We discuss distribution-free exact rank tests from partially ordered data that arise in various biological and other applications where the primary objective is to conduct testing of significance to assess the linear dependence or to compare different groups. The tests here are obtained by treating the usual rank statistics, based on the completely ordered data as “latent” or missing, and conceptualizing the “latent” $p$-value as the random probability under the null hypothesis of a test statistic that is as extreme, or more extreme, than the latent test statistics based on the completely ordered data. The latent $p$-value is then predicted by sampling linear extensions or the complete orderings that are consistent with the observed partially ordered data. The sampling methods explored here include importance sampling methods based on randomized topological sorting algorithms, Gibbs sampling methods, random-walk based Metropolis–Hasting sampling methods and random-walk based modern perfect Markov chain Monte Carlo sampling methods. We discuss running times of these sampling methods and their strength and weaknesses. A simulation experiment and three data examples are given. The simulation experiment illustrates how the exact rank tests from partially ordered data work when the desired result is known. The first data example concerns the light preference behavior of fruit flies and tests whether heterogeneity observed in average light-preference behavior can be explained by manipulations in serotonin signaling. The second one is a reanalysis of the lead absorption data in children of employees who worked in a lead battery factory and consolidates the results reported in Rosenbaum [Ann. Statist. 19 (1991) 1091–1097]. The third one reexamines the breast cosmesis data from Finkelstein [Biometrics 42 (1986) 845–854].
"Rank Tests from Partially Ordered Data Using Importance and MCMC Sampling Methods." Statist. Sci. 31 (3) 325 - 347, August 2016. https://doi.org/10.1214/16-STS549