Thanks for the quick response, and the simulation! Once the model is developed I intended to use PLM to make predictions under multiple scenarios where the term A is varied and then assess the difference in the exceedence frequency for each scenario using a cutpoint value. So for instance, if the cutpoint for identifying an exceedence is 0.50, then for row 239 the BLUP value is greater than 0.50 while the NOBLUP value is less than 0.50. In my case this makes a fairly substantial difference but now I am thinking that this means I should probably specify D as a fixed effect even though the overall objective is to evaluate the effects of A. ... View more

Thank you for your response. I did run the "manual" method and it is not really more computationally intensive so that's great. This work is for a client so I'm not able to post the graphics but a generalized version of the code is below where A and B are continuous and C is categorical and there are two interaction terms and a random intercepts term for D. The PLM predictions correspond to the PRED(ILINK NOBLUP), not the PRED(ILINK) . If I use the missing value trick, the random intercepts are incorporated. Perhaps I'm missing an option in PLM . I'm sure it's complicated to include the random effects unless you assume they are essentially fixed which I guess is what is happening when you score using the missing value trick? Thanks. PROC GLIMMIX DATA=LOGIT PLOTS = ALL ; CLASS C D; MODEL MARK(EVENT='1') = A B C A*B B*C / LINK=LOGIT DIST=BINARY SOLUTION; RANDOM INT / SUBJECT = D; OUTPUT OUT=D.TRANSECT_GLIMMIX PRED(ILINK)=PREDPROB PRED(ILINK NOBLUP)=FIX_PREDPROB; STORE D.TEST_PLM; RUN; PROC PLM RESTORE=D.TEST_PLM; SCORE DATA=D.TRANSECT_GLIMMIX OUT=D.SCORE_IT PREDICTED UCLM LCLM / ILINK; RUN; ... View more

I just noticed the same issue with PLM using Glimmix for a logistic model with  random intercepts. Even if i take the dataset output from the original model and then score it using the plm procedure i get different predicted values (thankfully i plotted both).  Is there another option besides the manual approach.I have several simulated datasets i need to score.  Seems like it should generate a warning in the log at least? ... View more