Files in 0liver0815/onc-crmpack-test

Object-Oriented Implementation of CRM Designs

.github/ISSUE_TEMPLATE/bug_report.md .github/ISSUE_TEMPLATE/clean-up-issue.md .github/ISSUE_TEMPLATE/feature_request.md .github/pull_request_template.md NEWS.md R/Data-class.R R/Data-methods.R R/Data-validity.R R/Design-class.R R/Design-methods.R R/McmcOptions-class.R R/McmcOptions-methods.R R/McmcOptions-validity.R R/Model-class.R R/Model-methods.R R/Model-validity.R R/Rules-class.R R/Rules-methods.R R/Rules-validity.R R/Samples-class.R R/Samples-methods.R R/Simulations-class.R R/Simulations-methods.R R/ZZ_IncrementsHSRBeta_DK.R R/ZZ_LogisticKadane2_DK.R R/ZZ_NextBestMTDCRM_DK.R R/ZZ_StoppingLowestDoseHSRBeta_DK.R R/ZZ_StoppingTargetProbPatientsNearHighestDose_DK.R R/ZZ_StoppingTargetProbPatientsNearLowestDose_DK.R R/ZZ_crmPack-package_DK.R R/crmPack-package.R R/fromQuantiles.R R/helpers.R R/helpers_jags.R R/logger.R R/mcmc.R R/utils.R R/x-source-bayer.R R/x_new_IncrementsHSRbeta.R R/x_new_StoppingLowestDoseHSRbeta.R R/y_bay_design_1GeneralSimulationsBay_summary.R R/y_bay_design_2GeneralSimulationsBay_show.R R/y_bay_design_3SimulationsBay_summary.R R/y_bay_design_BayDesign.R R/y_bay_design_BayDesign_examine.R R/y_bay_design_BayDesign_simulate.R R/y_bay_model_LogisticKadaneBayer.R R/y_bay_model_OneParExp.R R/y_bay_model_TwoPar.R R/y_bay_model_TwoParBayS.R R/y_bay_myfunction-outdated.R R/y_bay_myfunction.R R/y_bay_myfunction2.R R/y_bay_myproposal.R R/y_bay_rules_IncrementsAbsoluteMax.R R/y_bay_rules_IncrementsRelativeDLTmax.R R/y_bay_rules_IncrementsRelativeMax.R R/y_bay_rules_IncrementsSafetyStop.R R/y_bay_rules_IncrementsSafetyStopFix.R R/y_bay_rules_NextBestMTDprob.R R/y_bay_rules_NextBestMinDist.R R/y_bay_rules_StoppingHardFirst.R R/y_bay_rules_StoppingHardFirstFix.R R/y_bay_rules_StoppingMTDdistributionBay.R R/y_bay_rules_StoppingPatientsNearDose2.R R/y_bay_rules_StoppingProbBay.R README.Rmd README.md bayer/R-done/ZZ_IncrementsNumDoseLevelsMaxTested_DK.R bayer/R-done/ZZ_StoppingMTDCV_DK.R bayer/R-done/bay_rules_IncrementsNumDoseLevelsMax.R bayer/R-done/bay_rules_StoppingCV.R bayer/R-done/new_StoppingMTDCV.R bayer/R_DK/S4_experimental/Report-Show.R bayer/R_DK/S4_experimental/Simulations.R bayer/R_DK/S4_experimental/Summary.R bayer/R_DK/crmpack_R_programs_amended/ZZ_Model-class_DK.R bayer/R_DK/crmpack_R_programs_amended/ZZ_Rules-class_DK.R bayer/R_DK/crmpack_R_programs_amended/ZZ_Rules-methods_DK.R bayer/analysis_DK/PriorSamples_MSLN_TTC.R bayer/analysis_DK/Simulation_MSLN_TTC_DK.R bayer/analysis_DK/stopping rules test_DK.R bayer/analysis_examples_ob/18795 msln-ttc analyze oc.R bayer/analysis_examples_ob/18795 msln-ttc analyze oc_old.R bayer/analysis_examples_ob/18795 msln-ttc simulations.R bayer/analysis_examples_ob/example from JSS 2019 - section3.1.R bayer/analysis_examples_ob/example from JSS 2019 - section3.3.r bayer/analysis_examples_ob/func_ana_simres.r bayer/analysis_examples_ob/testStoppingLowestDoseHSRbeta.R bayer/analysis_examples_ob/threep3.R bayer/create_and_install_package.R bayer/examples-done/Rules-class-IncrementsNumDoseLevelsMax.R bayer/examples-done/Rules-class-StoppingMTDCV.R bayer/examples-done/Rules-method-maxDose-IncrementsNumDoseLevelsMax.R bayer/examples-done/Rules-method-stopTrial-StoppingMTDCV.R bayer/examples/Rules-class-IncrementsHSRBeta.R bayer/examples/Rules-class-StoppingLowestDoseHSRBeta.R bayer/examples/Rules-method-maxDose-IncrementsHSRBeta.R bayer/examples/Rules-method-stopTrial-StoppingLowestDoseHSRBeta.R bayer/guide-to-create-code.R