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The statement: "fixed-effect model matrix is rank deficient so dropping 1 column / coefficient" is not a side note. It means that you haven't properly set up your model to work with your data. Some one of your fixed effects is a linear combination of your other fixed effects. You say: In the case of the brain Region variable, this [reference] ...


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The answers at Proportion of explained variance in a mixed-effects model cite many sources which should give you abundant technical information on this question. I’ll add a few points for context. First, many have struggled with this question. Commonly cited sources such as the textbooks by Singer & Willett and by Fitzmaurice, Laird & Ware ...


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