Package: basksim 1.0.0

Lukas Baumann

basksim: 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. (2024) <doi:10.48550/arXiv.2309.06988>, Fujikawa et al. (2020) <doi:10.1002/bimj.201800404>, Berry et al. (2020) <doi:10.1177/1740774513497539>, Neuenschwander et al. (2016) <doi:10.1002/pst.1730> and Psioda et al. (2021) <doi:10.1093/biostatistics/kxz014>. For the latter three designs, the functions are mostly wrappers for functions provided by the packages 'bhmbasket' and 'bmabasket'.

Authors:Lukas Baumann [aut, cre], Lukas Sauer [ctb]

basksim_1.0.0.tar.gz
basksim_1.0.0.tar.gz(r-4.5-noble)basksim_1.0.0.tar.gz(r-4.4-noble)
basksim_1.0.0.tgz(r-4.4-emscripten)basksim_1.0.0.tgz(r-4.3-emscripten)
basksim.pdf |basksim.html
basksim/json (API)

# Install 'basksim' in R:
install.packages('basksim', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/lbau7/basksim/issues

Uses libs:
  • jags– Just Another Gibbs Sampler for Bayesian MCMC
  • c++– GNU Standard C++ Library v3

jagscpp

1.70 score 213 downloads 17 exports 43 dependencies

Last updated 8 months agofrom:b33d181aa3. Checks:OK: 2. Indexed: no.

TargetResultDate
Doc / VignettesOKDec 09 2024
R-4.5-linuxOKDec 09 2024

Exports:adjust_lambdaecdget_dataget_detailsget_resultsget_scenariosopt_designsetup_bhmsetup_bmasetup_cppsetup_cppglobalsetup_exnexsetup_fujikawasetup_jsdglobalsetup_mmlsetup_mmlglobaltoer

Dependencies:abindarrangementsbhmbasketbmabasketbootclicodacodetoolsdigestdoFuturedoRNGextraDistrforeachfuturefuture.applyglobalsgluegmpHDIntervaliteratorslatticelifecyclelistenvmagrittrmathjaxrparallellypartitionspolynomprogressrR2jagsR2WinBUGSR6rbibutilsRcppRcppArmadilloRdpackrjagsrlangrngtoolssetsstringistringrvctrs

Readme and manuals

Help Manual

Help pageTopics
Adjust Lambdaadjust_lambda
Adjust Lambda for the BHM Designadjust_lambda.bhm
Adjust Lambdaadjust_lambda.default
Adjust Lambda for the EXNEX Designadjust_lambda.exnex
Calculate the Expected Number of Correct Decisions for a Basket Trial Designecd
Simulate Data Based on a Binomial Distributionget_data
Get Details of a Basket Trial Simulationget_details
Get Details of a BHM Basket Trial Simulationget_details.bhm
Get Details of a BMA Basket Trial Simulationget_details.bma
Get Details of a Basket Trial Simulation with the Calibrated Power Prior Designget_details.cpp
Get Details of a Basket Trial Simulation with the Global Calibrated Power Prior Designget_details.cppglobal
Get Details of a Basket Trial Simulation with the EXNEX Designget_details.exnex
Get Details of a Basket Trial Simulation with Fujikawa's Designget_details.fujikawa
Get Details of a Basket Trial Simulation with the Power Prior Design Based on Global JSD Weightsget_details.jsdglobal
Get Details of a Basket Trial Simulation with the MML Designget_details.mml
Get Details of a Basket Trial Simulation with the Global MML Designget_details.mmlglobal
Get Results for Simulation of Basket Trial Designsget_results
Get Results for Simulation of a Basket Trial with the BHM Designget_results.bhm
Get Results for Simulation of a Basket Trial with the BMA Designget_results.bma
Get Results for Simulation of a Basket Trial with a Calibrated Power Prior Designget_results.cpp
Get Results for Simulation of a Basket Trial with a Global Calibrated Power Prior Designget_results.cppglobal
Get Results for Simulation of a Basket Trial with the EXNEX Designget_results.exnex
Get Results for Simulation of a Basket Trial with Fujikawa's Designget_results.fujikawa
Get Results for Simulation of a Basket Trial with the Power Prior Design Based on Global JSD Weightsget_results.jsdglobal
Get Results for Simulation of a Basket Trial with the MML Designget_results.mml
Get Results for Simulation of a Basket Trial with the Global MML Designget_results.mmlglobal
Create a Scenario Matrixget_scenarios
Optimize a Basket Trial Designopt_design
Setup BHM Design Objectsetup_bhm
Setup bma Design Objectsetup_bma
Setup Calibrated Power Prior Design Objectsetup_cpp
Setup Global Calibrated Power Prior Design Objectsetup_cppglobal
Setup EXNEX Design Objectsetup_exnex
Setup Fujikawa Design Objectsetup_fujikawa
Setup Global JSD Design Objectsetup_jsdglobal
Setup mml Design Objectsetup_mml
Setup mmlglobal Design Objectsetup_mmlglobal
Calculate the Type 1 Error Rate for a Basket Trial Designtoer