to answer your first question, it would be wasteful to discard data but if there's some reason for using the first obs for each patient you can reduce the data set using "proc sort data=data nodupkey; by patient; run;" you're right, however, with your second post, ie you likely want to use the repeated values for each patient. We would need to know more about the design of the study, eg the order the treatments were received, what exactly the outcome is etc. A cross over design is not uncommon and is maybe analogous. You can likely find SAS code examples online for a binary outcome. Note that you would not use proc logistic, in that case. Maybe you use proc nlmixed or genmod: https://support.sas.com/documentation/cdl/en/statug/63033/HTML/default/viewer.htm#statug_intromix_a0000000216.htm
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