├── .DS_Store ├── .Rbuildignore ├── .gitignore ├── CODE_OF_CONDUCT.md ├── DESCRIPTION ├── LICENSE ├── NAMESPACE ├── NEWS.md ├── R ├── .DS_Store ├── 01_model_inputs_functions.R ├── 02_decision_model_functions.R ├── 03_calibration_functions.R ├── 04_validation_functions.R ├── 05a_probabilistic_analysis_functions.R ├── 05b_deterministic_analysis_functions.R ├── darthpack.R ├── data_all_cause_mortality.R ├── data_calib_post_dist.R ├── data_calib_post_map.R ├── data_calibration_targets.R ├── data_cea_psa.R ├── data_init_params.R ├── data_posterior_summ.R ├── data_psa_object.R └── open_guide.R ├── README.Rmd ├── README.md ├── Shiny_framework.R ├── _pkgdown.yaml ├── analysis ├── 01_model_inputs.R ├── 02_decision_model.R ├── 03_calibration.R ├── 04_validation.R ├── 05a_probabilistic_analysis.R ├── 05b_deterministic_analysis.R ├── 05c_value_of_information.R └── _master.R ├── darthpack.Rproj ├── data-raw ├── .DS_Store ├── 01_all_cause_mortality.R ├── 01_all_cause_mortality.csv ├── 01_basecase_params.csv ├── 01_init_params.R ├── 01_init_params.csv ├── 03_imis_output.R └── 05a_psa_dataset.R ├── data ├── .DS_Store ├── 03_calibration_targets.RData ├── 03_summary_posterior.RData ├── 05a_probabilistic_cea_results.RData ├── all_cause_mortality.rda ├── df_params_init.rda ├── l_psa.rda ├── m_calib_post.rda └── v_calib_post_map.rda ├── docs ├── .DS_Store ├── CODE_OF_CONDUCT.html ├── LICENSE-text.html ├── articles │ ├── .DS_Store │ ├── aa-introduction.html │ ├── bb-inputs.html │ ├── cc-model.html │ ├── cc-model_files │ │ └── figure-html │ │ │ └── Sick-Sicker-Trace-1.png │ ├── darthpack.html │ ├── dd-calibration.html │ ├── dd-calibration_files │ │ └── kePrint-0.0.1 │ │ │ └── kePrint.js │ ├── ee-validation.html │ ├── ff-analysis.html │ ├── index.html │ └── zz-testing.html ├── authors.html ├── docsearch.css ├── docsearch.js ├── figs │ ├── .DS_Store │ ├── 02_model_diagram.png │ ├── 02_trace_plot.png │ ├── 03_posterior_distribution_joint.png │ ├── 03_posterior_distribution_marginal.png │ ├── 04_posterior_vs_targets_prevalence.png │ ├── 04_posterior_vs_targets_proportion_sicker.png │ ├── 04_posterior_vs_targets_survival.png │ ├── 05a_cea_frontier_psa.png │ ├── 05a_cea_plane_scatter.png │ ├── 05a_ceac_ceaf.png │ ├── 05a_elc.png │ ├── 05a_optimal_owsa_lrm_nmb.png │ ├── 05a_owsa_lrm_nmb.png │ ├── 05a_tornado_lrm_Treatment_nmb.png │ ├── 05a_twsa_lrm_uS1_uTrt_nmb.png │ ├── 05b_cea_frontier.png │ ├── 05b_cea_frontier_psa.png │ ├── 05b_cea_plane_scatter.png │ ├── 05b_ceac_ceaf.png │ ├── 05b_elc.png │ ├── 05b_optimal_owsa_lrm_nmb.png │ ├── 05b_optimal_owsa_nmb.png │ ├── 05b_owsa_lrm_nmb.png │ ├── 05b_owsa_nmb.png │ ├── 05b_tornado_Treatment_nmb.png │ ├── 05b_tornado_lrm_Treatment_nmb.png │ ├── 05b_twsa_lrm_uS1_uTrt_nmb.png │ ├── 05b_twsa_uS1_uTrt_nmb.png │ ├── 05c_evpi.png │ ├── darth-logo-small.png │ └── under_const.jpeg ├── index.html ├── link.svg ├── logo.png ├── news │ ├── index.html │ └── news-0.1.html ├── pkgdown.css ├── pkgdown.js ├── pkgdown.yml ├── reference │ ├── SickSicker_targets.html │ ├── all_cause_mortality.html │ ├── calculate_ce_out.html │ ├── calibration_out.html │ ├── check_sum_of_transition_array.html │ ├── check_transition_array.html │ ├── check_transition_probability.html │ ├── darthpack.html │ ├── data_summary.html │ ├── decision_model.html │ ├── df_cea_psa.html │ ├── df_params_init.html │ ├── df_posterior_summ.html │ ├── figures │ │ └── logo.png │ ├── generate_psa_params.html │ ├── index.html │ ├── l_psa.html │ ├── likelihood.html │ ├── load_all_params.html │ ├── load_mort_data.html │ ├── log_lik.html │ ├── log_post.html │ ├── log_prior.html │ ├── m_calib_post.html │ ├── open_guide.html │ ├── owsa_det.html │ ├── posterior.html │ ├── prior.html │ ├── sample.prior.html │ ├── twsa_det.html │ ├── update_param_list.html │ └── v_calib_post_map.html ├── sitemap.xml └── vignettes │ └── test_summary.png ├── figs ├── 02_model_diagram.png ├── 02_trace_plot.png ├── 03_posterior_distribution_joint.png ├── 03_posterior_distribution_marginal.png ├── 04_posterior_vs_targets_prevalence.png ├── 04_posterior_vs_targets_proportion_sicker.png ├── 04_posterior_vs_targets_survival.png ├── 05a_cea_frontier_psa.png ├── 05a_cea_plane_scatter.png ├── 05a_ceac_ceaf.png ├── 05a_elc.png ├── 05a_optimal_owsa_lrm_nmb.png ├── 05a_owsa_lrm_nmb.png ├── 05a_tornado_lrm_Treatment_nmb.png ├── 05a_twsa_lrm_uS1_uTrt_nmb.png ├── 05b_cea_frontier.png ├── 05b_optimal_owsa_nmb.png ├── 05b_owsa_nmb.png ├── 05b_tornado_Treatment_nmb.png ├── 05b_twsa_uS1_uTrt_nmb.png └── 05c_evpi.png ├── inst ├── .DS_Store ├── WORDLIST └── figs │ ├── .DS_Store │ ├── STD-Sick-Sicker-big-font-trans.png │ └── darthpack_hexsticker.png ├── man ├── SickSicker_targets.Rd ├── all_cause_mortality.Rd ├── calculate_ce_out.Rd ├── calibration_out.Rd ├── check_sum_of_transition_array.Rd ├── check_transition_probability.Rd ├── darthpack.Rd ├── data_summary.Rd ├── decision_model.Rd ├── df_cea_psa.Rd ├── df_params_init.Rd ├── df_posterior_summ.Rd ├── figures │ └── logo.png ├── generate_psa_params.Rd ├── l_psa.Rd ├── likelihood.Rd ├── load_all_params.Rd ├── load_mort_data.Rd ├── log_lik.Rd ├── log_post.Rd ├── log_prior.Rd ├── m_calib_post.Rd ├── open_guide.Rd ├── owsa_det.Rd ├── posterior.Rd ├── prior.Rd ├── sample.prior.Rd ├── twsa_det.Rd ├── update_param_list.Rd └── v_calib_post_map.Rd ├── output ├── 