Files in Roche/crmPack

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/CrmPackClass-class.R R/CrmPackClass-methods.R R/Data-class.R R/Data-methods.R R/Data-validity.R R/Design-class.R R/Design-methods.R R/Design-validity.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/ModelParams-class.R R/ModelParams-validity.R R/Rules-class.R R/Rules-methods.R R/Rules-validity.R R/Samples-class.R R/Samples-methods.R R/Samples-validity.R R/Simulations-class.R R/Simulations-methods.R R/Simulations-validity.R R/checkmate.R R/crmPack-package.R R/fromQuantiles.R R/helpers.R R/helpers_broom.R R/helpers_covr.R R/helpers_data.R R/helpers_design.R R/helpers_jags.R R/helpers_knitr.R R/helpers_knitr_CohortSize.R R/helpers_knitr_Design.R R/helpers_knitr_GeneralData.R R/helpers_knitr_GeneralModel.R R/helpers_knitr_Increments.R R/helpers_knitr_NextBest.R R/helpers_knitr_SafetyWindow.R R/helpers_knitr_Stopping.R R/helpers_model.R R/helpers_rules.R R/helpers_samples.R R/helpers_simulations.R R/logger.R R/mcmc.R R/utils-pipe.R R/utils.R README.Rmd README.md design/767-reporting-crmpack-objects/knit_print.R design/concise-tidy-design.Rmd design/devel/BayesLogit.R design/devel/Dual endpoint separate model 27012015.R design/devel/TestGPA.R design/devel/classes.R design/devel/classes2.R design/devel/combo.R design/devel/dual.R design/devel/dual2.R design/devel/dualPackage.R design/devel/dualTestcode.R design/devel/funs.R design/devel/project.R design/devel/projectWithPackage.R design/devel/projectWithPackageOld.R design/devel/reporters.R design/devel/rolling-crm-Simona.Rmd design/devel/three.R design/devel/tite-crm.R design/devel/varnames.R design/ordinal-crm.Rmd design/ordinal-crm.pdf design/ordinal-crm_JK.Rmd design/ordinal_crm.Rmd design/single_combo_grouped.Rmd design/stop-specific-dose.Rmd examples/CrmPackClass-method-tidy.R examples/Data-class-DataDA.R examples/Data-class-DataDual.R examples/Data-class-DataGrouped.R examples/Data-class-DataMixture.R examples/Data-class-DataOrdinal.R examples/Data-class-DataParts.R examples/Data-class.R examples/Data-method-dose_grid_range.R examples/Data-method-getEff.R examples/Data-method-ngrid.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-DataOrdinal.R examples/Data-method-update-DataParts.R examples/Data-method-update.R examples/DataOrdinal-method-dose_grid_range.R examples/DataOrdinal-method-plot.R examples/DataOrdinal-method-update.R examples/Design-class-DADesign.R examples/Design-class-Design.R examples/Design-class-DesignGrouped.R examples/Design-class-DesignOrdinal.R examples/Design-class-DualDesign.R examples/Design-class-DualResponsesDesign.R examples/Design-class-DualResponsesSamplesDesign.R examples/Design-class-RuleDesign.R examples/Design-class-RuleDesignOrdinal.R examples/Design-class-TDDesign.R examples/Design-class-TDsamplesDesign.R examples/Design-class-ThreePlusThreeDesign.R examples/Design-method-simulate-DesignGrouped.R examples/Design-method-tidyDualDesign.R examples/Effloglog-method-tidy.R examples/GeneralData-method-tidy.R examples/LogisticIndepBeta-method-tidy.R examples/McmcOptions-class-McmcOptions.R examples/McmcOptions-methods-saveSample.R examples/McmcOptions-methods-size.