├── .Rbuildignore ├── .github ├── .gitignore └── workflows │ ├── R-CMD-check.yaml │ ├── pkgdown.yaml │ └── test-coverage.yaml ├── .gitignore ├── DESCRIPTION ├── NAMESPACE ├── R ├── .Rapp.history ├── .gitignore ├── RcppExports.R ├── calibration.R ├── config-documentation.R ├── config-management.R ├── core.R ├── epicR.R ├── figures.R ├── input.R ├── misc │ ├── cancold_fev1.R │ └── lhs.R ├── package-init.R ├── report.R ├── sysdata.rda └── validation.R ├── README.md ├── _pkgdown.yml ├── claude.md ├── cleanup ├── configure ├── data-raw ├── BOLD.prevalence.xlsx ├── CanSim.052.0005.csv ├── CanSim.052.0005.xlsm ├── CanSim.105.0501.csv ├── CanSim.105.0501.xlsm ├── NHANES.SPM.Ref.csv ├── SmokingPrevalence.xlsx ├── data-raw.R └── lhs.csv ├── docs ├── 404.html ├── articles │ ├── GettingStarted.html │ ├── RecalibratingEPIC.html │ └── index.html ├── authors.html ├── index.html ├── link.svg ├── pkgdown.js ├── pkgdown.yml ├── reference │ ├── Cget_agent_events.html │ ├── Cget_all_events.html │ ├── Cget_all_events_matrix.html │ ├── Cget_event.html │ ├── Cget_events_by_type.html │ ├── Cget_inputs.html │ ├── Cget_n_events.html │ ├── Cget_output.html │ ├── Cget_output_ex.html │ ├── Cget_runtime_stats.html │ ├── Cget_settings.html │ ├── Cget_smith.html │ ├── Cset_input_var.html │ ├── Cset_settings_var.html │ ├── calibrate_COPD_inc.html │ ├── calibrate_explicit_mortality.html │ ├── calibrate_explicit_mortality2.html │ ├── calibrate_smoking.html │ ├── export_figures.html │ ├── express_matrix.html │ ├── get_agent_events.html │ ├── get_all_events.html │ ├── get_default_settings.html │ ├── get_errors.html │ ├── get_events_by_type.html │ ├── get_input.html │ ├── get_list_elements.html │ ├── get_sample_output.html │ ├── index.html │ ├── init_session.html │ ├── mvrnormArma.html │ ├── report_COPD_by_ctime.html │ ├── report_exacerbation_by_time.html │ ├── resume.html │ ├── run.html │ ├── sanity_COPD.html │ ├── sanity_check.html │ ├── terminate_session.html │ ├── test_case_detection.html │ ├── validate_COPD.html │ ├── validate_diagnosis.html │ ├── validate_exacerbation.html │ ├── validate_gpvisits.html │ ├── validate_lung_function.html │ ├── validate_medication.html │ ├── validate_mortality.html │ ├── validate_overdiagnosis.html │ ├── validate_payoffs.html │ ├── validate_population.html │ ├── validate_smoking.html │ ├── validate_survival.html │ ├── validate_symptoms.html │ └── validate_treatment.html └── sitemap.xml ├── epicR.Rproj ├── examples └── seed_example.R ├── inst ├── USCensus.csv ├── assets │ ├── vignette-scripts.js │ └── vignette-styles.css └── config │ ├── config_canada.json │ └── config_us.json ├── man ├── calc_event_stack_size.Rd ├── calibrate_COPD_inc.Rd ├── calibrate_explicit_mortality.Rd ├── calibrate_explicit_mortality2.Rd ├── calibrate_smoking.Rd ├── copy_configs_to_user.Rd ├── epicR-config.Rd ├── epicR-package.Rd ├── estimate_memory_required.Rd ├── export_figures.Rd ├── express_matrix.Rd ├── get_agent_events.Rd ├── get_agent_size_bytes.Rd ├── get_all_events.Rd ├── get_all_events_matrix.Rd ├── get_available_memory.Rd ├── get_default_model_input.Rd ├── get_default_settings.Rd ├── get_errors.Rd ├── get_event.Rd ├── get_events_by_type.Rd ├── get_input.Rd ├── get_inputs.Rd ├── get_list_elements.Rd ├── get_n_events.Rd ├── get_output.Rd ├── get_output_ex.Rd ├── get_progress.Rd ├── get_runtime_stats.Rd ├── get_sample_output.Rd ├── get_settings.Rd ├── get_smith.Rd ├── get_user_config_dir.Rd ├── init_session.Rd ├── list_available_jurisdictions.Rd ├── mvrnormArma.Rd ├── open_user_config_dir.Rd ├── report_COPD_by_ctime.Rd ├── report_exacerbation_by_time.Rd ├── reset_model_input.Rd ├── reset_user_configs.Rd ├── resume.Rd ├── run.Rd ├── sanity_COPD.Rd ├── sanity_check.Rd ├── set_input_var.Rd ├── set_settings_var.Rd ├── simulate.Rd ├── terminate_session.Rd ├── test_case_detection.Rd ├── user_config_exists.Rd ├── validate_COPD.Rd ├── validate_config.Rd ├── validate_diagnosis.Rd ├── validate_exacerbation.Rd ├── validate_gpvisits.Rd ├── validate_lung_function.Rd ├── validate_medication.Rd ├── validate_mortality.Rd ├── validate_overdiagnosis.Rd ├── validate_payoffs.Rd ├── validate_population.Rd ├── validate_smoking.Rd ├── validate_survival.Rd ├── validate_symptoms.Rd └── validate_treatment.Rd ├── src ├── .gitignore ├── Makevars ├── Makevars.in ├── Makevars.win ├── RcppExports.cpp ├── epic_model.h ├── model.cpp ├── model_events.cpp ├── model_globals.cpp ├── model_input.cpp ├── model_output.cpp └── model_random.cpp ├── tests ├── testthat.R └── testthat │ ├── test-ClosedCohort.R │ ├── test-config-reload.R │ ├── test-config-structure.R │ ├── test-input-functions.R │ ├── test-seed-reproducibility.R │ ├── test-timeHorizon.R │ ├── testDiagnosis.R │ ├── testExacerbations.R │ ├── testGPvisits.R │ ├── testIncidence.R │ ├── testSanity.R │ └── testSymptoms.R └── vignettes ├── .gitignore ├── AddingNewCountry.Rmd ├── BackgroundEPIC.Rmd ├── Canada_Calibrate_COPD_Exacerbations.Rmd ├── GettingStarted.Rmd ├── 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