Recommended tests and confidence intervals for paired binomial proportions

We describe, evaluate, and recommend statistical methods for the analysis of paired binomial proportions. A total of 24 methods are considered. The best tests for association include the asymptotic McNemar test and the McNemar mid-p test. For the difference between proportions, we recommend two simple confidence intervals with closed-form expressions and the asymptotic score interval. The asymptotic score interval is also recommended for the ratio of proportions, as is an interval with closed-form expression based on combining two Wilson score intervals for the single proportion. For the odds ratio, we recommend a transformation of the Wilson score interval and a transformation of the Clopper-Pearson mid-p interval. We illustrate the practical application of the methods using data from a recently published study of airway reactivity in children before and after stem cell transplantation and a matched case-control study of the association between floppy eyelid syndrome and obstructive sleep apnea-hypopnea syndrome. Copyright (C) 2014 John Wiley & Sons, Ltd.