Files in crmPack

Object-Oriented Implementation of Dose Escalation Designs

NEWS.md R/helpers_knitr_CohortSize.R R/helpers_knitr_SafetyWindow.R R/CrmPackClass-methods.R R/checkmate.R R/helpers_knitr.R R/Rules-methods.R R/helpers_knitr_Increments.R R/Data-validity.R R/utils-pipe.R R/Samples-class.R R/helpers_data.R R/Model-class.R R/McmcOptions-validity.R R/Design-methods.R R/McmcOptions-methods.R R/Rules-validity.R R/ModelParams-class.R R/Simulations-methods.R R/Simulations-validity.R R/mcmc.R R/helpers_knitr_Stopping.R R/Model-methods.R R/helpers_samples.R R/helpers_rules.R R/McmcOptions-class.R R/CrmPackClass-class.R R/helpers_knitr_NextBest.R R/Simulations-class.R R/Design-class.R R/logger.R R/Data-methods.R R/fromQuantiles.R R/helpers_covr.R R/Rules-class.R R/helpers_knitr_GeneralData.R R/helpers_knitr_Design.R R/ModelParams-validity.R R/helpers_broom.R R/helpers_model.R R/helpers_knitr_GeneralModel.R R/helpers_simulations.R R/helpers_design.R R/helpers.R R/helpers_jags.R R/Design-validity.R R/crmPack-package.R R/Model-validity.R R/utils.R R/Samples-validity.R R/Samples-methods.R R/Data-class.R inst/crmPack.pdf inst/doc/rolling-crm.Rmd inst/doc/tidy_method.R inst/doc/trial_simulation.R inst/doc/trial_analysis.R inst/doc/trial_definition.R inst/doc/parallel_computing_with_extensions.R inst/doc/knit_print.Rmd inst/doc/ordinal-crm.Rmd inst/doc/crmPack-jss-paper.Rmd inst/doc/upgrading_from_the_old_crmPack.Rmd inst/doc/parallel_computing_with_extensions.Rmd inst/doc/example.Rmd inst/doc/simulations.Rmd inst/doc/simulations.R inst/doc/tidy_method.Rmd inst/doc/trial_analysis.Rmd inst/doc/ordinal-crm.R inst/doc/trial_definition.Rmd inst/doc/trial_sanity_checks.Rmd inst/doc/trial_simulation.Rmd inst/doc/upgrading_from_the_old_crmPack.R tests/testthat.R tests/test-package-load.R tests/testthat/test-helpers_design.R tests/testthat/test-sas-results-part-2.R tests/testthat/test-Design-validity.R tests/testthat/test-fromQuantiles.R tests/testthat/test-Samples-class.R tests/testthat/test-mcmc.R tests/testthat/test-helpers_covr.R tests/testthat/test-logger.R tests/testthat/test-helpers_rules.R tests/testthat/helper-model.R tests/testthat/test-CrmPackClass-methods.R tests/testthat/test-utils.R tests/testthat/test-Rules-validity.R tests/testthat/test-checkmate.R tests/testthat/test-Simulations-validity.R tests/testthat/test-Model-class.R tests/testthat/test-helpers_samples.R tests/testthat/test-Data-methods.R tests/testthat/test-sas-results-part-1.R tests/testthat/test-Simulations-class.R tests/testthat/test-helpers_knitr_Design.R tests/testthat/helper-data.R tests/testthat/test-helpers_jags.R tests/testthat/test-accuracy-published.R tests/testthat/test-McmcOptions-class.R tests/testthat/test-Rules-methods.R tests/testthat/test-Validate-class.R tests/testthat/helper-testthat.R tests/testthat/test-Model-validity.R tests/testthat/helper-rules.R tests/testthat/test-ModelParams-class.R tests/testthat/test-CrmPackClass-class.R tests/testthat/test-Samples-methods.R tests/testthat/helper-modelparams.R tests/testthat/test-Model-methods.R tests/testthat/test-Simulations-methods.R tests/testthat/test-helpers_knitr_Stopping.R tests/testthat/test-Data-class.R tests/testthat/test-helpers_knitr_SafetyWindow.R tests/testthat/test-Samples-validity.R