Files in Calvagone/campsis
Generic PK/PD Simulation Platform CAMPSIS
.Rbuildignore
.github/.gitignore
.github/workflows/R-CMD-check.yaml
.github/workflows/test-coverage.yaml
.gitignore
DESCRIPTION
LICENSE.md
NAMESPACE
NEWS.md
R/arm.R
R/arms.R
R/bootstrap.R
R/check.R
R/covariate.R
R/covariates.R
R/data.R
R/dataset.R
R/dataset_config.R
R/dataset_summary.R
R/declare_settings.R
R/default_plot.R
R/distribution.R
R/dose_adaptation.R
R/dose_adaptations.R
R/event.R
R/event_logic.R
R/events.R
R/generic.R
R/global.R
R/hardware_settings.R
R/internal_settings.R
R/nocb_settings.R
R/observations.R
R/observations_set.R
R/occasion.R
R/occasions.R
R/outfun.R
R/parameter_uncertainty.R
R/plan_setup.R
R/progress_settings.R
R/protocol.R
R/results_processing.R
R/scenario.R
R/scenarios.R
R/seed.R
R/simulate.R
R/simulate_preprocess.R
R/simulation_engine.R
R/simulation_progress.R
R/simulation_settings.R
R/solver_settings.R
R/time_entry.R
R/time_utilities.R
R/treatment.R
R/treatment_entry.R
R/treatment_iov.R
R/treatment_iovs.R
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
man/BinomialDistribution.Rd
man/Bolus.Rd
man/Bootstrap.Rd
man/BootstrapDistribution.Rd
man/ConstantDistribution.Rd
man/Covariate.Rd
man/Dataset.Rd
man/DatasetConfig.Rd
man/DatasetSummary.Rd
man/Declare.Rd
man/DiscreteDistribution.Rd
man/DoseAdaptation.Rd
man/EtaDistribution.Rd
man/Event.Rd
man/EventCovariate.Rd
man/EventIteration.Rd
man/EventRelatedObservations.Rd
man/Events.Rd
man/FixedDistribution.Rd
man/FunctionDistribution.Rd
man/Hardware.Rd
man/IOV.Rd
man/Infusion.Rd
man/LogNormalDistribution.Rd
man/NOCB.Rd
man/NormalDistribution.Rd
man/Observations.Rd
man/Occasion.Rd
man/Outfun.Rd
man/PI.Rd
man/ParameterDistribution.Rd
man/Progress.Rd
man/Scenario.Rd
man/Scenarios.Rd
man/Settings.Rd
man/SimulationProgress.Rd
man/Solver.Rd
man/TimeVaryingCovariate.Rd
man/UniformDistribution.Rd
man/VPC.Rd
man/applyCompartmentCharacteristics.Rd
man/applyScenario.Rd
man/arm-class.Rd
man/arms-class.Rd
man/assignDoseNumber.Rd
man/bolus-class.Rd
man/bootstrap-class.Rd
man/bootstrap_distribution-class.Rd
man/campsis_handler.Rd
man/checkIIandADDL.Rd
man/computeIncrementalProgress.Rd
man/constant_distribution-class.Rd
man/convertTime.Rd
man/counterBalanceLocfMode.Rd
man/counterBalanceNocbMode.Rd
man/covariate-class.Rd
man/covariates-class.Rd
man/cutTableForEvent.Rd
man/dataset-class.Rd
man/dataset_config-class.Rd
man/days.Rd
man/declare_settings-class.Rd
man/distribution-class.Rd
man/dose_adaptation-class.Rd
man/dose_adaptations-class.Rd
man/dosingOnly.Rd
man/dropOthers.Rd
man/event-class.Rd
man/event_covariate-class.Rd
man/events-class.Rd
man/exportDelegate.Rd
man/exportTableDelegate.Rd
man/factorScenarios.Rd
man/figures/logo.png
man/figures/readme_plot-1.png
man/fillIOVOccColumns.Rd
man/fixed_covariate-class.Rd
man/fixed_distribution-class.Rd
man/function_distribution-class.Rd
man/generateIIV.Rd
man/generateIIV_.Rd
man/getAvailableTimeUnits.Rd
man/getColumn.Rd
man/getCovariates.Rd
man/getDatasetMaxTime.Rd
man/getEventCovariates.Rd
man/getEventIterations.Rd
man/getFixedCovariates.Rd
man/getFurrrScheduling.Rd
man/getIOVs.Rd
man/getInitialConditions.Rd
man/getOccasions.Rd
man/getRandomSeedValue.Rd
man/getSeed.Rd
man/getSeedForDatasetExport.Rd
man/getSeedForIteration.Rd
man/getSeedForParametersSampling.Rd
man/getSimulationEngineType.Rd
man/getSplittingConfiguration.Rd
