I am running this code: PROC GEE DATA=test DESCENDING ; CLASS id testcat(desc ref='0') fiscal_yr; MODEL ldl_lt100(REF='1')=testcat fiscal_yr /DIST=MULTINOMIAL LINK=GLOGIT TYPE3; REPEATED SUB=id/WITHIN=fiscal_yr; LSMEANS testcat/ILINK ODDSRATIO DIFF CL; RUN; My outcome is 0, 1 or 2. I want the reference group to be 1. Currently, the LSMEANS is showing this in the LSMEANS differences table: Table 1: ldl_lt100 testcat _testcat 2 2 1 2 2 0 2 1 0 1 2 1 1 2 0 1 1 0 However, I want: Table 2: ldl_lt100 testcat _testcat 2 2 1 2 2 0 2 1 0 0 2 1 0 2 0 0 1 0 The weird/interesting thing here is that I get the output I want (Table 2) in the unadjusted model, but as soon as I add covariates, it shows Table 1.
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