tests/testthat/test-Design-class.R tests/testthat/test-McmcOptions-validity.R tests/testthat/test-helpers.R tests/testthat/helper-McmcOptions.R tests/testthat/test-helpers_knitr_NextBest.R tests/testthat/test-helpers_model.R tests/testthat/test-helpers-simulations.R tests/testthat/helper-samples.R tests/testthat/helper-design.R tests/testthat/test-Design-methods.R tests/testthat/test-Rules-class.R tests/testthat/test-ModelParams-validity.R tests/testthat/test-McmcOptions-methods.R tests/testthat/test-helpers_knitr.R tests/testthat/helper-logger.R tests/testthat/test-Data-validity.R tests/testthat/fixtures/knit_print_data_classes_template.Rmd tests/testthat/fixtures/knit_print_template.Rmd tests/testthat/fixtures/knit_print_object_specific_template.Rmd tests/testthat/fixtures/make_persistent_objects_for_mocked_constructors.R vignettes/rolling-crm.Rmd vignettes/knit_print.Rmd vignettes/ordinal-crm.Rmd vignettes/crmPack-jss-paper.Rmd vignettes/upgrading_from_the_old_crmPack.Rmd vignettes/parallel_computing_with_extensions.Rmd vignettes/example.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 man/enable_logging.Rd man/plot-DualSimulations-missing-method.Rd man/GeneralModel-class.Rd man/DualResponsesSamplesDesign-class.Rd man/h_jags_get_model_inits.Rd man/plot-PseudoDualSimulations-missing-method.Rd man/plot-Samples-ModelTox-method.Rd man/StoppingPatientsNearDose-class.Rd man/h_info_theory_dist.Rd man/update-DataDA-method.Rd man/h_determine_dlts.Rd man/StoppingTDCIRatio-class.Rd man/IncrementsHSRBeta-class.Rd man/StoppingMinPatients-class.Rd man/check_probabilities.Rd man/plot-Data.Rd man/LogisticKadaneBetaGamma-class.Rd man/IncrementsMin-class.Rd man/h_default_if_empty.Rd man/NextBestThreePlusThree-class.Rd man/IncrementsDoseLevels-class.Rd man/NextBestNCRMLoss-class.Rd man/plotGain.Rd man/h_validate_common_data_slots.Rd man/LogisticNormal-class.Rd man/h_get_formatted_dosegrid.Rd man/Data-class.Rd man/summary-PseudoDualFlexiSimulations-method.Rd man/myBayesLogit.Rd man/LogisticKadane-class.Rd man/show-GeneralSimulationsSummary-method.Rd man/v_data_objects.Rd man/Validate.Rd man/maxSize.Rd man/v_next_best.Rd man/StoppingExternal-class.Rd man/minSize.Rd man/mcmc.Rd man/h_is_positive_definite.Rd man/h_unpack_stopit.Rd man/DALogisticLogNormal-class.Rd man/fit.Rd man/h_group_data.Rd man/h_jags_add_dummy.Rd man/StoppingTargetBiomarker-class.Rd man/h_quantiles_target_function.Rd man/StoppingMaxGainCIRatio-class.Rd man/plot-PseudoDualFlexiSimulations-missing-method.Rd man/v_increments.Rd man/h_next_best_mg_plot.Rd man/NextBestMaxGain-class.Rd man/ProbitLogNormalRel-class.Rd man/LogisticLogNormalGrouped-class.Rd man/h_convert_ordinal_data.Rd man/summary-PseudoDualSimulations-method.Rd man/PseudoSimulations-class.Rd man/h_next_best_mg_ci.Rd man/CohortSizeMax-class.Rd man/Design-class.Rd man/h_model_dual_endpoint_rho.Rd man/LogisticLogNormalMixture-class.Rd man/v_safety_window.Rd man/plot-SimulationsSummary-missing-method.Rd man/LogisticIndepBeta-class.Rd man/StoppingMTDCV-class.Rd man/logit.Rd man/Increments-class.Rd man/DualEndpointRW-class.Rd man/LogisticLogNormalSub-class.Rd man/simulate-DualResponsesSamplesDesign-method.Rd man/h_next_best_mg_doses_at_grid.Rd man/plot-PseudoDualSimulationsSummary-missing-method.Rd man/NextBestEWOC-class.Rd