man/getTimeVaryingCovariates.Rd
man/getTimeVaryingVariables.Rd
man/getTimes.Rd
man/hardware_settings-class.Rd
man/hours.Rd
man/importCampsismodToNamespace.Rd
man/infusion-class.Rd
man/internal_settings-class.Rd
man/isEmptyBootstrap.Rd
man/leftJoinIIV.Rd
man/length-arm-method.Rd
man/length-dataset-method.Rd
man/mergeTimeVaryingCovariates.Rd
man/minutes.Rd
man/months.Rd
man/mrgsolve_engine-class.Rd
man/nhanes.Rd
man/nocb_settings-class.Rd
man/obsOnly.Rd
man/observations-class.Rd
man/observations_set-class.Rd
man/occasion-class.Rd
man/occasions-class.Rd
man/onCI.Rd
man/onCran.Rd
man/output_function-class.Rd
man/preprocessArmColumn.Rd
man/preprocessDest.Rd
man/preprocessDosing.Rd
man/preprocessEvents.Rd
man/preprocessIds.Rd
man/preprocessNocbvars.Rd
man/preprocessOutfun.Rd
man/preprocessOutvars.Rd
man/preprocessReplicates.Rd
man/preprocessScenarios.Rd
man/preprocessSettings.Rd
man/preprocessSlices.Rd
man/preprocessTSLDAndTDOSColumn.Rd
man/preprocessTablefun.Rd
man/processAllTimeColumns.Rd
man/processArmLabels.Rd
man/processDropOthers.Rd
man/processSimulateArguments.Rd
man/progress_settings-class.Rd
man/protocol-class.Rd
man/removeInitialConditions.Rd
man/reorderColumns.Rd
man/retrieveParameterValue.Rd
man/rxode_engine-class.Rd
man/sample.Rd
man/sampleCovariatesList.Rd
man/sampleDistributionAsTibble.Rd
man/sampleTimeVaryingCovariates.Rd
man/scatterPlot.Rd
man/scenario-class.Rd
man/scenarios-class.Rd
man/seconds.Rd
man/setLabel.Rd
man/setSeed.Rd
man/setSubjects.Rd
man/setupPlanDefault.Rd
man/setupPlanSequential.Rd
man/shadedPlot.Rd
man/simulate.Rd
man/simulateDelegate.Rd
man/simulateDelegateCore.Rd
man/simulateScenarios.Rd
man/simulation_engine-class.Rd
man/simulation_progress-class.Rd
man/simulation_settings-class.Rd
man/solver_settings-class.Rd
man/spaghettiPlot.Rd
man/splitDataset.Rd
man/standardiseTime.Rd
man/time_varying_covariate-class.Rd
man/toDatasetSummary.Rd
man/toExplicitDistribution.Rd
man/treatment-class.Rd
man/treatment_iov-class.Rd
man/treatment_iovs-class.Rd
man/undefined_distribution-class.Rd
man/uniteColumns.Rd
man/vpcPlot.Rd
man/weeks.Rd
man/years.Rd
pkgdown/favicon/apple-touch-icon.png
pkgdown/favicon/favicon-96x96.png
pkgdown/favicon/favicon.ico
pkgdown/favicon/favicon.svg
pkgdown/favicon/site.webmanifest
pkgdown/favicon/web-app-manifest-192x192.png
pkgdown/favicon/web-app-manifest-512x512.png
tests/testthat.R
tests/testthat/_snaps/testDefaultPlots/scatterplot-colour-scenario.svg
tests/testthat/_snaps/testDefaultPlots/scatterplot-no-colour.svg
tests/testthat/_snaps/testDefaultPlots/shadedplot-colour-arm-strat-wt.svg
tests/testthat/_snaps/testDefaultPlots/shadedplot-colour-arm-wt-strat-wt.svg
tests/testthat/_snaps/testDefaultPlots/shadedplot-colour-scenario.svg
tests/testthat/_snaps/testDefaultPlots/spaghettiplot-colour-arm-strat-wt.svg
tests/testthat/_snaps/testDefaultPlots/spaghettiplot-colour-scenario.svg
tests/testthat/_snaps/testSimulateReplicates/vpc-specified-outfun.svg
tests/testthat/models/minimalist_model/model.campsis
tests/testthat/models/simple_tte_model/model.campsis
tests/testthat/models/simple_tte_model/omega.csv
tests/testthat/models/simple_tte_model/sigma.csv
tests/testthat/models/simple_tte_model/theta.csv
tests/testthat/models/weibull_model/model.campsis
tests/testthat/models/weibull_model/omega.csv
tests/testthat/models/weibull_model/sigma.csv
