├── .Rbuildignore ├── .covrignore ├── .github ├── .gitignore └── workflows │ ├── R-CMD-check.yaml │ ├── make-release.yaml │ ├── pkgdown.yaml │ └── test-coverage.yaml ├── .gitignore ├── DESCRIPTION ├── LICENSE ├── LICENSE.md ├── NAMESPACE ├── NEWS.md ├── R ├── align.R ├── assertions.R ├── beta.R ├── calibration.R ├── check.R ├── contact_matrices.R ├── data.R ├── drjacoby_utils.R ├── estimation.R ├── format_output.R ├── models.R ├── object.R ├── odin.R ├── parameters.R ├── particle.R ├── pmcmc.R ├── pmcmc_object.R ├── pmcmc_utils.R ├── population.R ├── projections.R ├── run.R ├── triggering.R ├── util.R └── zzz.R ├── README.Rmd ├── README.md ├── _pkgdown.yml ├── codecov.yml ├── data-raw ├── Hospital_Bed_Capacity_Predictions.Rds ├── Income_Strata_Predicted_Hospital_and_ICU_Beds.Rds ├── WPP_demog_matrix.csv ├── contact_matrices.rds ├── hospital_bed_capacity.csv └── prepare_raw_data.R ├── data ├── contact_matrices.rda ├── country_specific_healthcare_capacity.rda ├── elderly_pop.rda ├── income_group.rda ├── income_strata_healthcare_capacity.rda └── population.rda ├── images ├── Explicit_Healthcare_Mechanical_Ventilation_Decision_Tree.JPG ├── Explicit_Healthcare_Model_Structure.JPG └── Explicit_Healthcare_Oxygen_Decision_Tree.JPG ├── inst ├── extdata │ ├── example.csv │ ├── example_DZA.csv │ ├── example_DZA_intervention.csv │ ├── example_GIN.csv │ ├── example_guinea.csv │ └── example_intervention.csv ├── odin │ ├── .gitignore │ ├── SEIR.json │ ├── explicit_SEIR.R │ ├── explicit_SEIR.json │ ├── explicit_SEIR_deterministic.R │ ├── explicit_SEIR_deterministic.json │ ├── less_basic_model_for_js.R │ ├── less_basic_model_for_js.json │ ├── simple_SEIR.R │ └── simple_SEIR.json └── other │ ├── det_basic_SEIR.R │ ├── run_det_basic_SEIR.R │ ├── test_out │ └── test_out.zip ├── man ├── adjusted_eigen.Rd ├── align.Rd ├── beta_est.Rd ├── beta_est_explicit.Rd ├── beta_est_simple.Rd ├── calibrate.Rd ├── check_squire.Rd ├── check_time_change.Rd ├── compare_output.Rd ├── conduct_replicate.Rd ├── contact_matrices.Rd ├── country_specific_healthcare_capacity.Rd ├── create_master_chain.Rd ├── default_durations.Rd ├── default_probs.Rd ├── deterministic_model.Rd ├── div_pop.Rd ├── drjacoby_mcmc.Rd ├── elderly_pop.Rd ├── explicit_model.Rd ├── extract_ICU_occ.Rd ├── extract_deaths.Rd ├── extract_hospital_occ.Rd ├── extract_infection_incidence.Rd ├── figures │ ├── README-base plot-1.png │ ├── README-calibration-1.png │ ├── README-cases over time-1.png │ ├── README-change healthcare capacity-1.png │ ├── README-deaths over time-1.png │ ├── README-healthcare forecast over time-1.png │ ├── README-healthcare over time-1.png │ ├── README-orderly style-1.png │ ├── README-particle fit ints-1.png │ ├── README-particle fit no ints-1.png │ ├── README-particle gin alt proj-1.png │ ├── README-particle gin alt-1.png │ ├── README-particle gin forecast-1.png │ ├── README-particle gin plots-1.png │ ├── README-plot gcu-1.png │ ├── README-plot particle deaths-1.png │ ├── README-pressure-1.png │ ├── README-projection plotting absolute-1.png │ ├── README-projection plotting-1.png │ ├── README-projection relative beds-1.png │ ├── README-set R0 decrease-1.png │ ├── README-set contact matrix decrease and relax-1.png │ ├── README-set contact matrix decrease-1.png │ ├── README-set params-1.png │ ├── README-show grid fits probs-1.png │ ├── README-show grid fits-1.png │ ├── README-subset variables plot-1.png │ ├── README-subset variables plot2-1.png │ ├── README-total deaths projection-1.png │ └── README-untransformed-1.png ├── format_deterministic_output.Rd ├── format_output.Rd ├── format_output_simple_model.Rd ├── get_elderly_population.Rd ├── get_healthcare_capacity.Rd ├── get_lmic_countries.Rd ├── get_mixing_matrix.Rd ├── get_population.Rd ├── income_group.Rd ├── income_strata_healthcare_capacity.Rd ├── init_check.Rd ├── init_check_explicit.Rd ├── intervention_dates_for_odin.Rd ├── jc_prop_update.Rd ├── matrix_check.Rd ├── matrix_set.Rd ├── parameters_explicit_SEEIR.Rd ├── parameters_simple_SEEIR.Rd ├── parse_country_severity.Rd ├── particle_filter.Rd ├── particle_filter_data.Rd ├── plot.squire_scan.Rd ├── plot.squire_simulation.Rd ├── pmcmc.Rd ├── population.Rd ├── pos_num.Rd ├── print.squire_simulation.Rd ├── process_contact_matrix.Rd ├── process_contact_matrix_scaled_age.Rd ├── projection_plotting.Rd ├── projections.Rd ├── run_deterministic_SEIR_model.Rd ├── run_deterministic_comparison.Rd ├── run_explicit_SEEIR_model.Rd ├── run_particle_filter.Rd ├── run_simple_SEEIR_model.Rd ├── sample_3d_grid_scan.Rd ├── sample_drjacoby.Rd ├── sample_grid_scan.Rd ├── sample_pmcmc.Rd ├── scan_R0_date.Rd ├── scan_R0_date_Meff.Rd ├── simple_model.Rd ├── summary.squire_simulation.Rd └── trigger_projections.Rd ├── squire.Rproj ├── src ├── odin.c └── registration.c ├── tests ├── testthat.R └── testthat │ ├── test-align.R │ ├── test-assertions.R │ ├── test-beta.R │ ├── test-calibration.R │ ├── test-checks.R │ ├── test-data.R │ ├── 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