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-FractionalCRM.R examples/Model-class-LogisticIndepBeta.R examples/Model-class-LogisticKadane.R examples/Model-class-LogisticKadaneBetaGamma.R examples/Model-class-LogisticLogNormal.R examples/Model-class-LogisticLogNormalGrouped.R examples/Model-class-LogisticLogNormalMixture.R examples/Model-class-LogisticLogNormalOrdinal.R examples/Model-class-LogisticLogNormalSub.R examples/Model-class-LogisticNormal.R examples/Model-class-LogisticNormalFixedMixture.R examples/Model-class-LogisticNormalMixture.R examples/Model-class-OneParExpPrior.R examples/Model-class-OneParLogNormalPrior.R examples/Model-class-ProbitLogNormal.R examples/Model-class-ProbitLogNormalRel.R examples/Model-class-TITELogisticLogNormal.R examples/Model-method-biomarker.R examples/Model-method-dose.R examples/Model-method-doseFunction.R examples/Model-method-doseFunctionLogisticLogNormalOrdinal.R examples/Model-method-doseLogisticLogNormalOrdinal.R examples/Model-method-efficacy.R examples/Model-method-efficacyFunction.R examples/Model-method-gain.R examples/Model-method-gainNoSamples.R examples/Model-method-prob.R examples/Model-method-probFunction.R examples/Model-method-probFunctionLogisticLogNormalOrdinal.R examples/Model-method-update.R examples/Rules-class-CohortSizeConst.R examples/Rules-class-CohortSizeDLT.R examples/Rules-class-CohortSizeMax.R examples/Rules-class-CohortSizeMin.R examples/Rules-class-CohortSizeOrdinal.R examples/Rules-class-CohortSizeParts.R examples/Rules-class-CohortSizeRange.R examples/Rules-class-IncrementsDoseLevels.R examples/Rules-class-IncrementsHSRBeta.R examples/Rules-class-IncrementsMin.R examples/Rules-class-IncrementsOrdinal.R examples/Rules-class-IncrementsRelative-DataParts.R examples/Rules-class-IncrementsRelative.R examples/Rules-class-IncrementsRelativeDLT.R examples/Rules-class-IncrementsRelativeDLTCurrent.R examples/Rules-class-NextBestDualEndpoint.R examples/Rules-class-NextBestMTD.R examples/Rules-class-NextBestMaxGainSamples.R examples/Rules-class-NextBestMinDist.R examples/Rules-class-NextBestNCRM.R examples/Rules-class-NextBestNCRMLoss.R examples/Rules-class-NextBestOrdinal.R examples/Rules-class-NextBestProbMTDLTE.R examples/Rules-class-NextBestProbMTDMinDist.R examples/Rules-class-NextBestTDsamples.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-StoppingExternal.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-StoppingMaxGainCIRatio.R examples/Rules-class-StoppingMinCohorts.R examples/Rules-class-StoppingMinPatients.R examples/Rules-class-StoppingMissingDose.R examples/Rules-class-StoppingOrdinal.R examples/Rules-class-StoppingPatientsNearDose.R examples/Rules-class-StoppingSpecificDose.R examples/Rules-class-StoppingTDCIRatio.R examples/Rules-class-StoppingTargetBiomarker.R examples/Rules-class-StoppingTargetProb.R examples/Rules-method-CohortSizeDLT.R examples/Rules-method-CohortSizeRange.R examples/Rules-method-CombiningStoppingRulesAndOr.