Journal of Data Science

We introduce the stepp packages for R and Stata that implement the subpopulation treatment effect pattern plot (STEPP) method. STEPP is a nonparametric graphical tool aimed at examining possible heterogeneous treatment effects in subpopulations defined on a continuous covariate or composite score. More pecifically, STEPP considers overlapping subpopulations defined with respect to a continuous covariate (or risk index) and it estimates a treatment effect for each subpopulation. It also produces confidence regions and tests for treatment effect heterogeneity among the subpopulations. The original method has been extended in different directions such as different survival contexts, outcome types, or more efficient procedures for identifying the overlapping subpopulations. In this paper, we also introduce a novel method to determine the number of subjects within the subpopulations by minimizing the variability of the sizes of the subpopulations generated by a specific parameter combination. We illustrate the packages using both synthetic data and publicly available data sets. The most intensive computations in R are implemented in Fortran, while the Stata version exploits the powerful Mata language.

Abstract: In this paper we consider clinical trials with two treatments and a non-normally distributed response variable. In addition, we focus on ap plications which include only discrete covariates and their interactions. For such applications, the semi-parametric Area Under the ROC Curve (AUC) regression model proposed by Dodd and Pepe (2003) can be used. However, because a logistic regression procedure is used to obtain parameter estimates and a bootstrapping method is needed for computing parameter standard errors, their method may be cumbersome to implement. In this paper we propose to use a set of AUC estimates to obtain parameter estimates and combine DeLong’s method and the delta method for computing parameter standard errors. Our new method avoids heavy computation associated with the Dodd and Pepe’s method and hence is easy to implement. We conduct simulation studies to show that the two methods yield similar results. Finally, we illustrate our new method using data from urinary incontinence clinical trials.