Binary longitudinal data are often collected in clinical trials when intere
st is on assessing the effect of a treatment over time. Our application is
a recent study of opiate addiction that examined the effect of a new treatm
ent on repeated urine tests to assess opiate use over an extended follow-up
. Drug addiction is episodic, and a new treatment may affect various featur
es of the opiate-use process such as the proportion of positive urine tests
over follow-up and the time to the first occurrence of a positive test. Co
mplications in this trial were the large amounts of dropout and intermitten
t missing data and the large number of observations on each subject. We dev
elop a transitional model for longitudinal binary data subject to nonignora
ble missing data and propose an EM algorithm for parameter estimation. We u
se the transitional model to derive summary measures of the opiate-use proc
ess that can be compared across treatment groups to assess treatment effect
. Through analyses and simulations, we show the importance of property acco
unting for the missing data mechanism when assessing the treatment effect i
n our example.