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-IncrementsDoseLevels.R examples/Rules-method-maxDose-IncrementsHSRBeta.R examples/Rules-method-maxDose-IncrementsMin.R examples/Rules-method-maxDose-IncrementsOrdinal.R examples/Rules-method-maxDose-IncrementsRelative.R examples/Rules-method-maxDose-IncrementsRelativeDLT.R examples/Rules-method-maxDose-IncrementsRelativeDLTCurrent.R examples/Rules-method-maxDose-IncrementsRelativeParts.R examples/Rules-method-maxSize.R examples/Rules-method-minSize.R examples/Rules-method-nextBest-NextBestDualEndpoint.R examples/Rules-method-nextBest-NextBestMTD.R examples/Rules-method-nextBest-NextBestMaxGain.R examples/Rules-method-nextBest-NextBestMaxGainSamples.R examples/Rules-method-nextBest-NextBestMinDist.R examples/Rules-method-nextBest-NextBestNCRM-DataParts.R examples/Rules-method-nextBest-NextBestNCRM.R examples/Rules-method-nextBest-NextBestNCRMLoss.R examples/Rules-method-nextBest-NextBestOrdinal.R examples/Rules-method-nextBest-NextBestProbMTDLTE.R examples/Rules-method-nextBest-NextBestProbMtdMinDist.R examples/Rules-method-nextBest-NextBestTD.R examples/Rules-method-nextBest-NextBestTDsamples.R examples/Rules-method-nextBest-NextBestThreePlusThree.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-CohortSizeOrdinal.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-StoppingExternal.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-StoppingMissingDose.R examples/Rules-method-stopTrial-StoppingOrdinal.R examples/Rules-method-stopTrial-StoppingPatientsNearDose.R examples/Rules-method-stopTrial-StoppingSpecificDose.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-tidyCohortSizeDLT.R examples/Rules-method-tidyCohortSizeMax.R examples/Rules-method-tidyCohortSizeMin.R examples/Rules-method-tidyCohortSizeParts.R examples/Rules-method-tidyCohortSizeRange.R examples/Rules-method-tidyIncrementsMax.R examples/Rules-method-tidyIncrementsMin.R examples/Rules-method-tidyIncrementsRelative.R examples/Rules-method-tidyIncrementsRelativeDLT.R examples/Rules-method-tidyIncrementsRelativeParts.R examples/Rules-method-tidyNextBestNCRM.R examples/Rules-method-tidyNextBestNCRMLoss.R examples/Rules-method-windowLength-SafetyWindowConst.R examples/Rules-method-windowLength-SafetyWindowSize.R examples/Rules-methodTidy.R examples/Sample-methods-approximate.R examples/Sample-methods-fit-DualEndpoint.R examples/Sample-methods-fit-LogisticLogNormalOrdinal.R examples/Sample-methods-fit.R examples/Sample-methods-get.R examples/Sample-methods-plot-DualEndpoint.R examples/Sample-methods-plot.R examples/Samples-class.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/Samples-method-tidy.R examples/Samples-methods-names.R examples/Samples-methods-size.R examples/Simulation-method-show-ReportLabels.R examples/Simulations-class-DualSimulations.R examples/Simulations-class-GeneralSimulations.R examples/Simulations-class-Simulations.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-show-SimulationsSummary_additionalStats.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/Simulations-method-tidy.R examples/design-method-examine-DADesign.R examples/design-method-examine-Design.R examples/design-method-examine-RuleDesign.R examples/design-method-simulate-DADesign.R examples/design-method-simulate-Design.R examples/design-method-simulate-DualDesign.R examples/design-method-simulate-RuleDesign.R examples/design-method-simulateDualResponsesDesign.R examples/design-method-simulateDualResponsesSamplesDesign.R examples/design-method-simulateTDDesign.R