Simulation-Based Calculation of Basket Trial Operating Characteristics

Provides a unified syntax for the simulation-based comparison of different single-stage basket trial designs with a binary endpoint and equal sample sizes in all baskets. Methods include the designs by Baumann et al. (2025) , Schmitt and Baumann (2025) , Fujikawa et al. (2020) , Berry et al. (2020) , and Neuenschwander et al. (2016) . For the latter two designs, the functions are mostly wrappers for functions provided by the package 'bhmbasket'.

basksim

Overview

basksim calculates the operating characteristics of different basket trial designs based on simulation.

Installation

Install the development version with:

# install.packages("devtools")
pak::pak("lbau7/basksim")

Usage

With basksim you can calculate the operating characteristics such as rejection probabilities and mean squared error of single-stage basket trials with different designs.

At first, you have to create a design-object using a setup-function. For example to create a design-object for Fujikawa’s design (Fujikawa et al., 2020):

library(basksim)
design <- setup_fujikawa(k = 3, shape1 = 1, shape2 = 1, p0 = 0.2)

k is the number of baskets, shape1 and shape2 are the shape parameters of the Beta-prior of the response probabilities of each baskets and p0 is the response probability that defines the null hypothesis.

Use get_details to estimate several important operating characteristics:

set.seed(123)
get_details(
  design = design,
  n = c(15, 20, 25),
  p1 = c(0.2, 0.5, 0.5),
  lambda = 0.95,
  epsilon = 1.5,
  tau = 0,
  iter = 5000
)

# $Rejection_Probabilities
# [1] 0.4226 0.9824 0.9874
# 
# $FWER
# [1] 0.4226
# 
# $EWP
# [1] 0.999
# 
# $Mean
# [1] 0.2992626 0.4823250 0.4836304
# 
# $MSE
# [1] 0.020532553 0.007330251 0.006862607
# 
# $Lower_CL
# [1] 0.1517281 0.3407342 0.3440962
# 
# $Upper_CL
# [1] 0.4574680 0.6241900 0.6234426
# 
# $ECD
# [1] 2.5472
# 
# $Rejection_Probabilities_SE
# [1] 0.006985832 0.001859583 0.001577418
# 
# $FWER_SE
# [1] 0.006985832
# 
# $EWP_SE
# [1] 0.0004469899
# 
# $ECD_SE
# [1] 0.007147353