this:
What is the difference between the two model matrices?