tests/testthat/models/weibull_model/theta.csv
tests/testthat/non_regression/3_bolus_iov_on_f1_cp.csv
tests/testthat/non_regression/3_boluses_iiv_alag1.csv
tests/testthat/non_regression/3_boluses_iiv_f1.csv
tests/testthat/non_regression/3_boluses_iiv_iov_alag1.csv
tests/testthat/non_regression/3_boluses_iiv_iov_alag1_cp.csv
tests/testthat/non_regression/3_boluses_iiv_iov_f1.csv
tests/testthat/non_regression/3_boluses_iiv_iov_f1_cp.csv
tests/testthat/non_regression/3_boluses_iov_cl_cp.csv
tests/testthat/non_regression/3_boluses_iov_ka_1.csv
tests/testthat/non_regression/3_boluses_iov_ka_1_cp.csv
tests/testthat/non_regression/3_boluses_iov_ka_2.csv
tests/testthat/non_regression/3_boluses_iov_ka_2_cp.csv
tests/testthat/non_regression/3_infusions_iiv_d1.csv
tests/testthat/non_regression/3_infusions_iiv_iov_d1.csv
tests/testthat/non_regression/3_infusions_iiv_iov_d1_cp.csv
tests/testthat/non_regression/advan1_trans1_conc.csv
tests/testthat/non_regression/bolus_2arms.csv
tests/testthat/non_regression/bolus_2arms_bioavailability.csv
tests/testthat/non_regression/bolus_2arms_cp.csv
tests/testthat/non_regression/bolus_2arms_cp_arm.csv
tests/testthat/non_regression/bolus_fixed_lag_time_cp.csv
tests/testthat/non_regression/bolus_fixed_lag_time_dataset.csv
tests/testthat/non_regression/bolus_fixed_lag_time_model.csv
tests/testthat/non_regression/bolus_infusion_same_cmt.csv
tests/testthat/non_regression/bolus_infusion_same_cmt_cp.csv
tests/testthat/non_regression/clear_central_event_cp.csv
tests/testthat/non_regression/dose_adaptation_by_bw.csv
tests/testthat/non_regression/dose_adaptation_by_bw_a_test.csv
tests/testthat/non_regression/dose_adaptation_by_bw_cp.csv
tests/testthat/non_regression/dose_adaptation_by_bw_infusion.csv
tests/testthat/non_regression/dose_adaptation_by_bw_infusion_cp.csv
tests/testthat/non_regression/dose_adaptation_ctrough_cp_dose.csv
tests/testthat/non_regression/ds_export_parallel_disabled_wt_iov_covariate.csv
tests/testthat/non_regression/ds_export_parallel_enabled_wt_iov_covariate.csv
tests/testthat/non_regression/event_daily_dose_cp.csv
tests/testthat/non_regression/event_in_multiple_arms_cp.csv
tests/testthat/non_regression/event_interruption_at_dose_cp.csv
tests/testthat/non_regression/event_interruption_at_dose_iov_cp.csv
tests/testthat/non_regression/event_varying_bw_2arms_ind_cp.csv
tests/testthat/non_regression/event_varying_bw_cp.csv
tests/testthat/non_regression/full_uncertainty_cp.csv
tests/testthat/non_regression/full_uncertainty_y.csv
tests/testthat/non_regression/infusion_duration.csv
tests/testthat/non_regression/infusion_duration_cp.csv
tests/testthat/non_regression/infusion_rate_lag_time1_dataset.csv
tests/testthat/non_regression/infusion_rate_lag_time1_dataset_cp.csv
tests/testthat/non_regression/infusion_rate_lag_time2_dataset.csv
tests/testthat/non_regression/infusion_rate_lag_time2_dataset_cp.csv
tests/testthat/non_regression/initial_conditions_cp.csv
tests/testthat/non_regression/layer_added_to_multiple_arm_dataset.csv
tests/testthat/non_regression/minimalist_model_a_central.csv
tests/testthat/non_regression/objects_defined_in_different_order.csv
tests/testthat/non_regression/occ_as_time_varying_cov.csv
tests/testthat/non_regression/occ_as_time_varying_cov_cp.csv
tests/testthat/non_regression/replicates_in_parallel_conc.csv
tests/testthat/non_regression/scenarios_few_changes_on_dataset_scenario_cp.csv