03_imis_output.RData └── 05a_psa_dataset.RData ├── packages.bib ├── report ├── .DS_Store ├── 01-inputs.Rmd ├── 02-decision_model.Rmd ├── 03-calibration.Rmd ├── 04-validation.Rmd ├── 05-analysis.Rmd ├── 06-references.Rmd ├── README.md ├── _book │ ├── analysis.html │ ├── calibration.html │ ├── index.html │ ├── inputs.html │ ├── libs │ │ ├── gitbook-2.6.7 │ │ │ ├── css │ │ │ │ ├── fontawesome │ │ │ │ │ └── fontawesome-webfont.ttf │ │ │ │ ├── plugin-bookdown.css │ │ │ │ ├── plugin-fontsettings.css │ │ │ │ ├── plugin-highlight.css │ │ │ │ ├── plugin-search.css │ │ │ │ ├── plugin-table.css │ │ │ │ └── style.css │ │ │ └── js │ │ │ │ ├── app.min.js │ │ │ │ ├── jquery.highlight.js │ │ │ │ ├── lunr.js │ │ │ │ ├── plugin-bookdown.js │ │ │ │ ├── plugin-fontsettings.js │ │ │ │ ├── plugin-search.js │ │ │ │ └── plugin-sharing.js │ │ ├── jquery-2.2.3 │ │ │ └── jquery.min.js │ │ └── kePrint-0.0.1 │ │ │ └── kePrint.js │ ├── references.html │ ├── report.epub │ ├── report.pdf │ ├── report.tex │ ├── report_files │ │ └── figure-html │ │ │ └── Sick-Sicker-Trace-1.png │ ├── search_index.json │ ├── simulation.html │ ├── style.css │ └── validation.html ├── _bookdown.yml ├── _bookdown_files │ └── report_files │ │ ├── figure-html │ │ └── Sick-Sicker-Trace-1.png │ │ └── figure-latex │ │ └── Sick-Sicker-Trace-1.pdf ├── _output.yml ├── book.bib ├── figs │ ├── 02_model_diagram.png │ ├── 03_posterior_distribution_joint.png │ ├── 03_posterior_distribution_marginal.png │ ├── 04_posterior_vs_targets_prevalence.png │ ├── 04_posterior_vs_targets_proportion_sicker.png │ ├── 04_posterior_vs_targets_survival.png │ ├── 05a_cea_frontier.png │ ├── 05a_cea_frontier_psa.png │ ├── 05a_cea_plane_scatter.png │ ├── 05a_ceac_ceaf.png │ ├── 05a_elc.png │ ├── 05a_optimal_owsa_lrm_nmb.png │ ├── 05a_optimal_owsa_nmb.png │ ├── 05a_owsa_lrm_nmb.png │ ├── 05a_owsa_nmb.png │ ├── 05a_tornado_Treatment_nmb.png │ ├── 05a_tornado_lrm_Treatment_nmb.png │ ├── 05a_twsa_lrm_uS1_uTrt_nmb.png │ ├── 05a_twsa_uS1_uTrt_nmb.png │ ├── 05b_cea_frontier.png │ ├── 05b_cea_frontier_psa.png │ ├── 05b_cea_plane_scatter.png │ ├── 05b_ceac_ceaf.png │ ├── 05b_elc.png │ ├── 05b_optimal_owsa_lrm_nmb.png │ ├── 05b_optimal_owsa_nmb.png │ ├── 05b_owsa_lrm_nmb.png │ ├── 05b_owsa_nmb.png │ ├── 05b_tornado_Treatment_nmb.png │ ├── 05b_tornado_lrm_Treatment_nmb.png │ ├── 05b_twsa_lrm_uS1_uTrt_nmb.png │ ├── 05b_twsa_uS1_uTrt_nmb.png │ └── 05c_evpi.png ├── index.Rmd ├── packages.bib ├── preamble.tex ├── report.Rproj ├── report.log └── style.css ├── tables ├── 03_summary_posterior.RData ├── 03_summary_posterior.csv ├── 05a_probabilistic_cea_results.RData ├── 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