bayer/testthat/IncrementsHSRBeta-test-Rules-class.R bayer/testthat/IncrementsHSRBeta-test-Rules-methods.R bayer/testthat/IncrementsHSRBeta-test-Rules-validity.R bayer/testthat/StoppingLowestDoseHSRBeta-test-Rules-class.R bayer/testthat/StoppingLowestDoseHSRBeta-test-Rules-methods.R bayer/testthat/StoppingLowestDoseHSRBeta-test-Rules-validity.R bayer/testthat/helper-data.R devel/BayesLogit.R devel/Dual endpoint separate model 27012015.R devel/TestGPA.R devel/classes.R devel/classes2.R devel/combo.R devel/dual.R devel/dual2.R devel/dualPackage.R devel/dualTestcode.R devel/funs.R devel/project.R devel/projectWithPackage.R devel/projectWithPackageOld.R devel/reporters.R devel/rolling-crm-Simona.Rmd devel/three.R devel/tite-crm.R devel/varnames.R examples/Data-class-DataDA.R examples/Data-class-DataDual.R examples/Data-class-DataMixture.R examples/Data-class-DataParts.R examples/Data-class.R examples/Data-method-getEff.R examples/Data-method-plot-DataDA.R examples/Data-method-plot-DataDual.R examples/Data-method-plot.R examples/Data-method-update-DataDA.R examples/Data-method-update-DataDual.R examples/Data-method-update-DataParts.R examples/Data-method-update.R examples/McmcOptions-class-McmcOptions.R examples/McmcOptions-methods-sampleSize.R examples/McmcOptions-methods-saveSample.R examples/MinimalInformative.R examples/Model-class-DALogisticLogNormal.R examples/Model-class-DualEndpointBeta.R examples/Model-class-DualEndpointEmax.R examples/Model-class-DualEndpointRW.R examples/Model-class-EffFlexi.R examples/Model-class-Effloglog.R examples/Model-class-LogisticIndepBeta.R examples/Model-class-LogisticKadane.R examples/Model-class-LogisticLogNormal.R examples/Model-class-LogisticLogNormalMixture.R examples/Model-class-LogisticLogNormalSub.R examples/Model-class-LogisticNormal.R examples/Model-class-LogisticNormalFixedMixture.R examples/Model-class-LogisticNormalMixture.R examples/Model-class-ProbitLogNormal.R examples/Model-class-ProbitLogNormalRel.R examples/Model-method-ExpEff.R examples/Model-method-ExpEffFlexi.R examples/Model-method-ExpEffNoSamples.R examples/Model-method-biomLevel.R examples/Model-method-dose.R examples/Model-method-doseFunction.R examples/Model-method-gain.R examples/Model-method-gainFlexi.R examples/Model-method-gainNoSamples.R examples/Model-method-prob.R examples/Model-method-probFunction.R examples/Model-method-updateEffFlexi.R examples/Model-method-updateEffloglog.R examples/Model-method-updateLogisticIndepBeta.R examples/Rules-class-CohortSizeConst.R examples/Rules-class-CohortSizeDLT.R examples/Rules-class-CohortSizeMax.R examples/Rules-class-CohortSizeMin.R examples/Rules-class-CohortSizeParts.R examples/Rules-class-CohortSizeRange.R examples/Rules-class-IncrementMin.R examples/Rules-class-IncrementsHSRBeta.R examples/Rules-class-IncrementsNumDoseLevels.R examples/Rules-class-IncrementsRelative-DataParts.R examples/Rules-class-IncrementsRelative.R examples/Rules-class-IncrementsRelativeDLT.R examples/Rules-class-NextBestDualEndpoint.R examples/Rules-class-NextBestMTD.R examples/Rules-class-NextBestMaxGain.R examples/Rules-class-NextBestMaxGainSamples.R examples/Rules-class-NextBestNCRM.R examples/Rules-class-NextBestTD.R examples/Rules-class-NextBestTDsamples.R examples/Rules-class-NextBestThreePlusThree.R examples/Rules-class-SafetyWindowConst.R examples/Rules-class-SafetyWindowSize.R examples/Rules-class-StoppingAll.R examples/Rules-class-StoppingAny.R examples/Rules-class-StoppingCohortsNearDose.R examples/Rules-class-StoppingGstarCIRatio.R