examples/design-method-simulateTDsamplesDesign.R examples/helpers-jags_add_dummy.R examples/helpers-jags_get_data.R examples/helpers-jags_get_model_inits.R examples/helpers-jags_write_model.R examples/helpers-rapply.R examples/mcmc-DualEndpointBeta.R examples/mcmc-DualEndpointRW.R examples/mcmc-EffFlexi.R examples/mcmc-Effloglog.R examples/mcmc-LogisticIndepBeta.R examples/mcmc-LogisticLogNormalOrdinal.R examples/mcmc.R examples/utils-dapply.R inst/crmPack.pdf man/CohortSize-class.Rd man/CohortSizeConst-class.Rd man/CohortSizeDLT-class.Rd man/CohortSizeMax-class.Rd man/CohortSizeMin-class.Rd man/CohortSizeOrdinal-class.Rd man/CohortSizeParts-class.Rd man/CohortSizeRange-class.Rd man/CrmPackClass.Rd man/DADesign-class.Rd man/DALogisticLogNormal-class.Rd man/DASimulations-class.Rd man/DASimulations.Rd man/DLTLikelihood.Rd man/Data-class.Rd man/DataDA-class.Rd man/DataDual-class.Rd man/DataGrouped-class.Rd man/DataMixture-class.Rd man/DataOrdinal-class.Rd man/DataParts-class.Rd man/Design-class.Rd man/DesignGrouped-class.Rd man/DesignOrdinal-class.Rd man/DualDesign-class.Rd man/DualEndpoint-class.Rd man/DualEndpointBeta-class.Rd man/DualEndpointEmax-class.Rd man/DualEndpointRW-class.Rd man/DualResponsesDesign-class.Rd man/DualResponsesSamplesDesign-class.Rd man/DualSimulations-class.Rd man/DualSimulationsSummary-class.Rd man/EffFlexi-class.Rd man/Effloglog-class.Rd man/FractionalCRM-class.Rd man/GeneralData-class.Rd man/GeneralModel-class.Rd man/GeneralSimulations-class.Rd man/GeneralSimulationsSummary-class.Rd man/Increments-class.Rd man/IncrementsDoseLevels-class.Rd man/IncrementsHSRBeta-class.Rd man/IncrementsMin-class.Rd man/IncrementsOrdinal-class.Rd man/IncrementsRelative-class.Rd man/IncrementsRelativeDLT-class.Rd man/IncrementsRelativeDLTCurrent-class.Rd man/IncrementsRelativeParts-class.Rd man/LogisticIndepBeta-class.Rd man/LogisticKadane-class.Rd man/LogisticKadaneBetaGamma-class.Rd man/LogisticLogNormal-class.Rd man/LogisticLogNormalGrouped-class.Rd man/LogisticLogNormalMixture-class.Rd man/LogisticLogNormalOrdinal-class.Rd man/LogisticLogNormalSub-class.Rd man/LogisticNormal-class.Rd man/LogisticNormalFixedMixture-class.Rd man/LogisticNormalMixture-class.Rd man/McmcOptions-class.Rd man/MinimalInformative.Rd man/ModelEff-class.Rd man/ModelLogNormal-class.Rd man/ModelParamsNormal-class.Rd man/ModelPseudo-class.Rd man/ModelTox-class.Rd man/NextBest-class.Rd man/NextBestDualEndpoint-class.Rd man/NextBestInfTheory-class.Rd man/NextBestMTD-class.Rd man/NextBestMaxGain-class.Rd man/NextBestMaxGainSamples-class.Rd man/NextBestMinDist-class.Rd man/NextBestNCRM-class.Rd man/NextBestNCRMLoss-class.Rd man/NextBestOrdinal-class.Rd man/NextBestProbMTDLTE-class.Rd man/NextBestProbMTDMinDist-class.Rd man/NextBestTD-class.Rd man/NextBestTDsamples-class.Rd man/NextBestThreePlusThree-class.Rd man/OneParExpPrior-class.Rd man/OneParLogNormalPrior-class.Rd man/ProbitLogNormal-class.Rd man/ProbitLogNormalRel-class.Rd man/PseudoDualFlexiSimulations-class.Rd man/PseudoDualFlexiSimulations.Rd man/PseudoDualSimulations-class.Rd man/PseudoDualSimulationsSummary-class.Rd man/PseudoSimulations-class.Rd man/PseudoSimulationsSummary-class.Rd man/Quantiles2LogisticNormal.Rd