man/h_in_range.Rd man/SimulationsSummary-class.Rd man/SafetyWindowConst-class.Rd man/NextBestProbMTDLTE-class.Rd man/h_plot_doses_tried.Rd man/efficacyFunction.Rd man/v_design.Rd man/h_convert_ordinal_samples.Rd man/h_model_dual_endpoint_sigma2betaw.Rd man/McmcOptions-class.Rd man/h_pseudo_sim_inverse_dose.Rd man/CohortSizeDLT-class.Rd man/show-DualSimulationsSummary-method.Rd man/knit_print.Rd man/plot-Data-ModelTox-method.Rd man/CohortSizeRange-class.Rd man/Stopping-class.Rd man/MinimalInformative.Rd man/h_pseudo_sim_fit_summary.Rd man/or-StoppingAny-Stopping.Rd man/h_covr_helpers.Rd man/h_format_number.Rd man/RuleDesignOrdinal-class.Rd man/v_pseudo_simulations.Rd man/simulate-TDDesign-method.Rd man/nextBest.Rd man/update-Data-method.Rd man/check_probability.Rd man/update-DataDual-method.Rd man/plot-PseudoSimulationsSummary-missing-method.Rd man/h_barplot_percentages.Rd man/plotDualResponses.Rd man/show-SimulationsSummary-method.Rd man/h_test_named_numeric.Rd man/StoppingOrdinal-class.Rd man/IncrementsOrdinal-class.Rd man/summary-PseudoSimulations-method.Rd man/h_convert_ordinal_model.Rd man/stopTrial.Rd man/EffFlexi-class.Rd man/NextBestProbMTDMinDist-class.Rd man/PseudoSimulationsSummary-class.Rd man/CohortSizeParts-class.Rd man/Simulations-class.Rd man/h_validate_combine_results.Rd man/plot-Samples-GeneralModel-method.Rd man/IncrementsRelativeParts-class.Rd man/saveSample.Rd man/biomarker.Rd man/qinvGamma.Rd man/h_plot_data_cohort_lines.Rd man/h_simulations_output_format.Rd man/h_prepare_labels.Rd man/h_plot_simulation_trajectory.Rd man/ModelLogNormal-class.Rd man/ngrid.Rd man/StoppingAny-class.Rd man/plot-GeneralSimulations-missing-method.Rd man/simulate-DualResponsesDesign-method.Rd man/DataOrdinal-class.Rd man/windowLength.Rd man/get-Samples-character-method.Rd man/DataDA-class.Rd man/PseudoDualSimulationsSummary-class.Rd man/DualEndpointBeta-class.Rd man/h_next_best_eligible_doses.Rd man/Quantiles2LogisticNormal.Rd man/DualSimulations-class.Rd man/TDDesign-class.Rd man/StoppingLowestDoseHSRBeta-class.Rd man/DualEndpoint-class.Rd man/v_samples_objects.Rd man/update-DataParts-method.Rd man/crmPack.Rd man/v_starting_dose.Rd man/and-Stopping-Stopping-method.Rd man/plot-Samples-DualEndpoint-method.Rd man/check_equal.Rd man/h_jags_write_model.Rd man/h_all_equivalent.Rd man/TDsamplesDesign-class.Rd man/NextBestMinDist-class.Rd man/IncrementsMaxToxProb-class.Rd man/OneParLogNormalPrior-class.Rd man/ProbitLogNormal-class.Rd man/plot-GeneralSimulationsSummary-missing-method.Rd man/efficacy.Rd man/IncrementsRelativeDLT-class.Rd man/h_find_interval.Rd man/examine.Rd man/LogisticNormalMixture-class.Rd man/set_seed.Rd man/LogisticNormalFixedMixture-class.Rd man/update-DataOrdinal-method.Rd man/StoppingCohortsNearDose-class.Rd man/CohortSizeMin-class.Rd man/StoppingMinCohorts-class.Rd man/size.Rd man/plot-Samples-ModelEff-method.Rd man/doseFunction.Rd man/NextBestTD-class.Rd man/h_next_best_tdsamples_plot.Rd man/h_summarize_add_stats.Rd man/fitPEM.Rd man/h_rapply.Rd man/h_jags_extract_samples.Rd man/h_calc_report_label_percentage.Rd man/h_this_truth.Rd man/NextBestMaxGainSamples-class.Rd man/StoppingMTDdistribution-class.Rd man/simulate-DADesign-method.Rd man/show-PseudoDualSimulationsSummary-method.Rd man/h_next_best_mgsamples_plot.Rd