examples/Rules-class-StoppingHighestDose.R examples/Rules-class-StoppingList.R examples/Rules-class-StoppingLowestDoseHSRBeta.R examples/Rules-class-StoppingMTDCV.R examples/Rules-class-StoppingMTDdistribution.R examples/Rules-class-StoppingMinCohorts.R examples/Rules-class-StoppingMinPatients.R examples/Rules-class-StoppingPatientsNearDose.R examples/Rules-class-StoppingTDCIRatio.R examples/Rules-class-StoppingTargetBiomarker.R examples/Rules-class-StoppingTargetProb.R examples/Rules-method-CombiningStoppingRulesAndOr.R examples/Rules-method-NextBestDualEndpoint.R examples/Rules-method-NextBestMTD.R examples/Rules-method-NextBestNCRM-DataParts.R examples/Rules-method-NextBestNCRM.R examples/Rules-method-NextBestThreePlusThree.R examples/Rules-method-and-stopping-stopping.R examples/Rules-method-and-stopping-stoppingAll.R examples/Rules-method-and-stoppingAll-stopping.R examples/Rules-method-maxDose-IncrementMin.R examples/Rules-method-maxDose-IncrementsHSRBeta.R examples/Rules-method-maxDose-IncrementsNumDoseLevels.R examples/Rules-method-maxDose-IncrementsRelative.R examples/Rules-method-maxDose-IncrementsRelativeDLT.R examples/Rules-method-maxDose-IncrementsRelativeParts.R examples/Rules-method-maxSize.R examples/Rules-method-minSize.R examples/Rules-method-nextbest_MaxGain.R examples/Rules-method-nextbest_MaxGainSamples.R examples/Rules-method-nextbest_TD.R examples/Rules-method-nextbest_TDsamples.R examples/Rules-method-or-stopping-stopping.R examples/Rules-method-or-stopping-stoppingAny.R examples/Rules-method-or-stoppingAny-stopping.R examples/Rules-method-size-CohortSizeConst.R examples/Rules-method-size-CohortSizeDLT.R examples/Rules-method-size-CohortSizeMax.R examples/Rules-method-size-CohortSizeMin.R examples/Rules-method-size-CohortSizeParts.R examples/Rules-method-size-CohortSizeRange.R examples/Rules-method-stopTrial-StoppingAll.R examples/Rules-method-stopTrial-StoppingAny.R examples/Rules-method-stopTrial-StoppingCohortsNearDose.R examples/Rules-method-stopTrial-StoppingHighestDose.R examples/Rules-method-stopTrial-StoppingList.R examples/Rules-method-stopTrial-StoppingLowestDoseHSRBeta.R examples/Rules-method-stopTrial-StoppingMTDCV.R examples/Rules-method-stopTrial-StoppingMTDdistribution.R examples/Rules-method-stopTrial-StoppingMinCohorts.R examples/Rules-method-stopTrial-StoppingMinPatients.R examples/Rules-method-stopTrial-StoppingPatientsNearDose.R examples/Rules-method-stopTrial-StoppingTargetBiomarker.R examples/Rules-method-stopTrial-StoppingTargetProb.R examples/Rules-method-stopTrialCIMaxGain.R examples/Rules-method-stopTrialCIMaxGainSamples.R examples/Rules-method-stopTrialCITD.R examples/Rules-method-stopTrialCITDsamples.R examples/Rules-method-windowLength-SafetyWindowConst.R examples/Rules-method-windowLength-SafetyWindowSize.R examples/Sample-class-Samples.R examples/Sample-methods-approximate.R examples/Sample-methods-fit-DualEndpoint.R examples/Sample-methods-fit.R examples/Sample-methods-get.R examples/Sample-methods-plot-DualEndpoint.R examples/Sample-methods-plot.R examples/Samples-method-fitDLE.R examples/Samples-method-fitEff.R examples/Samples-method-fitEffFlexi.R examples/Samples-method-fitGain.R examples/Samples-method-fitPEM-DALogisticLogNormal.R examples/Samples-method-plotDualResponses.R examples/Samples-method-plotDualResponsesNoSamples.R examples/Samples-method-plotGain.R examples/Samples-method-plotGainNoSamples.R examples/Samples-method-plotModelEff.R examples/Samples-method-plotModelEffNoSamples.R examples/Samples-method-plotModelTox.R