man/Report.Rd man/RuleDesign-class.Rd man/RuleDesignOrdinal-class.Rd man/SafetyWindow-class.Rd man/SafetyWindowConst-class.Rd man/SafetyWindowSize-class.Rd man/Samples-class.Rd man/Simulations-class.Rd man/SimulationsSummary-class.Rd man/StartingDose-class.Rd man/Stopping-class.Rd man/StoppingAll-class.Rd man/StoppingAny-class.Rd man/StoppingCohortsNearDose-class.Rd man/StoppingExternal-class.Rd man/StoppingHighestDose-class.Rd man/StoppingList-class.Rd man/StoppingLowestDoseHSRBeta-class.Rd man/StoppingMTDCV-class.Rd man/StoppingMTDdistribution-class.Rd man/StoppingMaxGainCIRatio-class.Rd man/StoppingMinCohorts-class.Rd man/StoppingMinPatients-class.Rd man/StoppingMissingDose-class.Rd man/StoppingOrdinal-class.Rd man/StoppingPatientsNearDose-class.Rd man/StoppingSpecificDose-class.Rd man/StoppingTDCIRatio-class.Rd man/StoppingTargetBiomarker-class.Rd man/StoppingTargetProb-class.Rd man/TDDesign-class.Rd man/TDsamplesDesign-class.Rd man/TITELogisticLogNormal-class.Rd man/Validate.Rd man/and-Stopping-Stopping-method.Rd man/and-Stopping-StoppingAll-method.Rd man/and-StoppingAll-Stopping-method.Rd man/approximate.Rd man/assertions.Rd man/biomarker.Rd man/check_equal.Rd man/check_format.Rd man/check_length.Rd man/check_probabilities.Rd man/check_probability.Rd man/check_probability_range.Rd man/check_range.Rd man/crmPack-package.Rd man/crmPackExample.Rd man/crmPackHelp.Rd man/dapply.Rd man/dinvGamma.Rd man/dose.Rd man/doseFunction.Rd man/dose_grid_range.Rd man/efficacy.Rd man/efficacyFunction.Rd man/enable_logging.Rd man/examine.Rd man/fit.Rd man/fitGain.Rd man/fitPEM.Rd man/gain.Rd man/get-Samples-character-method.Rd man/getEff.Rd man/get_result_list.Rd man/h_all_equivalent.Rd man/h_barplot_percentages.Rd man/h_blind_plot_data.Rd man/h_calc_report_label_percentage.Rd man/h_check_fun_formals.Rd man/h_convert_ordinal_data.Rd man/h_convert_ordinal_model.Rd man/h_convert_ordinal_samples.Rd man/h_covr_helpers.Rd man/h_default_if_empty.Rd man/h_determine_dlts.Rd man/h_find_interval.Rd man/h_format_number.Rd man/h_get_formatted_dosegrid.Rd man/h_get_min_inf_beta.Rd man/h_group_data.Rd man/h_in_range.Rd man/h_info_theory_dist.Rd man/h_is_positive_definite.Rd man/h_jags_add_dummy.Rd man/h_jags_extract_samples.Rd man/h_jags_get_data.Rd man/h_jags_get_model_inits.Rd man/h_jags_join_models.Rd man/h_jags_write_model.Rd man/h_model_dual_endpoint_beta.Rd man/h_model_dual_endpoint_rho.Rd man/h_model_dual_endpoint_sigma2W.Rd man/h_model_dual_endpoint_sigma2betaW.Rd man/h_next_best_eligible_doses.Rd man/h_next_best_mg_ci.Rd man/h_next_best_mg_doses_at_grid.Rd man/h_next_best_mg_plot.Rd man/h_next_best_mgsamples_plot.Rd man/h_next_best_ncrm_loss_plot.Rd man/h_next_best_td_plot.Rd man/h_next_best_tdsamples_plot.Rd man/h_null_if_na.Rd man/h_obtain_dose_grid_range.Rd man/h_plot_data_cohort_lines.Rd man/h_plot_data_df.Rd man/h_prepare_labels.Rd man/h_prepare_units.Rd man/h_rapply.Rd man/h_simulations_output_format.Rd man/h_slots.Rd man/h_summarize_add_stats.Rd man/h_test_named_numeric.Rd man/h_this_truth.Rd man/h_unpack_stopit.Rd man/h_validate_combine_results.Rd man/h_validate_common_data_slots.Rd man/is.wholenumber.Rd man/knit_print.Rd man/logit.Rd man/match_within_tolerance.Rd man/maxDose.Rd