I am running a GEE to test the effect of an ordinal and a nominal independent factor on an ordinal dependent variable. The GEE will use one of each factors conditions as the reference value. For the ordinal value it makes sense to select a descending ordering. However I am not sure how the reference category is determined for the nominal factor. Is it based on the size of the effect ? Is it based on the order in which it appears in the data set? Can you self select the reference category?
Thanks in advance.