examples/Samples-method-plotModelToxNoSamples.R examples/Simulations-method-plot-DualSimulations.R examples/Simulations-method-plot-DualSimulationsSummary.R examples/Simulations-method-plot-SimulationsSummary.R examples/Simulations-method-plotSIMDual.R examples/Simulations-method-plotSIMDualFlexi.R examples/Simulations-method-plotSIMsingle.R examples/Simulations-method-plotSUMDual.R examples/Simulations-method-plotSUMsingle.R examples/Simulations-method-show-DualSimulationsSummary.R examples/Simulations-method-show-SimulationsSummary.R examples/Simulations-method-showSIMDual.R examples/Simulations-method-showSIMsingle.R examples/Simulations-method-summary-DualSimulations.R examples/Simulations-method-summary.R examples/Simulations-method-summarySIMDual.R examples/Simulations-method-summarySIMDualFlexi.R examples/Simulations-method-summarySIMsingle.R examples/design-class-DADesign.R examples/design-class-Design.R examples/design-class-DualDesign.R examples/design-class-DualResponsesDesign.R examples/design-class-DualResponsesSamplesDesign.R examples/design-class-RuleDesign.R examples/design-class-TDDesign.R examples/design-class-TDsamplesDesign.R examples/design-class-ThreePlusThreeDesign.R examples/design-method-examine-DADesign.R 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man/show-GeneralSimulationsSummary-method.Rd man/show-GeneralSimulationsSummaryBay-method.Rd man/show-PseudoDualSimulationsSummary-method.Rd man/show-PseudoSimulationsSummary-method.Rd man/show-SimulationsSummary-method.Rd man/simulate-BayDesign-method.Rd man/simulate-DADesign-method.Rd man/simulate-Design-method.Rd man/simulate-DualDesign-method.Rd man/simulate-DualResponsesDesign-method.Rd man/simulate-DualResponsesSamplesDesign-method.Rd man/simulate-RuleDesign-method.Rd man/simulate-TDDesign-method.Rd man/simulate-TDsamplesDesign-method.Rd man/size.Rd man/stopTrial.Rd man/summary-DualSimulations-method.Rd man/summary-GeneralSimulations-method.Rd man/summary-GeneralSimulationsBay-method.Rd man/summary-PseudoDualFlexiSimulations-method.Rd man/summary-PseudoDualSimulations-method.Rd man/summary-PseudoSimulations-method.Rd man/summary-Simulations-method.Rd man/summary-SimulationsBay-method.Rd man/update-Data-method.Rd man/update-DataDA-method.Rd man/update-DataDual-method.Rd man/update-DataParts-method.Rd man/update-EffFlexi-method.Rd man/update-Effloglog-method.Rd man/update-LogisticIndepBeta-method.Rd man/validate_data_objects.Rd man/validate_increments.Rd man/validate_mcmcoptions_objects.Rd man/validate_model_objects.Rd man/validate_stopping.Rd man/windowLength.Rd tests/testthat.R tests/testthat/_snaps/helpers_jags.md tests/testthat/helper-McmcOptions.R tests/testthat/helper-data.R tests/testthat/helper-logger.R tests/testthat/helper-model.R tests/testthat/helper-samples.R tests/testthat/helper-testthat.R tests/testthat/test-Data-class.R tests/testthat/test-Data-methods.R tests/testthat/test-Data-validity.R tests/testthat/test-McmcOptions-class.R tests/testthat/test-McmcOptions-methods.R tests/testthat/test-McmcOptions-validity.R tests/testthat/test-Model-class.R tests/testthat/test-Model-methods.R tests/testthat/test-Model-validity.R tests/testthat/test-Rules-class.R tests/testthat/test-Rules-methods.R tests/testthat/test-Rules-validity.R tests/testthat/test-Validate-class.R tests/testthat/test-helpers.R tests/testthat/test-helpers_jags.R tests/testthat/test-logger.R tests/testthat/test-mcmc.R tests/testthat/test-utils.R vignettes/rolling-crm.Rmd vignettes/schematic.pdf vignettes/simulations.Rmd