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For example, if you fit sex as an environmental factor, GCTA will fit only one main effect in the model, i. the mean difference between males and females. The levels of each factor can be represented by a single character, word or numerical number. NOTE: the design matrix of the mean in the model (which is a vector of all ones) is always a linear combination of the design matrix of a discrete covariate so that not all the effects of the levels (or classes, e.