trialr: Bayesian Clinical Trial Designs in R and Stan

Abstract

This manuscript introduces an \proglang{R} package called \pkg{trialr} that implements a collection of clinical trial methods in \proglang{Stan} and \proglang{R}. In this article, we explore three methods in detail. The first is the continual reassessment method for conducting phase I dose-finding trials that seek a maximum tolerable dose. The second is EffTox, a dose-finding design that scrutinises doses by joint efficacy and toxicity outcomes. The third is the augmented binary method for modelling the probability of treatment success in phase II oncology trials with reference to repeated measures of continuous tumour size and binary indicators of treatment failure. We emphasise in this article the benefits that stem from having access to posterior samples, including flexible inference and powerful visualisation. We hope that this package encourages the use of Bayesian methods in clinical trials.