Reference-based sensitivity analysis for repeated count outcomes using negative binomial margins and a Gaussian copula
Reference-based multiple imputation is used in longitudinal clinical trials to assess sensitivity to assumptions about outcomes unobserved after intercurrent events. Most existing methods target continuous outcomes and use multivariate normal working models. Scheduled count outcomes require a model that preserves integer support, skewness, overdispersion, longitudinal dependence, and an exposure-based rate interpretation. We propose visit-specific negative binomial (NB) margins linked by a Gaussian copula. Covariate-adjusted log rate models define the margins, while the copula captures longitudinal dependence. For missing outcomes in the active arm after a prespecified event, termed the trigger, assigned arm continuation retains the fitted active arm marginal mean, jump to reference uses the corresponding reference arm marginal mean, and the intermediate rule interpolates between these means on the log rate scale. Combined with the copula, the resulting NB margins determine an imputation distribution conditional on the retained history. We account for discreteness through randomized probability integral transform augmentation and fit the model with a custom Metropolis-within-Gibbs sampler. In targeted simulations, the model recovered the generating marginal and dependence parameters with little bias. In simulations with incomplete data, treatment effect estimates were closest to the corresponding complete data estimates when the imputation rule matched the mechanism governing outcomes after the trigger. We illustrate the method using repeated incontinence episode counts from a published trial in overactive bladder. Estimated rate ratios comparing active treatment with placebo remained below 1 under all reference-based assumptions, with modest attenuation toward the null and the greatest separation between rules at the final visit.