Package: BayesianPlatformDesignTimeTrend 1.2.0

BayesianPlatformDesignTimeTrend: Simulate and Analyse Bayesian Platform Trial with Time Trend

Simulating the sequential multi-arm multi-stage or platform trial with Bayesian approach using the 'rstan' package, which provides the R interface for the Stan. This package supports fixed ratio and Bayesian adaptive randomization approaches for randomization. Additionally, it allows for the study of time trend problems in platform trials. There are demos available for a multi-arm multi-stage trial with two different null scenarios, as well as for Bayesian trial cutoff screening. The Bayesian adaptive randomisation approaches are described in: Trippa et al. (2012) <doi:10.1200/JCO.2011.39.8420> and Wathen et al. (2017) <doi:10.1177/1740774517692302>. The randomisation algorithm is described in: Zhao W <doi:10.1016/j.cct.2015.06.008>. The analysis methods of time trend effect in platform trial are described in: Saville et al. (2022) <doi:10.1177/17407745221112013> and Bofill Roig et al. (2022) <doi:10.1186/s12874-022-01683-w>.

Authors:Ziyan Wang [aut, cre], David Woods [ctb]

BayesianPlatformDesignTimeTrend_1.2.0.tar.gz
BayesianPlatformDesignTimeTrend_1.2.0.zip(r-4.5)BayesianPlatformDesignTimeTrend_1.2.0.zip(r-4.4)BayesianPlatformDesignTimeTrend_1.2.0.zip(r-4.3)
BayesianPlatformDesignTimeTrend_1.2.0.tgz(r-4.4-x86_64)BayesianPlatformDesignTimeTrend_1.2.0.tgz(r-4.4-arm64)BayesianPlatformDesignTimeTrend_1.2.0.tgz(r-4.3-x86_64)BayesianPlatformDesignTimeTrend_1.2.0.tgz(r-4.3-arm64)
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BayesianPlatformDesignTimeTrend.pdf |BayesianPlatformDesignTimeTrend.html
BayesianPlatformDesignTimeTrend/json (API)
NEWS

# Install 'BayesianPlatformDesignTimeTrend' in R:
install.packages('BayesianPlatformDesignTimeTrend', repos = c('https://zxw834.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/zxw834/bayesianplatformdesigntimetrend/issues

Uses libs:
  • c++– GNU Standard C++ Library v3
Datasets:
  • OPC_Trial.simulation - Operation characteristic table for Trial.simulation() null scenario
  • OPC_alt - Operation characteristic table for alternative scenario
  • OPC_null - Operation characteristic table for null scenario
  • dataloginformd - Cutoff screening example: the details of grid
  • optimdata_asy - A list of data from Gaussian process and trial simulation for asymmetric cutoff screening.
  • optimdata_sym - A list of data from Gaussian process for symmetric cutoff screening.
  • predictedtpIEinformd - Cutoff screening example: the predicted value from quadratic model
  • recommandloginformd - Cutoff screening example: the recommended grid value at each time point

On CRAN:

analysisbayesian-adaptive-randomisationclinial-trialgroup-sequential-designsmultiarm-multistage-trialsplatform-trialssimulation

4.38 score 12 scripts 391 downloads 34 exports 102 dependencies

Last updated 1 years agofrom:5a86705bb6. Checks:OK: 1 NOTE: 8. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 26 2024
R-4.5-win-x86_64NOTEOct 26 2024
R-4.5-linux-x86_64NOTEOct 26 2024
R-4.4-win-x86_64NOTEOct 26 2024
R-4.4-mac-x86_64NOTEOct 26 2024
R-4.4-mac-aarch64NOTEOct 26 2024
R-4.3-win-x86_64NOTEOct 26 2024
R-4.3-mac-x86_64NOTEOct 26 2024
R-4.3-mac-aarch64NOTEOct 26 2024

Exports:AdaptiveRandomisationalphaspendingARmethodBoundaryconstructionconjuncativepower_or_FWERdemo_Cutoffscreeningdemo_Cutoffscreening.GPdemo_multscenariodisconjunctivepowerfuncGP.optimibetabinomial.postInitializetrialparameterintbiasMeanfuncmodelinf.funNfuncOutputStats.initialisingperHtypeIerror_marginalpowerfuncRandomisation.infresultrtostatsresultrtostats.randresultstantoRfuncresultstantoRfunc.randSave.resulttoRDatafilesimulatetrialSperarmfuncstan.logisticmodeltransStopboundinftesting_and_armdroppingTimetrend.funTrial.simulationtrtbiastrteffectvarfunc