tests/testthat/non_regression/scenarios_few_changes_on_model_scenario_cp.csv
tests/testthat/non_regression/simple_bolus.csv
tests/testthat/non_regression/simple_bolus_bioavailability.csv
tests/testthat/non_regression/simple_bolus_bioavailability_cp.csv
tests/testthat/non_regression/simple_bolus_cp.csv
tests/testthat/non_regression/simple_tte_model_a_survival_trigger.csv
tests/testthat/non_regression/trim_covariate_my_cov.csv
tests/testthat/non_regression/weibull_model_conc.csv
tests/testthat/non_regression/wt_as_time_varying_cov.csv
tests/testthat/non_regression/wt_as_time_varying_cov_locf_cp.csv
tests/testthat/non_regression/wt_as_time_varying_cov_nocb_cp.csv
tests/testthat/testArm.R
tests/testthat/testArms.R
tests/testthat/testBootstrap.R
tests/testthat/testCompilationError.R
tests/testthat/testCovariate.R
tests/testthat/testCovariates.R
tests/testthat/testDataset.R
tests/testthat/testDatasetExportParallelisation.R
tests/testthat/testDefaultPlots.R
tests/testthat/testDistribution.R
tests/testthat/testDoseAdaptation.R
tests/testthat/testEvent.R
tests/testthat/testEvents.R
tests/testthat/testObservations.R
tests/testthat/testOccasion.R
tests/testthat/testOccasions.R
tests/testthat/testParameterUncertainty.R
tests/testthat/testScenario.R
tests/testthat/testScenarios.R
tests/testthat/testSeed.R
tests/testthat/testSettings.R
tests/testthat/testShowMethod.R
tests/testthat/testSimulateArguments.R
tests/testthat/testSimulateBioavailability.R
tests/testthat/testSimulateBolus.R
tests/testthat/testSimulateBolusInfusionSameCmt.R
tests/testthat/testSimulateDeclare.R
tests/testthat/testSimulateDoseAdaptation.R
tests/testthat/testSimulateDosingInfo.R
tests/testthat/testSimulateEvents.R
tests/testthat/testSimulateEventsLogic.R
tests/testthat/testSimulateIOV.R
tests/testthat/testSimulateInfusion.R
tests/testthat/testSimulateInit.R
tests/testthat/testSimulateLagTime.R
tests/testthat/testSimulateMinimalistModel.R
tests/testthat/testSimulateNoOmega.R
tests/testthat/testSimulateNocbLocf.R
tests/testthat/testSimulateOutvars.R
tests/testthat/testSimulateRUV.R
tests/testthat/testSimulateReplicates.R
tests/testthat/testSimulateScenarios.R
tests/testthat/testSimulateTSLD.R
tests/testthat/testSimulateTTEModels.R
tests/testthat/testSimulateTable.R
tests/testthat/testSimulateTimeVaryingCovariates.R
tests/testthat/testSimulateWeirdCases.R
tests/testthat/testTimeUtilities.R
tests/testthat/testTreatment.R
tests/testthat/testTreatmentEntry.R
tests/testthat/testUtils.R
vignettes/campsis.Rmd
vignettes/resources/Targets_Squeletton/R/my_script.R
vignettes/resources/Targets_Squeletton/_targets.R
vignettes/resources/Targets_Squeletton_Parallel/R/my_script.R
vignettes/resources/Targets_Squeletton_Parallel/_targets.R
vignettes/resources/readme_plot.png
vignettes/v01_dataset.Rmd
vignettes/v02_uncertainties.Rmd
vignettes/v03_covariates.Rmd
vignettes/v04_bioavailability.Rmd
vignettes/v05_lag_time.Rmd
vignettes/v06_infusions.Rmd
vignettes/v07_iov.Rmd
vignettes/v08_initial_conditions.Rmd
vignettes/v09_dose_adaptation.Rmd
vignettes/v10_replicate_study.Rmd
vignettes/v11_scenarios.Rmd
vignettes/v12_time_varying_covariates.Rmd
vignettes/v13_events.Rmd
vignettes/v14_complex_pkpd_models.Rmd
vignettes/v15_pkpd_model_library.Rmd
vignettes/v16_progress_bar.Rmd
vignettes/v17_run_simulation_in_parallel.Rmd
