├── .Rbuildignore ├── .github ├── .gitignore └── workflows │ ├── R-CMD-check.yaml │ └── test-coverage.yaml ├── .gitignore ├── DESCRIPTION ├── LICENSE.md ├── NAMESPACE ├── NEWS.md ├── R ├── arm.R ├── arms.R ├── bootstrap.R ├── check.R ├── covariate.R ├── covariates.R ├── data.R ├── dataset.R ├── dataset_config.R ├── dataset_summary.R ├── declare_settings.R ├── default_plot.R ├── distribution.R ├── dose_adaptation.R ├── dose_adaptations.R ├── event.R ├── event_logic.R ├── events.R ├── generic.R ├── global.R ├── hardware_settings.R ├── internal_settings.R ├── nocb_settings.R ├── observations.R ├── observations_set.R ├── occasion.R ├── occasions.R ├── outfun.R ├── plan_setup.R ├── progress_settings.R ├── protocol.R ├── repeated_schedule.R ├── results_processing.R ├── scenario.R ├── scenarios.R ├── seed.R ├── simulate.R ├── simulate_preprocess.R ├── simulation_engine.R ├── simulation_progress.R ├── simulation_settings.R ├── solver_settings.R ├── time_entry.R ├── time_utilities.R ├── treatment.R ├── treatment_entry.R ├── treatment_iov.R ├── treatment_iovs.R └── utilities.R ├── README.Rmd ├── README.md ├── _pkgdown.yml ├── campsis.Rproj ├── codecov.yml ├── cran-comments.md ├── data-raw └── nhanes_database.R ├── data └── nhanes.rda ├── man ├── Arm.Rd ├── BinomialDistribution.Rd ├── Bolus.Rd ├── Bootstrap.Rd ├── BootstrapDistribution.Rd ├── ConstantDistribution.Rd ├── Covariate.Rd ├── CyclicSchedule.Rd ├── Dataset.Rd ├── DatasetConfig.Rd ├── DatasetSummary.Rd ├── Declare.Rd ├── DiscreteDistribution.Rd ├── DoseAdaptation.Rd ├── EtaDistribution.Rd ├── Event.Rd ├── EventCovariate.Rd ├── EventIteration.Rd ├── EventRelatedObservations.Rd ├── Events.Rd ├── FixedDistribution.Rd ├── FunctionDistribution.Rd ├── Hardware.Rd ├── IOV.Rd ├── Infusion.Rd ├── LogNormalDistribution.Rd ├── NOCB.Rd ├── NormalDistribution.Rd ├── Observations.Rd ├── Occasion.Rd ├── Outfun.Rd ├── PI.Rd ├── ParameterDistribution.Rd ├── Progress.Rd ├── RepeatAtSchedule.Rd ├── Scenario.Rd ├── Scenarios.Rd ├── Settings.Rd ├── SimulationProgress.Rd ├── Solver.Rd ├── TimeVaryingCovariate.Rd ├── UniformDistribution.Rd ├── VPC.Rd ├── applyCompartmentCharacteristics.Rd ├── applyScenario.Rd ├── arm-class.Rd ├── arms-class.Rd ├── assignDoseNumber.Rd ├── bolus-class.Rd ├── bolus_wrapper-class.Rd ├── bootstrap-class.Rd ├── bootstrap_distribution-class.Rd ├── campsis_handler.Rd ├── checkIIandADDL.Rd ├── computeIncrementalProgress.Rd ├── constant_distribution-class.Rd ├── convertTime.Rd ├── counterBalanceLocfMode.Rd ├── counterBalanceNocbMode.Rd ├── covariate-class.Rd ├── covariates-class.Rd ├── cutTableForEvent.Rd ├── cyclic_schedule-class.Rd ├── dataset-class.Rd ├── dataset_config-class.Rd ├── days.Rd ├── declare_settings-class.Rd ├── distribution-class.Rd ├── dose_adaptation-class.Rd ├── dose_adaptations-class.Rd ├── dosingOnly.Rd ├── dropOthers.Rd ├── event-class.Rd ├── event_covariate-class.Rd ├── events-class.Rd ├── exportDelegate.Rd ├── exportTableDelegate.Rd ├── factorScenarios.Rd ├── figures │ ├── logo.png │ └── readme_plot-1.png ├── fillIOVOccColumns.Rd ├── fixed_covariate-class.Rd ├── fixed_distribution-class.Rd ├── function_distribution-class.Rd ├── generateIIV.Rd ├── generateIIV_.Rd ├── getAvailableTimeUnits.Rd ├── getColumn.Rd ├── getCompartmentMapping.Rd ├── getCovariates.Rd ├── getDatasetMaxTime.Rd ├── getEventCovariates.Rd ├── getEventIterations.Rd ├── getFixedCovariates.Rd ├── getFurrrScheduling.Rd ├── getIOVs.Rd ├── getInitialConditions.Rd ├── getOccasions.Rd ├── getRandomSeedValue.Rd ├── getSeed.Rd ├── getSeedForDatasetExport.Rd ├── getSeedForIteration.Rd ├── getSeedForParametersSampling.Rd ├── getSimulationEngineType.Rd ├── getSplittingConfiguration.Rd ├── getTimeVaryingCovariates.Rd ├── getTimeVaryingVariables.Rd ├── getTimes.Rd ├── hardware_settings-class.Rd ├── hours.Rd ├── importCampsismodToNamespace.Rd ├── infusion-class.Rd ├── infusion_wrapper-class.Rd ├── internal_settings-class.Rd ├── isEmptyBootstrap.Rd ├── leftJoinIIV.Rd ├── length-arm-method.Rd ├── length-cyclic_schedule-method.Rd ├── length-dataset-method.Rd ├── length-repeat_at_schedule-method.Rd ├── mergeTimeVaryingCovariates.Rd ├── minutes.Rd ├── months.Rd ├── mrgsolve_engine-class.Rd ├── nhanes.Rd ├── nocb_settings-class.Rd ├── obsOnly.Rd ├── observations-class.Rd ├── observations_set-class.Rd ├── occasion-class.Rd ├── occasions-class.Rd ├── onCI.Rd ├── onCran.Rd ├── output_function-class.Rd ├── preprocessArmColumn.Rd ├── preprocessDest.Rd ├── preprocessDosing.Rd ├── preprocessEvents.Rd ├── preprocessIds.Rd ├── preprocessNocbvars.Rd ├── preprocessOutfun.Rd ├── preprocessOutvars.Rd ├── preprocessReplicates.Rd ├── preprocessScenarios.Rd ├── preprocessSettings.Rd ├── preprocessSlices.Rd ├── preprocessTSLDAndTDOSColumn.Rd ├── preprocessTablefun.Rd ├── processAllTimeColumns.Rd ├── processArmLabels.Rd ├── processDropOthers.Rd ├── processSimulateArguments.Rd ├── progress_settings-class.Rd ├── protocol-class.Rd ├── removeInitialConditions.Rd ├── reorderColumns.Rd ├── repeatSchedule.Rd ├── repeat_at_schedule-class.Rd ├── repeated_schedule-class.Rd ├── retrieveParameterValue.Rd ├── rxode_engine-class.Rd ├── sample.Rd ├── sampleCovariatesList.Rd ├── sampleDistributionAsTibble.Rd ├── sampleTimeVaryingCovariates.Rd ├── scatterPlot.Rd ├── scenario-class.Rd ├── scenarios-class.Rd ├── seconds.Rd ├── setLabel.Rd ├── setSeed.Rd ├── setSubjects.Rd ├── setupPlanDefault.Rd ├── setupPlanSequential.Rd ├── shadedPlot.Rd ├── simulate.Rd ├── simulateDelegate.Rd ├── simulateDelegateCore.Rd ├── simulateScenarios.Rd ├── simulation_engine-class.Rd ├── simulation_progress-class.Rd ├── simulation_settings-class.Rd ├── solver_settings-class.Rd ├── spaghettiPlot.Rd ├── splitDataset.Rd ├── standardiseTime.Rd ├── time_varying_covariate-class.Rd ├── toDatasetSummary.Rd ├── toExplicitDistribution.Rd ├── treatment-class.Rd ├── treatment_iov-class.Rd ├── treatment_iovs-class.Rd ├── undefined_distribution-class.Rd ├── undefined_schedule-class.Rd ├── uniteColumns.Rd ├── unwrapTreatment.Rd ├── updateADDL.Rd ├── updateAmount.Rd ├── updateII.Rd ├── updateRepeat.Rd ├── vpcPlot.Rd ├── weeks.Rd └── years.Rd ├── pkgdown └── favicon │ ├── apple-touch-icon.png │ ├── favicon-96x96.png │ ├── favicon.ico │ ├── favicon.svg │ ├── site.webmanifest │ ├── web-app-manifest-192x192.png │ └── web-app-manifest-512x512.png ├── tests ├── testthat.R └── testthat │ ├── _snaps │ ├── testDefaultPlots │ │ ├── scatterplot-colour-scenario.svg │ │ ├── scatterplot-no-colour.svg │ │ ├── shadedplot-colour-arm-strat-wt.svg │ │ ├── shadedplot-colour-arm-wt-strat-wt.svg │ │ ├── shadedplot-colour-scenario.svg │ │ ├── spaghettiplot-colour-arm-strat-wt.svg │ │ └── spaghettiplot-colour-scenario.svg │ └── testSimulateReplicates │ │ └── vpc-specified-outfun.svg │ ├── models │ ├── minimalist_model │ │ └── model.campsis │ ├── simple_tte_model │ │ ├── model.campsis │ │ ├── omega.csv │ │ ├── sigma.csv │ │ └── theta.csv │ └── weibull_model │ │ ├── model.campsis │ │ ├── omega.csv │ │ ├── sigma.csv │ │ └── theta.csv │ ├── non_regression │ ├── 3_bolus_iov_on_f1_cp.csv │ ├── 3_boluses_iiv_alag1.csv │ ├── 3_boluses_iiv_f1.csv │ ├── 3_boluses_iiv_iov_alag1.csv │ ├── 3_boluses_iiv_iov_alag1_cp.csv │ ├── 3_boluses_iiv_iov_f1.csv │ ├── 3_boluses_iiv_iov_f1_cp.csv │ ├── 3_boluses_iov_cl_cp.csv │ ├── 3_boluses_iov_ka_1.csv │ ├── 3_boluses_iov_ka_1_cp.csv │ ├── 3_boluses_iov_ka_2.csv │ ├── 3_boluses_iov_ka_2_cp.csv │ ├── 3_infusions_iiv_d1.csv │ ├── 3_infusions_iiv_iov_d1.csv │ ├── 3_infusions_iiv_iov_d1_cp.csv │ ├── advan1_trans1_conc.csv │ ├── bolus_2arms.csv │ ├── bolus_2arms_bioavailability.csv │ ├── bolus_2arms_cp.csv │ ├── bolus_2arms_cp_arm.csv │ ├── bolus_fixed_lag_time_cp.csv │ ├── bolus_fixed_lag_time_dataset.csv │ ├── bolus_fixed_lag_time_model.csv │ ├── bolus_infusion_same_cmt.csv │ ├── bolus_infusion_same_cmt_cp.csv │ ├── clear_central_event_cp.csv │ ├── dose_adaptation_by_bw.csv │ ├── dose_adaptation_by_bw_a_test.csv │ ├── dose_adaptation_by_bw_cp.csv │ ├── dose_adaptation_by_bw_infusion.csv │ ├── dose_adaptation_by_bw_infusion_cp.csv │ ├── dose_adaptation_ctrough_cp_dose.csv │ ├── ds_export_parallel_disabled_wt_iov_covariate.csv │ ├── ds_export_parallel_enabled_wt_iov_covariate.csv │ ├── event_daily_dose_cp.csv │ ├── event_in_multiple_arms_cp.csv │ ├── event_interruption_at_dose_cp.csv │ ├── event_interruption_at_dose_iov_cp.csv │ ├── event_varying_bw_2arms_ind_cp.csv │ ├── event_varying_bw_cp.csv │ ├── full_uncertainty_cp.csv │ ├── full_uncertainty_y.csv │ ├── infusion_duration.csv │ ├── infusion_duration_cp.csv │ ├── infusion_rate_lag_time1_dataset.csv │ ├── infusion_rate_lag_time1_dataset_cp.csv │ ├── infusion_rate_lag_time2_dataset.csv │ ├── infusion_rate_lag_time2_dataset_cp.csv │ ├── initial_conditions_cp.csv │ ├── layer_added_to_multiple_arm_dataset.csv │ ├── minimalist_model_a_central.csv │ ├── multiple_doses_repeat_option_cp.csv │ ├── objects_defined_in_different_order.csv │ ├── occ_as_time_varying_cov.csv │ ├── occ_as_time_varying_cov_cp.csv │ ├── replicates_in_parallel_conc.csv │ ├── scenarios_few_changes_on_dataset_scenario_cp.csv │ ├── scenarios_few_changes_on_model_scenario_cp.csv │ ├── simple_bolus.csv │ ├── simple_bolus_bioavailability.csv │ ├── simple_bolus_bioavailability_cp.csv │ ├── simple_bolus_cp.csv │ ├── simple_tte_model_a_survival_trigger.csv │ ├── trim_covariate_my_cov.csv │ ├── vectorised_compartment_properties.csv │ ├── weibull_model_conc.csv │ ├── wt_as_time_varying_cov.csv │ ├── wt_as_time_varying_cov_locf_cp.csv │ └── wt_as_time_varying_cov_nocb_cp.csv │ ├── testArm.R │ ├── testArms.R │ ├── testBootstrap.R │ ├── testCompilationError.R │ ├── testCovariate.R │ ├── testCovariates.R │ ├── testDataset.R │ ├── testDatasetExportParallelisation.R │ ├── testDefaultPlots.R │ ├── testDistribution.R │ ├── testDoseAdaptation.R │ ├── testEvent.R │ ├── testEvents.R │ ├── testObservations.R │ ├── testOccasion.R │ ├── testOccasions.R │ ├── testRepeatedSchedule.R │ ├── testScenario.R │ ├── testScenarios.R │ ├── testSeed.R │ ├── testSettings.R │ ├── testShowMethod.R │ ├── testSimulateArguments.R │ ├── testSimulateBioavailability.R │ ├── testSimulateBolus.R │ ├── testSimulateBolusInfusionSameCmt.R │ ├── testSimulateDeclare.R │ ├── testSimulateDoseAdaptation.R │ ├── testSimulateDosingInfo.R │ ├── testSimulateEvents.R │ ├── testSimulateEventsLogic.R │ ├── testSimulateIOV.R │ ├── testSimulateInfusion.R │ ├── testSimulateInit.R │ ├── testSimulateLagTime.R │ ├── testSimulateMinimalistModel.R │ ├── testSimulateNoOmega.R │ ├── testSimulateNocbLocf.R │ ├── testSimulateOutvars.R │ ├── testSimulateRUV.R │ ├── testSimulateReplicates.R │ ├── testSimulateScenarios.R │ ├── testSimulateTSLD.R │ ├── testSimulateTTEModels.R │ ├── testSimulateTable.R │ ├── testSimulateTimeVaryingCovariates.R │ ├── testSimulateWeirdCases.R │ ├── testTimeUtilities.R │ ├── testTreatment.R │ ├── testTreatmentEntry.R │ └── testUtils.R └── vignettes ├── campsis.Rmd ├── resources ├── Targets_Squeletton │ ├── R │ │ 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