├── .Rbuildignore ├── .circleci └── config.yml ├── .gitignore ├── COPYING ├── DESCRIPTION ├── NAMESPACE ├── R ├── RcppExports.R ├── acceptability_curve.R ├── calibration.R ├── cluster.R ├── combine.R ├── compatability.R ├── complexity.r ├── correct_counts.R ├── covariance.R ├── define_transition.R ├── density.R ├── dispatch_strategy.R ├── efficiency_frontier.R ├── error_codes.R ├── evpi.R ├── evppi_define.R ├── evppi_eval.R ├── evppi_print.R ├── expand.R ├── formula.R ├── gho_mortality.R ├── heRomod.R ├── hero.R ├── hero_bc.R ├── hero_dsa.R ├── hero_scenario.R ├── hero_sensitivity_analysis.R ├── hero_threshold.R ├── hero_twsa.r ├── hero_vbp.r ├── hero_xlsx.R ├── look_up.R ├── matrix_define.R ├── matrix_eval.R ├── matrix_plot.R ├── matrix_sparse.R ├── newdata.R ├── parallelsugar.R ├── param_define.R ├── param_eval.R ├── param_print.R ├── part_surv.R ├── resamp_define.R ├── resamp_eval.R ├── resamp_print.R ├── run_model_define.R ├── run_model_summary.R ├── sensitivity_define.R ├── sensitivity_eval.R ├── sensitivity_print.R ├── states_define.R ├── states_eval.R ├── states_print.R ├── strategy_define.R ├── strategy_eval.R ├── strategy_print.R ├── sysdata.rda ├── tabular_input.R ├── theme_ggplot.R ├── transform.R ├── update.R ├── utils.R ├── vbp_define.R ├── vbp_eval.R ├── vbp_print.R └── zzz.R ├── README.md ├── codecov.yml ├── data ├── data-raw └── save_gho_mortality.R ├── inst ├── compat │ ├── checkimab.json │ ├── checkimab.rds │ ├── custompsm.json │ ├── custompsm.rds │ ├── fit.json │ ├── fit.rds │ ├── groups.json │ ├── groups.rds │ ├── markov.json │ ├── markov.rds │ ├── psm.json │ ├── psm.rds │ ├── ta447.json │ └── ta447.rds ├── examples │ ├── example_calibration.R │ ├── example_define_calibration_fn.R │ ├── example_define_evppi.R │ ├── example_define_parameters.R │ ├── example_define_resample.R │ ├── example_define_state.R │ ├── example_define_strategy.R │ ├── example_define_transition.R │ ├── example_eval_parameters.R │ ├── example_eval_strategy.R │ ├── example_eval_strategy_newdata.R │ ├── example_look_up.R │ ├── example_plot.run_model.R │ ├── example_run_dsa.R │ ├── example_run_model.R │ ├── example_run_psa.R │ ├── example_run_vbp.R │ ├── example_transform.R │ └── example_update.R ├── hero │ ├── advanced_surv_modeling │ │ ├── bc_res.rds │ │ ├── dsa_res.rds │ │ ├── model.rds │ │ └── vbp_res.rds │ ├── example_simple_psm │ │ ├── bc_res.rds │ │ ├── dsa_res.rds │ │ ├── model.rds │ │ └── vbp_res.rds │ ├── groups │ │ ├── bc_res.rds │ │ ├── dsa_res.rds │ │ ├── model.rds │ │ ├── scen_res.rds │ │ ├── scen_vbp_res.rds │ │ ├── twsa_res.rds │ │ └── vbp_res.rds │ ├── markov_model │ │ ├── .DS_Store │ │ ├── bc_res.rds │ │ ├── dsa_res.rds │ │ ├── model.rds │ │ ├── scen_res.rds │ │ ├── scen_vbp_res.rds │ │ ├── twsa_res.rds │ │ └── vbp_res.rds │ ├── psm_responders │ │ ├── .DS_Store │ │ ├── bc_res.rds │ │ ├── dsa_res.rds │ │ ├── model.rds │ │ └── vbp_res.rds │ ├── shared_st │ │ ├── bc_res.rds │ │ ├── dsa_res.rds │ │ ├── model.rds │ │ ├── psa_res.rds │ │ ├── scen_res.rds │ │ └── vbp_res.rds │ ├── sparse │ │ ├── bc_res.rds │ │ └── model.rds │ ├── ta447 │ │ ├── bc_res.rds │ │ ├── dsa_res.rds │ │ ├── model.rds │ │ └── vbp_res.rds │ └── time-dependency │ │ ├── bc_res.rds │ │ └── model.rds ├── media │ └── logo.png └── tabular │ ├── surv │ ├── example_oncOptions.csv │ ├── example_oncParams.csv │ ├── example_oncParams_explicit_dists.csv │ ├── example_oncParams_nomatrix.csv │ ├── example_oncSpecs.csv │ ├── example_oncSpecs_explicit_dists.csv │ ├── example_oncSpecs_mixed.csv │ ├── example_oncSpecs_nomatrix.csv │ ├── example_oncSpecs_nomatrix_join.csv │ ├── example_oncSpecs_nomatrix_run.csv │ ├── example_oncSpecs_test_part_surv.csv │ ├── example_oncStates.csv │ ├── example_oncTransitionProbs.csv │ ├── example_use_fits_explicit_dists.csv │ ├── fake_fit_tib.csv │ ├── set_definitions_1.csv │ ├── set_definitions_2.csv │ ├── set_definitions_error_1.csv │ ├── surv_def_ok.csv │ ├── surv_table.csv │ ├── survival_data │ │ ├── OS.A.surv.fits.RData │ │ ├── OS.B.surv.fits.RData │ │ ├── PFS.A.surv.fits.RData │ │ ├── PFS.B.surv.fits.RData │ │ ├── set_def_pfs_os.csv │ │ ├── set_definitions.csv │ │ ├── surv_data_OS.csv │ │ ├── surv_data_OS_eventcode.csv │ │ ├── surv_data_PFS.csv │ │ └── surv_data_PFS_eventcode.csv │ ├── survival_info.csv │ ├── survival_info_eventcode.csv │ ├── survival_info_eventcode_error.csv │ ├── survival_info_explicit_dists.csv │ ├── survival_info_nomatrix_run.csv │ ├── use_fits.csv │ ├── use_fits_example0.csv │ ├── use_fits_join.csv │ └── use_fits_mixed.csv │ ├── test │ ├── .gitignore │ ├── REFERENCE_1probmissing.csv │ ├── REFERENCE_missingfunctions.csv │ ├── THR_options.csv │ ├── THR_parameters.csv │ ├── THR_test_states.csv │ ├── THR_test_transition_probs.csv │ ├── THR_test_transition_probs_1missing.csv │ ├── THR_test_transition_probs_2.csv │ ├── THR_test_transition_probs_bad.csv │ ├── bad_REFERENCE.csv │ ├── example_multinom_params.csv │ ├── example_multinom_params_dup_name.csv │ ├── survival_spec_1.csv │ ├── survival_spec_2.csv │ ├── survival_spec_error_1.csv │ ├── survival_spec_error_2.csv │ ├── test_diff_mod_name │ │ ├── REFERENCE.csv │ │ ├── THR_states.csv │ │ └── THR_transition_probs.csv │ ├── test_no_output_dir │ │ ├── REFERENCE.csv │ │ ├── THR_demographic_table.csv │ │ ├── THR_options.csv │ │ ├── THR_parameters.csv │ │ ├── THR_states.csv │ │ ├── THR_transition_probs.csv │ │ └── input_dataframes │ │ │ └── mr_table.xlsx │ ├── test_no_overwrite │ │ ├── REFERENCE.csv │ │ ├── THR_demographic_table.csv │ │ ├── THR_options.csv │ │ ├── THR_parameters.csv │ │ ├── THR_states.csv │ │ ├── THR_transition_probs.csv │ │ ├── input_dataframes │ │ │ └── mr_table.xlsx │ │ └── output │ │ │ └── state_count_plot_standard.png │ ├── testing_CSV_file_with_comment_col.csv │ ├── testing_XLSX_file_with_comment_col.xlsx │ ├── testing_XLS_file_with_comment_col.xls │ ├── thr_trans │ │ ├── .gitignore │ │ ├── REFERENCE.csv │ │ ├── REFERENCE_2core.csv │ │ ├── THR_demographic_table.csv │ │ ├── THR_options.csv │ │ ├── THR_options_2core.csv │ │ ├── THR_parameters.csv │ │ ├── THR_state_trans.csv │ │ ├── THR_states.csv │ │ ├── THR_transition_probs.csv │ │ └── input_dataframes │ │ │ └── mr_table.xlsx │ ├── toedit_REFERENCE.csv │ └── wrong_ext.tab │ └── thr │ ├── .gitignore │ ├── REFERENCE.csv │ ├── REFERENCE_2core.csv │ ├── THR_demographic_table.csv │ ├── THR_options.csv │ ├── THR_options_2core.csv │ ├── THR_parameters.csv │ ├── THR_states.csv │ ├── THR_transition_probs.csv │ └── input_dataframes │ └── mr_table.xlsx ├── man ├── acceptability_curve.Rd ├── as_expr_list.Rd ├── by_group.Rd ├── by_group_hack.Rd ├── by_strategy.Rd ├── c_linear.Rd ├── calibrate_model.Rd ├── ce_strategy.Rd ├── check_matrix.Rd ├── check_names.Rd ├── check_states.Rd ├── check_strategy_index.Rd ├── clean_factors.Rd ├── cluster.Rd ├── combine_models.Rd ├── combine_probs.Rd ├── compute_counts.Rd ├── compute_evppi.Rd ├── compute_icer.Rd ├── compute_values.Rd ├── create_demographic_table.Rd ├── create_df_from_tabular.Rd ├── create_matrix_from_tabular.Rd ├── create_model_from_tabular.Rd ├── create_model_list_from_tabular.Rd ├── create_options_from_tabular.Rd ├── create_parameters_from_tabular.Rd ├── create_states_from_tabular.Rd ├── define_calibration_fn.Rd ├── define_correlation.Rd ├── define_dsa.Rd ├── define_evppi.Rd ├── define_inflow.Rd ├── define_init.Rd ├── define_parameters.Rd ├── define_part_surv.Rd ├── define_part_surv_custom.Rd ├── define_psa.Rd ├── define_starting_values.Rd ├── define_state.Rd ├── define_state_list.Rd ├── define_state_transition.Rd ├── define_state_transition_list.Rd ├── define_strategy.Rd ├── define_transition.Rd ├── define_vbp.Rd ├── discount.Rd ├── discount_hack.Rd ├── dispatch_strategy.Rd ├── dispatch_strategy_hack.Rd ├── distributions.Rd ├── eval_models_from_tabular.Rd ├── eval_parameters.Rd ├── eval_resample.Rd ├── eval_state_list.Rd ├── eval_strategy.Rd ├── eval_strategy_newdata.Rd ├── eval_transition.Rd ├── export_savi.Rd ├── file-checkers.Rd ├── filter_blanks.Rd ├── gather_model_info.Rd ├── get_counts.Rd ├── get_frontier.Rd ├── get_matrix_order.Rd ├── get_parameter_names.Rd ├── get_state_names.Rd ├── get_state_number.Rd ├── get_state_value_names.Rd ├── get_transition.Rd ├── get_values.Rd ├── heRomod.Rd ├── heRomod_scale.Rd ├── insert.Rd ├── interpolate.Rd ├── is.wholenumber.Rd ├── list_all_same.Rd ├── look_up.Rd ├── make_names.Rd ├── mclapply.Rd ├── mclapply_socket.Rd ├── modify.Rd ├── p_comp.Rd ├── param_in_strategy.Rd ├── parse_multi_spec.Rd ├── plot.dsa.Rd ├── plot.evppi_res.Rd ├── plot.psa.Rd ├── plot.run_model.Rd ├── plot.vbp.Rd ├── plur.Rd ├── probability.Rd ├── read_file.Rd ├── reexports.Rd ├── reindent_transition.Rd ├── rescale_discount_rate.Rd ├── resolve_dependencies.default.Rd ├── run_bcea.Rd ├── run_dsa.Rd ├── run_model.Rd ├── run_model_tabular.Rd ├── run_psa.Rd ├── run_vbp.Rd ├── safe_conversion.Rd ├── save_outputs.Rd ├── summary.run_model.Rd ├── summary.vbp.Rd ├── update_model.Rd ├── who_mortality.Rd └── wtd_summary.Rd ├── src ├── .gitignore ├── RcppExports-ed4ceba3.o.tmp ├── RcppExports.cpp ├── code-3d31645c.o.tmp └── code.cpp ├── tests ├── testthat.R └── testthat │ ├── .gitignore │ ├── _snaps │ ├── hero.md │ └── threshold.md │ ├── helper_compat.R │ ├── helper_hero.R │ ├── results.json │ ├── test_calibration.R │ ├── test_check_init.R │ ├── test_code_preview.R │ ├── test_compat.R │ ├── test_dmhee.R │ ├── test_efficiency_frontier.R │ ├── test_evppi.R │ ├── test_expand.R │ ├── test_hero.R │ ├── test_heterogeneity.R │ ├── test_look_up.R │ ├── test_matrix.R │ ├── test_model.R │ ├── test_parallel.R │ ├── test_param_in_strategy.R │ ├── test_parameters.R │ ├── test_part_surv.R │ ├── test_probabilistic.R │ ├── test_run_model.R │ ├── test_sensitivity.R │ ├── test_states.R │ ├── test_tabular_input.R │ ├── test_threshold.R │ ├── test_transform.R │ ├── test_transition.R │ ├── test_twsa.r │ └── test_vbp.R └── vignettes ├── .gitignore ├── a_introduction.R ├── a_introduction.Rmd ├── b_time_dependency.R ├── 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