Package: BayesianMCPMod 1.3.2

Stephan Wojciekowski

BayesianMCPMod: Simulate, Evaluate, and Analyze Dose Finding Trials with Bayesian MCPMod

Bayesian MCPMod (Fleischer et al. (2022) <doi:10.1002/pst.2193>) is an innovative method that improves the traditional MCPMod by systematically incorporating historical data, such as previous placebo group data. This package offers functions for simulating, analyzing, and evaluating Bayesian MCPMod trials with normally and binary distributed endpoints. It enables the assessment of trial designs incorporating historical data across various true dose-response relationships and sample sizes. Robust mixture prior distributions, such as those derived with the Meta-Analytic-Predictive approach (Schmidli et al. (2014) <doi:10.1111/biom.12242>), can be specified for each dose group. Resulting mixture posterior distributions are used in the Bayesian Multiple Comparison Procedure and modeling steps. The modeling step also includes a weighted model averaging approach (Pinheiro et al. (2014) <doi:10.1002/sim.6052>). Estimated dose-response relationships can be bootstrapped and visualized.

Authors:Boehringer Ingelheim Pharma GmbH & Co. KG [cph, fnd], Stephan Wojciekowski [aut, cre], Lars Andersen [aut], Jonas Schick [ctb], Sebastian Bossert [aut]

BayesianMCPMod_1.3.2.tar.gz
BayesianMCPMod_1.3.2.zip(r-4.7)BayesianMCPMod_1.3.2.zip(r-4.6)BayesianMCPMod_1.3.2.zip(r-4.5)
BayesianMCPMod_1.3.2.tgz(r-4.6-any)BayesianMCPMod_1.3.2.tgz(r-4.5-any)
BayesianMCPMod_1.3.2.tar.gz(r-4.7-any)BayesianMCPMod_1.3.2.tar.gz(r-4.6-any)
BayesianMCPMod_1.3.2.tgz(r-4.6-emscripten)
manual.pdf |manual.html
DESCRIPTION |NEWS
card.svg |card.png
BayesianMCPMod/json (API)

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

Bug tracker:https://github.com/boehringer-ingelheim/bayesianmcpmod/issues

Pkgdown/docs site:https://boehringer-ingelheim.github.io

On CRAN:

Conda:

6.95 score 10 stars 7 scripts 610 downloads 12 exports 106 dependencies

Last updated from:d234ace44e. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64OK265
source / vignettesOK437
linux-release-x86_64OK253
macos-release-arm64OK130
macos-oldrel-arm64OK169
windows-develOK201
windows-releaseOK219
windows-oldrelOK193
wasm-releaseOK170

Exports:assessDesigngetBootstrapQuantilesgetBootstrapSamplesgetContrgetCritProbgetESSgetMEDgetModelFitsgetPosteriorperformBayesianMCPperformBayesianMCPModsimulateData

Dependencies:abindassertthatbackportsbayesplotBHbitbit64bootbroomcallrcheckmateclicliprcodetoolscpp11crayondescdistributionalDoseFindingdplyrfarverforcatsforeachFormulaformula.toolsgenericsggplot2ggridgesglmnetgluegridExtragtablehavenhmsinlineisobanditeratorsjomojsonlitelabelinglatticelifecyclelme4logistfloomagrittrMASSMatrixmatrixStatsmgcvmiceminqamitmlmvtnormnlmenloptrnnetnumDerivoperator.toolsordinalotelpanpillarpkgbuildpkgconfigplyrposteriorprettyunitsprocessxprogresspspurrrQuickJSRR6RBesTrbibutilsRColorBrewerRcppRcppEigenRcppParallelRdpackreadrreformulasreshape2rlangrpartrstanrstantoolsS7scalesshapeStanHeadersstringistringrsurvivaltensorAtibbletidyrtidyselecttzdbucminfutf8vctrsviridisLitevroomwithr

Trial Analysis Example of Bayesian MCPMod for Binary Data
Scale Conventions in BayesianMCPMod | Calculation of a MAP Prior | 1) Establish MAP prior (beta mixture distribution) | 2) Robustify prior | 3) Translate prior to logit scale (to approximate via normal mixture model) | Specification of reference scale (this follows the idea of [@Neuenschwander2016]). | Specify a prior list | Trial Data | Posterior Calculation | Bayesian MCPMod Test Step | Model Fitting and Visualization | Assessment of the Minimally Efficacious Dose | Additional Note

Last update: 2026-05-13
Started: 2026-02-15

Trial Simulation Example of Bayesian MCPMod for Binary Data
Background and Data | Calculation of a MAP Prior | Specification of the New Trial Design | Calculation of the Success Probabilities

Last update: 2026-05-13
Started: 2026-02-15

Trial Analysis Example of Bayesian MCPMod for Continuous Data
Introduction | Calculation of a MAP Prior | Dose-Response Model Shapes | Trial Data | Posterior Calculation | Bayesian MCPMod Test Step | Model Fitting and Visualization | Assessment of the Minimally Efficacious Dose | Additional Note

Last update: 2026-02-23
Started: 2023-10-20

Trial Simulation Example of Bayesian MCPMod for Continuous Data
Background and Data | Calculation of a MAP Prior | Specification of the New Trial Design | Calculation of the Success Probabilities | Assessment of the Minimally Efficacious Dose

Last update: 2026-02-23
Started: 2023-10-20

Comparison of Bayesian MCPMod and MCPMod
Introduction | Varying the Expected Effect for Maximum Dose | Convergence of Power Values

Last update: 2026-02-15
Started: 2025-02-06

Readme and manuals

Help Manual

Help pageTopics
assessDesignassessDesign
getBootstrapQuantilesgetBootstrapQuantiles
getBootstrapSamplesgetBootstrapSamples
getContrgetContr
getCritProbgetCritProb
getESSgetESS
getMEDgetMED
getModelFitsgetModelFits
getPosteriorgetPosterior
performBayesianMCPperformBayesianMCP
performBayesianMCPModperformBayesianMCPMod
plot.modelFitsplot.modelFits
predict.modelFitspredict.modelFits
simulateDatasimulateData