Exact confidence intervals for functions of parameters in the k-sample multinomial problem

When the target of inference is a real-valued function of probability parameters in the k-sample multinomial problem, variance estimation may be challenging. In small samples, methods like the nonparametric bootstrap or delta method may perform poorly. We propose a novel general method in this setting for computing exact p-values and confidence intervals which means that type I error rates are correctly bounded and confidence intervals have at least nominal coverage at all sample sizes. Our method is applicable to any real-valued function of multinomial probabilities, accommodating an arbitrary number of samples with varying category counts. We describe the method and provide an implementation of it in R, with some computational optimization to ensure broad applicability. Simulations demonstrate our method's ability to maintain correct coverage rates in settings where the nonparametric bootstrap fails.