Design of the DEFUSE3 Trial

In ASSISTant: Adaptive Subgroup Selection in Group Sequential Trials

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title: "Design of the DEFUSE3 Trial" author: "Tze Leung Lai, Philip W. Lavori, Olivia Liao, Ka Wai Tsang and Balasubramanian Narasimhan" date: 'r Sys.Date()' bibliography: assistant.bib output: html_document: theme: cerulean toc: yes toc_depth: 2 vignette: > %\VignetteIndexEntry{Design of the DEFUSE3 Trial} %\VignetteEngine{knitr::rmarkdown} \usepackage[utf8]{inputenc}

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### get knitr just the way we like it

knitr::opts_chunk$set(
  message = FALSE,
  warning = FALSE,
  error = FALSE,
  tidy = FALSE,
  cache = FALSE
)

Introduction

Here, we present the calculations for the initial design of the DEFUSE3 trial based on [@Lai2014191] and [@Lai201593]. The trial parameters are fixed as follows.

library(ASSISTant)
##Fix randomization vector N, errors, eps
trialParameters <- list(N = c(200, 340, 476), type1Error = 0.025,
                        eps = 1/2, type2Error = 0.1)

The design parameters are the following for various scenarios.

designParameters <- list(
    nul0 = list(prevalence = rep(1/6, 6), mean = matrix(0, 2, 6),
                sd = matrix(1, 2, 6)),
    alt1 = list(prevalence = rep(1/6, 6), mean = rbind(rep(0, 6),
                                                       c(0.5, 0.4, 0.3, 0, 0, 0)),
                sd = matrix(1, 2, 6)),
    alt2 = list(prevalence = rep(1/6, 6), mean = rbind(rep(0, 6),
                                                     c(0.5, 0.5, 0, 0, 0, 0)),
                sd = matrix(1,2, 6)),
    alt3 = list(prevalence = rep(1/6, 6), mean = rbind(rep(0, 6), rep(0.36, 6)),
                sd = matrix(1,2, 6)),
    alt4 = list(prevalence = rep(1/6, 6), mean = rbind(rep(0, 6), rep(0.30, 6)),
                sd = matrix(1,2, 6)),
    alt5 = list(prevalence = rep(1/6, 6), mean = rbind(rep(0, 6),
                                                       c(0.4, 0.3, 0.2, 0, 0, 0)),
                sd = matrix(1,2, 6)),
    alt6 = list(prevalence = rep(1/6, 6), mean = rbind(rep(0, 6),
                                                       c(0.5, 0.5, 0.3, 0.3, 0.1, 0.1)),
                sd = matrix(1,2, 6))
)

The NULL Scenario

defuse3 <- DEFUSE3Design$new(trialParameters = trialParameters,
                             numberOfSimulations = 25000,
                             designParameters = designParameters$nul0,
                             showProgress = FALSE)
print(defuse3)

result <- defuse3$explore(numberOfSimulations = 25000,
                          rngSeed = 283768,
                          showProgress = FALSE)
analysis <- defuse3$analyze(result)
print(defuse3$summary(analysis))

The ALT1 Scenario

result <- defuse3$explore(numberOfSimulations = 25000,
                          rngSeed = 873782,
                          trueParameters = designParameters$alt1,
                          showProgress = FALSE)
analysis <- defuse3$analyze(result)
print(defuse3$summary(analysis))

The ALT2 Scenario

result <- defuse3$explore(numberOfSimulations = 25000,
                          rngSeed = 45242,
                          trueParameters = designParameters$alt2,
                          showProgress = FALSE)
analysis <- defuse3$analyze(result)
print(defuse3$summary(analysis))

The ALT3 Scenario

result <- defuse3$explore(numberOfSimulations = 25000,
                          rngSeed = 833722,
                          trueParameters = designParameters$alt3,
                          showProgress = FALSE)
analysis <- defuse3$analyze(result)
print(defuse3$summary(analysis))

The ALT4 Scenario

result <- defuse3$explore(numberOfSimulations = 25000,
                          rngSeed = 434272,
                          trueParameters = designParameters$alt4,
                          showProgress = FALSE)
analysis <- defuse3$analyze(result)
print(defuse3$summary(analysis))

The ALT5 Scenario

result <- defuse3$explore(numberOfSimulations = 25000,
                          rngSeed = 132323,
                          trueParameters = designParameters$alt5,
                          showProgress = FALSE)
analysis <- defuse3$analyze(result)
print(defuse3$summary(analysis))

The ALT6 Scenario

result <- defuse3$explore(numberOfSimulations = 25000,
                          rngSeed = 653221,
                          trueParameters = designParameters$alt6,
                          showProgress = FALSE)
analysis <- defuse3$analyze(result)
print(defuse3$summary(analysis))

References

ASSISTant documentation built on Dec. 2, 2022, 5:12 p.m.