Dependencies:abindbackportsBHBiocManagerbootbroomcallrcarcarDatacheckmatecliclustercodetoolscolorspacecorrplotcowplotcpp11DerivdescdirectlabelsdistributionaldoBydoParalleldplyrfansifarverforeachFormulagenericsggplot2ggpubrggrepelggsciggsignifgluegridExtragtableinlineisobanditeratorslabelinglaGPlatticelhslifecyclelme4loomagrittrmaptreeMASSMatrixMatrixModelsmatrixStatsmgcvmicrobenchmarkminqamodelrmunsellnlmenloptrnnetnumDerivpbkrtestpillarpkgbuildpkgconfigplyrpolynomposteriorprocessxpspurrrquadprogquantregQuickJSRR6RColorBrewerRcppRcppEigenRcppParallelreshapereshape2rlangrpartrstanrstantoolsrstatixscalesSparseMStanHeadersstringistringrsurvivaltensorAtgptibbletidyrtidyselectutf8vctrsviridisLitewithr

MAMS-CutoffScreening-GP-Asymmetric-tutorial

Rendered fromMAMS-CutoffScreening-GP-Asymmetric-tutorial.Rmdusingknitr::rmarkdownon Oct 26 2024.

Last update: 2023-10-04
Started: 2023-10-04

MAMS-CutoffScreening-GP-Symmetric-tutorial

Rendered fromMAMS-CutoffScreening-GP-Symmetric-tutorial.Rmdusingknitr::rmarkdownon Oct 26 2024.

Last update: 2023-10-04
Started: 2023-10-04

MAMS-CutoffScreening-tutorial

Rendered fromMAMS-CutoffScreening-tutorial.Rmdusingknitr::rmarkdownon Oct 26 2024.

Last update: 2023-07-10
Started: 2023-03-07

MAMS-trial-simulation-tutorial

Rendered fromMAMS-trial-simulation-tutorial.Rmdusingknitr::rmarkdownon Oct 26 2024.

Last update: 2023-07-10
Started: 2023-03-07

Readme and manuals

Help Manual

Help pageTopics
The 'BayesianPlatformDesignTimeTrend' package.BayesianPlatformDesignTimeTrend-package BayesianPlatformDesignTimeTrend
AdaptiveRandomisationAdaptiveRandomisation
alphaspendingalphaspending
ARmethodARmethod
BoundaryconstructionBoundaryconstruction
conjuncativepower_or_FWERconjuncativepower_or_FWER
Cutoff screening example: the details of griddataloginformd
demo_Cutoffscreeningdemo_Cutoffscreening
A demo for cutoff screening using Bayesian optimisationdemo_Cutoffscreening.GP
demo_multscenariodemo_multscenario
disconjunctivepowerfuncdisconjunctivepowerfunc
GP.optim: optimiser to give the next cutoff for evaluationGP.optim
ibetabinomial.postibetabinomial.post
InitializetrialparameterInitializetrialparameter
intbiasintbias
MeanfuncMeanfunc
modelinf.funmodelinf.fun
NfuncNfunc
Operation characteristic table for alternative scenarioOPC_alt
Operation characteristic table for null scenarioOPC_null
Operation characteristic table for Trial.simulation() null scenarioOPC_Trial.simulation
A list of data from Gaussian process and trial simulation for asymmetric cutoff screening.optimdata_asy
A list of data from Gaussian process for symmetric cutoff screening.optimdata_sym
OutputStats.initialisingOutputStats.initialising
perHtypeIerror_powerfuncperHtypeIerror_marginalpowerfunc
Cutoff screening example: the predicted value from quadratic modelpredictedtpIEinformd
Randomisation.infRandomisation.inf
Cutoff screening example: the recommended grid value at each time pointrecommandloginformd
resultrtostatsresultrtostats
resultrtostats.randresultrtostats.rand
resultstantoRfuncresultstantoRfunc
resultstantoRfunc.randresultstantoRfunc.rand
Save.resulttoRDatafileSave.resulttoRDatafile
simulatetrialsimulatetrial
SperarmfuncSperarmfunc
stan.logisticmodeltransstan.logisticmodeltrans
StopboundinfStopboundinf
Titletesting_and_armdropping
Timetrend.funTimetrend.fun
Trial simulationTrial.simulation
trtbiastrtbias
trteffecttrteffect
varfuncvarfunc