As indicated in the codes, the predicted probabilities were calculated using LSmeans/ilink.   Thanks,   Yinghui ... View more

Thank you so much. This is very helpful. ... View more

If you fit a model with a covariate equal to the response variable, odd things can happen, mostly because you are fitting some sort of adjusted response - essentially the response being fit is now equal to response_variable - response_variable * beta_hat, where beta_hat reflects a slope estimate. Since your means are relatively close, I suspect beta_hat is near, but not equal to, zero.   SteveDenham ... View more

StatDave codes work well. You don't need dummy variables. Especially dummy variable for treatment and time interaction term will not work. ... View more