man/GeneralSimulations-class.Rd man/v_stopping.Rd man/h_jags_join_models.Rd man/h_check_fun_formals.Rd man/rinvGamma.Rd man/maxDose.Rd man/v_cohort_size.Rd man/check_length.Rd man/plot-DualSimulationsSummary-missing-method.Rd man/DataParts-class.Rd man/simulate-DesignGrouped-method.Rd man/v_general_simulations.Rd man/NextBestTDsamples-class.Rd man/DataGrouped-class.Rd man/PseudoDualFlexiSimulations-class.Rd man/NextBestDualEndpoint-class.Rd man/DualDesign-class.Rd man/pipe.Rd man/DASimulations-class.Rd man/StoppingList-class.Rd man/summary-DualSimulations-method.Rd man/CrmPackClass.Rd man/StoppingAll-class.Rd man/PseudoDualSimulations-class.Rd man/prob.Rd man/dinvGamma.Rd man/ModelTox-class.Rd man/SafetyWindow-class.Rd man/SafetyWindowSize-class.Rd man/crmPackExample.Rd man/probit.Rd man/ModelPseudo-class.Rd man/CohortSizeOrdinal-class.Rd man/IncrementsRelative-class.Rd man/plot-DataDual-ModelEff-method.Rd man/StartingDose-class.Rd man/h_blind_plot_data.Rd man/h_model_dual_endpoint_sigma2w.Rd man/plot-DataDual-missing-method.Rd man/DualSimulationsSummary-class.Rd man/h_obtain_dose_grid_range.Rd man/DualEndpointEmax-class.Rd man/v_mcmcoptions_objects.Rd man/FractionalCRM-class.Rd man/check_format.Rd man/fitGain.Rd man/DADesign-class.Rd man/check_probability_range.Rd man/LogisticLogNormalOrdinal-class.Rd man/gain.Rd man/approximate.Rd man/and-StoppingAll-Stopping-method.Rd man/Effloglog-class.Rd man/NextBest-class.Rd man/dapply.Rd man/Samples-class.Rd man/h_plot_data_df.Rd man/h_next_best_td_plot.Rd man/probFunction.Rd man/h_get_min_inf_beta.Rd man/NextBestMTD-class.Rd man/or-Stopping-Stopping.Rd man/DualResponsesDesign-class.Rd man/StoppingHighestDose-class.Rd man/LogisticLogNormal-class.Rd man/GeneralSimulationsSummary-class.Rd man/v_model_objects.Rd man/DataDual-class.Rd man/printVignette.Rd man/NextBestNCRM-class.Rd man/simulate-TDsamplesDesign-method.Rd man/plot.gtable.Rd man/DesignGrouped-class.Rd man/CohortSizeConst-class.Rd man/simulate-Design-method.Rd man/positive_number.Rd man/tidy.Rd man/dose_grid_range.Rd man/match_within_tolerance.Rd man/h_prepare_units.Rd man/DLTLikelihood.Rd man/names-Samples-method.Rd man/simulate-DualDesign-method.Rd man/TITELogisticLogNormal-class.Rd man/CohortSize-class.Rd man/plot-DataDA-missing-method.Rd man/ModelEff-class.Rd man/or-Stopping-StoppingAny.Rd man/crmPackHelp.Rd man/h_slots.Rd man/NextBestInfTheory-class.Rd man/DesignOrdinal-class.Rd man/h_model_dual_endpoint_beta.Rd man/getEff.Rd man/NextBestOrdinal-class.Rd man/h_null_if_na.Rd man/plot-Samples-DALogisticLogNormal-method.Rd man/get_result_list.Rd man/DataMixture-class.Rd man/IncrementsRelativeDLTCurrent-class.Rd man/GeneralData-class.Rd man/assertions.Rd man/check_range.Rd man/h_jags_get_data.Rd man/summary-Simulations-method.Rd man/ModelParamsNormal-class.Rd man/v_model_params.Rd man/h_get_quantiles_start_values.Rd man/pinvGamma.Rd man/StoppingMissingDose-class.Rd man/h_next_best_ncrm_loss_plot.Rd man/h_knit_format_func.Rd man/show-PseudoSimulationsSummary-method.Rd man/RuleDesign-class.Rd man/StoppingTargetProb-class.Rd man/update-ModelPseudo-method.Rd man/and-Stopping-StoppingAll-method.Rd man/OneParExpPrior-class.Rd man/summary-GeneralSimulations-method.Rd man/dose.Rd man/StoppingSpecificDose-class.Rd man/simulate-RuleDesign-method.Rd