├── .Rbuildignore ├── .github ├── .gitignore ├── CODEOWNERS ├── CONTRIBUTING.md ├── ISSUE_TEMPLATE │ ├── bug_report.md │ ├── feature_request.md │ ├── maintenance.md │ └── scientific-improvement.md ├── PULL_REQUEST_TEMPLATE │ ├── pull_request_template.md │ └── vulnerability.md ├── SUPPORT.md └── workflows │ ├── pkgdown.yaml │ └── r-cmd-check.yaml ├── .gitignore ├── .lintr ├── .pre-commit-config.yaml ├── .secrets.baseline ├── DESCRIPTION ├── LICENSE ├── NAMESPACE ├── NEWS.md ├── R ├── checkers.R ├── compile_model.R ├── data.R ├── delay_distribs.R ├── figures.R ├── generate_simulated_data.R ├── get_draws.R ├── get_params.R ├── get_stan_data.R ├── initialization.R ├── model_component_fwd_sim.R ├── model_diagnostics.R ├── preprocessing.R ├── utils.R ├── validate.R ├── wwinference-package.R └── wwinference.R ├── README.md ├── _pkgdown.yml ├── data-raw ├── covid_pmfs.R └── vignette_data.R ├── data ├── default_covid_gi.rda ├── default_covid_inf_to_hosp.rda ├── hosp_data.rda ├── hosp_data_eval.rda ├── subpop_hosp_data.rda ├── subpop_hosp_data_eval.rda ├── true_global_rt.rda ├── ww_data.rda └── ww_data_eval.rda ├── inst ├── extdata │ └── example_params.toml └── stan │ ├── functions │ ├── ar1.stan │ ├── convolve.stan │ ├── diff_ar1.stan │ ├── expgamma_lpdf.stan │ ├── hospitalization.stan │ ├── infections.stan │ ├── observation_model.stan │ └── utils.stan │ └── wwinference.stan ├── man ├── .DS_Store ├── add_pmfs.Rd ├── add_time_indexing.Rd ├── assert_cols_det_unique_row.Rd ├── assert_daily_data.Rd ├── assert_dates_within_frame.Rd ├── assert_df_not_empty.Rd ├── assert_elements_non_neg.Rd ├── assert_equivalent_indexing.Rd ├── assert_int_or_char.Rd ├── assert_no_dates_after_max.Rd ├── assert_no_repeated_elements.Rd ├── assert_non_missingness.Rd ├── assert_req_count_cols_present.Rd ├── assert_req_ww_cols_present.Rd ├── assert_rt_correct_length.Rd ├── assert_single_value.Rd ├── assert_site_lab_indices_align.Rd ├── assert_sufficient_days_of_data.Rd ├── assert_ww_site_pops_lt_total.Rd ├── autoescape_brackets.Rd ├── calc_rt.Rd ├── compile_model.Rd ├── convert_to_logmean.Rd ├── convert_to_logsd.Rd ├── create_dir.Rd ├── create_site_lab_map.Rd ├── default_covid_gi.Rd ├── default_covid_inf_to_hosp.Rd ├── downsample_for_frequency.Rd ├── drop_first_and_renormalize.Rd ├── figures │ ├── .DS_Store │ ├── logo.svg │ ├── wwinference_package_workflow.svg │ └── wwinference_workflow.png ├── flag_ww_outliers.Rd ├── format_hosp_data.Rd ├── format_subpop_hosp_data.Rd ├── format_ww_data.Rd ├── generate_simulated_data.Rd ├── get_count_data_sizes.Rd ├── get_count_indices.Rd ├── get_count_values.Rd ├── get_date_time_spine.Rd ├── get_draws.Rd ├── get_global_rt.Rd ├── get_ind_m.Rd ├── get_inits_for_one_chain.Rd ├── get_input_count_data_for_stan.Rd ├── get_input_ww_data_for_stan.Rd ├── get_lab_site_site_spine.Rd ├── get_lab_site_subpop_spine.Rd ├── get_mcmc_options.Rd ├── get_model_diagnostic_flags.Rd ├── get_model_spec.Rd ├── get_params.Rd ├── get_plot_forecasted_counts.Rd ├── get_plot_global_rt.Rd ├── get_plot_subpop_rt.Rd ├── get_plot_ww_conc.Rd ├── get_pred_obs_conc.Rd ├── get_pred_subpop_gen_per_n.Rd ├── get_site_subpop_spine.Rd ├── get_stan_data.Rd ├── get_time_varying_daily_ihr.Rd ├── get_ww_data_sizes.Rd ├── get_ww_indices_and_values.Rd ├── hosp_data.Rd ├── hosp_data_eval.Rd ├── indicate_ww_exclusions.Rd ├── make_hospital_onset_delay_pmf.Rd ├── make_incubation_period_pmf.Rd ├── make_reporting_delay_pmf.Rd ├── parameter_diagnostics.Rd ├── preprocess_count_data.Rd ├── preprocess_ww_data.Rd ├── simulate_double_censored_pmf.Rd ├── subpop_hosp_data.Rd ├── subpop_hosp_data_eval.Rd ├── subpop_inf_process.Rd ├── subpop_rt_process.Rd ├── summary_diagnostics.Rd ├── throw_type_error.Rd ├── to_simplex.Rd ├── true_global_rt.Rd ├── truncate_for_latency.Rd ├── validate_count_data.Rd ├── validate_data_jointly.Rd ├── validate_paramlist.Rd ├── validate_pmf.Rd ├── validate_ww_conc_data.Rd ├── ww_data.Rd ├── ww_data_eval.Rd ├── 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