# Assessing non-inferiority for binary matched-pairs data with missing values: a powerful and flexible GEE approach based on the risk difference

## TL;DR

This paper introduces a new GEE method for analyzing non-inferiority in clinical studies with missing data, offering higher power and flexibility.

## Contribution

A novel GEE approach for non-inferiority testing with binary matched-pairs data that handles missing values and improves statistical power.

## Key findings

- The proposed GEE method performs similarly to existing methods for complete data in moderate to large samples.
- It provides higher power and narrower confidence intervals when data are missing at random.
- The method reduces required sample size compared to alternatives in observational studies.

## Abstract

Clinical studies often aim to test the non-inferiority of a treatment compared to an alternative intervention with binary matched-pairs data. These studies are often planned with methods for completely observed pairs only. However, if missingness is more frequent than expected or is anticipated in the planning phase, methods are needed that allow the inclusion of partially observed pairs to improve statistical power.

We propose a flexible generalized estimating equations (GEE) approach to estimate confidence intervals for the risk difference, which accommodates partially observed pairs. Using simulated data, we compare this approach to alternative methods for completely observed pairs only and to those that also include pairs with missing observations. Additionally, we reconsider the study sample size calculation by applying these methods to a study with binary matched-pairs setting.

In moderate to large sample sizes, the proposed GEE approach performs similarly to alternative methods for completely observed pairs only. It even results in a higher power and narrower interval widths in scenarios with missing data and where missingness follows a missing (completely) at random (MCAR / MAR) mechanism. The GEE approach is also non-inferior to alternative methods, such as multiple imputation or confidence intervals explicitly developed for missing data settings. Reconsidering the sample size calculation for an observational study, our proposed approach leads to a considerably smaller sample size than the alternative methods.

Our results indicate that the proposed GEE approach is a powerful alternative to existing methods and can be used for testing non-inferiority, even if the initial sample size calculation was based on a different statistical method. Furthermore, it increases the analytical flexibility by allowing the inclusion of additional covariates, in contrast to other methods.

The online version contains supplementary material available at 10.1186/s12874-025-02497-2.