Package: bhmbasket 0.9.5
bhmbasket: Bayesian Hierarchical Models for Basket Trials
Provides functions for the evaluation of basket trial designs with binary endpoints. Operating characteristics of a basket trial design are assessed by simulating trial data according to scenarios, analyzing the data with Bayesian hierarchical models (BHMs), and assessing decision probabilities on stratum and trial-level based on Go / No-go decision making. The package is build for high flexibility regarding decision rules, number of interim analyses, number of strata, and recruitment. The BHMs proposed by Berry et al. (2013) <doi:10.1177/1740774513497539> and Neuenschwander et al. (2016) <doi:10.1002/pst.1730>, as well as a model that combines both approaches are implemented. Functions are provided to implement Bayesian decision rules as for example proposed by Fisch et al. (2015) <doi:10.1177/2168479014533970>. In addition, posterior point estimates (mean/median) and credible intervals for response rates and some model parameters can be calculated. For simulated trial data, bias and mean squared errors of posterior point estimates for response rates can be provided.
Authors:
bhmbasket_0.9.5.tar.gz
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bhmbasket.pdf |bhmbasket.html✨
bhmbasket/json (API)
NEWS
# Install 'bhmbasket' in R: |
install.packages('bhmbasket', repos = c('https://wojcieko.r-universe.dev', 'https://cloud.r-project.org')) |
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated 3 years agofrom:3e96ad7d87. Checks:OK: 7. Indexed: yes.
Target | Result | Date |
---|---|---|
Doc / Vignettes | OK | Nov 01 2024 |
R-4.5-win | OK | Nov 01 2024 |
R-4.5-linux | OK | Nov 01 2024 |
R-4.4-win | OK | Nov 01 2024 |
R-4.4-mac | OK | Nov 01 2024 |
R-4.3-win | OK | Nov 01 2024 |
R-4.3-mac | OK | Nov 01 2024 |
Exports:combinePriorParameterscontinueRecruitmentcreateTrialgetEstimatesgetGoDecisionsgetGoProbabilitiesgetMuVargetPriorParametersinvLogitloadAnalysesloadScenarioslogitnegateGoDecisionsperformAnalysessaveAnalysessaveScenariosscaleRoundListsetPriorParametersBerrysetPriorParametersExNexsetPriorParametersExNexAdjsetPriorParametersPooledsetPriorParametersStratifiedsimulateScenarios
Dependencies:abindbootclicodacodetoolsdigestdoRNGforeachglueiteratorslatticelifecyclemagrittrR2jagsR2WinBUGSrjagsrlangrngtoolsstringistringrvctrs
Reproducing Parts of Neuenschwander et al. (2016)
Rendered fromreproduceExNex.Rmd
usingknitr::rmarkdown
on Nov 01 2024.Last update: 2022-01-18
Started: 2021-02-15
Running bhmbasket on HPC
Rendered fromRunning_bhmbasket_on_HPC.Rmd
usingknitr::rmarkdown
on Nov 01 2024.Last update: 2022-02-14
Started: 2022-01-18
Readme and manuals
Help Manual
Help page | Topics |
---|---|
combinePriorParameters | combinePriorParameters |
continueRecruitment | continueRecruitment |
createTrial | createTrial |
getEstimates | getEstimates |
getGoDecisions | getGoDecisions |
getGoProbabilities | getGoProbabilities |
getMuVar | getMuVar |
getPriorParameters | getPriorParameters |
invLogit | invLogit |
loadAnalyses | loadAnalyses |
loadScenarios | loadScenarios |
logit | logit |
negateGoDecisions | negateGoDecisions |
performAnalyses | performAnalyses |
saveAnalyses | saveAnalyses |
saveScenarios | saveScenarios |
scaleRoundList | scaleRoundList |
setPriorParametersBerry | setPriorParametersBerry |
setPriorParametersExNex | setPriorParametersExNex |
setPriorParametersExNexAdj | setPriorParametersExNexAdj |
setPriorParametersPooled | setPriorParametersPooled |
setPriorParametersStratified | setPriorParametersStratified |
simulateScenarios | simulateScenarios |