man/maxSize.Rd man/mcmc.Rd man/minSize.Rd man/myBayesLogit.Rd man/names-Samples-method.Rd man/nextBest.Rd man/ngrid.Rd man/or-Stopping-Stopping.Rd man/or-Stopping-StoppingAny.Rd man/or-StoppingAny-Stopping.Rd man/pinvGamma.Rd man/pipe.Rd man/plot-Data-ModelTox-method.Rd man/plot-Data.Rd man/plot-DataDA-missing-method.Rd man/plot-DataDual-ModelEff-method.Rd man/plot-DataDual-missing-method.Rd man/plot-DualSimulations-missing-method.Rd man/plot-DualSimulationsSummary-missing-method.Rd man/plot-GeneralSimulations-missing-method.Rd man/plot-GeneralSimulationsSummary-missing-method.Rd man/plot-PseudoDualFlexiSimulations-missing-method.Rd man/plot-PseudoDualSimulations-missing-method.Rd man/plot-PseudoDualSimulationsSummary-missing-method.Rd man/plot-PseudoSimulationsSummary-missing-method.Rd man/plot-Samples-DALogisticLogNormal-method.Rd man/plot-Samples-DualEndpoint-method.Rd man/plot-Samples-GeneralModel-method.Rd man/plot-Samples-ModelEff-method.Rd man/plot-Samples-ModelTox-method.Rd man/plot-SimulationsSummary-missing-method.Rd man/plot.gtable.Rd man/plotDualResponses.Rd man/plotGain.Rd man/positive_number.Rd man/printVignette.Rd man/prob.Rd man/probFunction.Rd man/probit.Rd man/qinvGamma.Rd man/rinvGamma.Rd man/safeInteger.Rd man/saveSample.Rd man/set_seed.Rd man/show-DualSimulationsSummary-method.Rd man/show-GeneralSimulationsSummary-method.Rd man/show-PseudoDualSimulationsSummary-method.Rd man/show-PseudoSimulationsSummary-method.Rd man/show-SimulationsSummary-method.Rd man/simulate-DADesign-method.Rd man/simulate-Design-method.Rd man/simulate-DesignGrouped-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-PseudoDualFlexiSimulations-method.Rd man/summary-PseudoDualSimulations-method.Rd man/summary-PseudoSimulations-method.Rd man/summary-Simulations-method.Rd man/tidy.Rd man/update-Data-method.Rd man/update-DataDA-method.Rd man/update-DataDual-method.Rd man/update-DataOrdinal-method.Rd man/update-DataParts-method.Rd man/update-ModelPseudo-method.Rd man/v_cohort_size.Rd man/v_data_objects.Rd man/v_design.Rd man/v_general_simulations.Rd man/v_increments.Rd man/v_mcmcoptions_objects.Rd man/v_model_objects.Rd man/v_model_params.Rd man/v_next_best.Rd man/v_pseudo_simulations.Rd man/v_safety_window.Rd man/v_samples_objects.Rd man/v_starting_dose.Rd man/v_stopping.Rd man/windowLength.Rd tests/test-package-load.R tests/testthat.R tests/testthat/_snaps/Design-methods.md tests/testthat/_snaps/Model-class.md tests/testthat/_snaps/Model-methods.md tests/testthat/_snaps/Model-validity.md tests/testthat/_snaps/Rules-methods.md tests/testthat/_snaps/Samples-methods.md tests/testthat/_snaps/helpers_jags.md tests/testthat/_snaps/helpers_knitr.md tests/testthat/fixtures/knit_print_data_classes_template.Rmd tests/testthat/fixtures/knit_print_object_specific_template.Rmd tests/testthat/fixtures/knit_print_template.Rmd vignettes/crmPack-jss-paper.Rmd vignettes/example.Rmd vignettes/migration_from_the_old_crmPack.Rmd vignettes/ordinal-crm.Rmd vignettes/parallel_computing_with_extensions.Rmd vignettes/rolling-crm.Rmd vignettes/simulations.Rmd vignettes/tidy_method.Rmd vignettes/trial_analysis.Rmd vignettes/trial_definition.Rmd vignettes/trial_sanity_checks.Rmd vignettes/trial_simulation.Rmd