ANOVAN: How to use MSE of nested factor to calculate F stat for the nesting factor?
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Im using anovan for a model with multiple factors and multiple levels of nesting (all effects are fixed). The anovan function uses MSE of the error term to calculate the F statistic for all the factors in the model. Since the MSE is very small this leads to inflated F values. I would like instead to use MS of the nested factor as the denominator for the nesting factor. For instance, if A is the nesting factor, and B is the nested factor, I would like to use MSA/MSB to calculate F for A, instead of MSA/MSE. Is there a way to this other than manually?
Thank you
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