├── .Rbuildignore ├── .github ├── .gitignore ├── CONTRIBUTING.md ├── ISSUE_TEMPLATE │ ├── bug_report.md │ ├── config.yml │ ├── documentation.md │ ├── feature_request.md │ └── other_issue.md ├── PULL_REQUEST_TEMPLATE.md ├── dependabot.yml └── workflows │ ├── R-CMD-as-cran-check.yaml │ ├── R-CMD-check.yaml │ ├── document.yaml │ ├── lint-only-changed-files.yaml │ ├── lint-package.yaml │ ├── pkgdown.yaml │ ├── pr-commands.yaml │ ├── render-EpiNow2.yaml │ ├── render-epinow.yaml │ ├── render-estimate_infections_options.yaml │ ├── render-estimate_infections_workflow.yaml │ ├── render-readme.yaml │ ├── render-stan-docs.yaml │ ├── stan-model-benchmark.yaml │ ├── synthetic-validation.yaml │ ├── test-coverage.yaml │ ├── test-full.yaml │ ├── touchstone-comment.yaml │ ├── touchstone-receive.yaml │ ├── update-citation-cff.yaml │ └── update-r-multiverse.yaml ├── .gitignore ├── .lintr ├── .pre-commit-config.yaml ├── CITATION.cff ├── CLAUDE.md ├── CODE_OF_CONDUCT.md ├── DESCRIPTION ├── EpiNow2.Rproj ├── LICENSE ├── LICENSE.md ├── NAMESPACE ├── NEWS.md ├── R ├── EpiNow2-package.R ├── checks.R ├── create.R ├── data.R ├── deprecated.R ├── dist_spec.R ├── epinow-internal.R ├── epinow.R ├── estimate_delay.R ├── estimate_infections.R ├── estimate_secondary.R ├── estimate_truncation.R ├── extract.R ├── fit.R ├── format.R ├── get.R ├── opts.R ├── plot.R ├── preprocessing.R ├── regional_epinow.R ├── report.R ├── setup.R ├── simulate_infections.R ├── simulate_secondary.R ├── stan.R ├── stanmodels.R ├── summarise.R └── utilities.R ├── README.Rmd ├── README.md ├── _pkgdown.yml ├── codecov.yml ├── configure ├── configure.win ├── cran-comments.md ├── data-raw ├── estimate-infections.R ├── generation-time.R ├── gi.rds ├── incubation-period.R ├── reporting-delay.R └── truncated.R ├── data ├── example_confirmed.rda ├── example_generation_time.rda ├── example_incubation_period.rda ├── example_reporting_delay.rda └── example_truncated.rda ├── inst ├── WORDLIST ├── dev │ ├── accumulation.Rmd │ ├── accumulation.md │ ├── benchmark-compare.R │ ├── benchmark-functions.R │ ├── benchmark-single.R │ ├── design_dist.md │ ├── design_obs.md │ ├── design_s3.md │ ├── load-stan-functions.R │ ├── make_hexsticker.R │ ├── recover-synthetic │ │ ├── eval_rt.R │ │ ├── plot.R │ │ └── rt.R │ ├── stan-to-R.R │ └── synthetic_recovery.md ├── extdata │ ├── example_estimate_infections.rds │ ├── example_regional_epinow.rds │ ├── example_truncated.rds │ └── example_truncation_data.rds ├── include │ └── stan_meta_header.hpp └── stan │ ├── data │ ├── backcalc.stan │ ├── delays.stan │ ├── estimate_infections_params.stan │ ├── estimate_secondary_params.stan │ ├── gaussian_process.stan │ ├── observation_model.stan │ ├── observations.stan │ ├── params.stan │ ├── rt.stan │ ├── secondary.stan │ ├── simulation_delays.stan │ ├── simulation_observation_model.stan │ └── simulation_rt.stan │ ├── dist_fit.stan │ ├── docs │ ├── Doxyfile │ ├── DoxygenLayout.xml │ ├── doxygen-awesome │ │ ├── doxygen-awesome-darkmode-toggle.js │ │ ├── doxygen-awesome-fragment-copy-button.js │ │ ├── doxygen-awesome-interactive-toc.js │ │ ├── doxygen-awesome-paragraph-link.js │ │ ├── doxygen-awesome-sidebar-only-darkmode-toggle.css │ │ ├── doxygen-awesome-sidebar-only.css │ │ ├── doxygen-awesome-tabs.js │ │ └── doxygen-awesome.css │ ├── function_groups.stan │ └── mainpage.md │ ├── estimate_infections.stan │ ├── estimate_secondary.stan │ ├── estimate_truncation.stan │ ├── functions │ ├── convolve.stan │ ├── delays.stan │ ├── gaussian_process.stan │ ├── generated_quantities.stan │ ├── helpers.stan │ ├── infections.stan │ ├── observation_model.stan │ ├── params.stan │ ├── pmfs.stan │ ├── rt.stan │ └── secondary.stan │ ├── include │ └── license.stan │ ├── simulate_infections.stan │ └── simulate_secondary.stan ├── man ├── Distributions.Rd ├── EpiNow2-package.Rd ├── R_to_growth.Rd ├── add_breakpoints.Rd ├── add_day_of_week.Rd ├── add_horizon.Rd ├── allocate_delays.Rd ├── allocate_empty.Rd ├── apply_default_cdf_cutoff.Rd ├── apply_tolerance.Rd ├── apply_zero_threshold.Rd ├── backcalc_opts.Rd ├── bootstrapped_dist_fit.Rd ├── bound_dist.Rd ├── c.dist_spec.Rd ├── calc_CrI.Rd ├── calc_CrIs.Rd ├── calc_summary_measures.Rd ├── calc_summary_stats.Rd ├── cash-.estimate_secondary.Rd ├── check_generation_time.Rd ├── check_reports_valid.Rd ├── check_sparse_pmf_tail.Rd ├── check_stan_delay.Rd ├── check_truncation_length.Rd ├── clean_nowcasts.Rd ├── clean_regions.Rd ├── collapse.Rd ├── construct_output.Rd ├── convert_to_logmean.Rd ├── convert_to_logsd.Rd ├── convert_to_natural.Rd ├── convolve_and_scale.Rd ├── copy_results_to_latest.Rd ├── create_backcalc_data.Rd ├── create_delay_inits.Rd ├── create_future_rt.Rd ├── create_gp_data.Rd ├── create_infection_summary.Rd ├── create_initial_conditions.Rd ├── create_obs_model.Rd ├── create_rt_data.Rd ├── create_sampling_log_message.Rd ├── create_shifted_cases.Rd ├── create_stan_args.Rd ├── create_stan_data.Rd ├── create_stan_delays.Rd ├── create_stan_params.Rd ├── default_fill_missing_obs.Rd ├── delay_opts.Rd ├── discrete_pmf.Rd ├── discretise.Rd ├── dist_fit.Rd ├── dist_skel.Rd ├── epinow.Rd ├── epinow2_cmdstan_model.Rd ├── epinow2_rstan_model.Rd ├── epinow2_stan_model.Rd ├── equals-.dist_spec.Rd ├── estimate_delay.Rd ├── estimate_infections.Rd ├── estimate_secondary.Rd ├── estimate_truncation.Rd ├── estimates_by_report_date.Rd ├── example_confirmed.Rd ├── example_generation_time.Rd ├── example_incubation_period.Rd ├── example_reporting_delay.Rd ├── example_truncated.Rd ├── expose_stan_fns.Rd ├── extract_CrIs.Rd ├── extract_delays.Rd ├── extract_inits.Rd ├── extract_latent_state.Rd ├── extract_parameter_samples.Rd ├── extract_parameters.Rd ├── extract_params.Rd ├── extract_samples.Rd ├── extract_single_dist.Rd ├── extract_stan_param.Rd ├── figures │ ├── lifecycle-archived.svg │ ├── lifecycle-defunct.svg │ ├── lifecycle-deprecated.svg │ ├── lifecycle-experimental.svg │ ├── lifecycle-maturing.svg │ ├── lifecycle-questioning.svg │ ├── lifecycle-soft-deprecated.svg │ ├── lifecycle-stable.svg │ ├── lifecycle-superseded.svg │ └── logo.png ├── fill_missing.Rd ├── filter_leading_zeros.Rd ├── filter_opts.Rd ├── fit_model.Rd ├── fit_model_approximate.Rd ├── fit_model_with_nuts.Rd ├── fix_dist.Rd ├── fix_parameters.Rd ├── forecast_infections.Rd ├── forecast_opts.Rd ├── forecast_secondary.Rd ├── format_fit.Rd ├── format_samples_with_dates.Rd ├── format_simulation_output.Rd ├── generation_time_opts.Rd ├── get_distribution.Rd ├── get_element.Rd ├── get_parameters.Rd ├── get_pmf.Rd ├── get_predictions.Rd ├── get_raw_result.Rd ├── get_regional_results.Rd ├── get_regions.Rd ├── get_regions_with_most_reports.Rd ├── get_samples.Rd ├── get_seeding_time.Rd ├── gp_opts.Rd ├── growth_to_R.Rd ├── is_constrained.Rd ├── lapply_func.Rd ├── lower_bounds.Rd ├── make_conf.Rd ├── make_param.Rd ├── map_prob_change.Rd ├── match_output_arguments.Rd ├── max.dist_spec.Rd ├── mean.dist_spec.Rd ├── natural_params.Rd ├── ndist.Rd ├── new_dist_spec.Rd ├── obs_opts.Rd ├── opts_list.Rd ├── pad_reported_cases.Rd ├── plot.dist_spec.Rd ├── plot.epinow.Rd ├── plot.estimate_infections.Rd ├── plot.estimate_secondary.Rd ├── plot.estimate_truncation.Rd ├── plot.forecast_infections.Rd ├── plot.forecast_secondary.Rd ├── plot_CrIs.Rd ├── plot_estimates.Rd ├── plot_summary.Rd ├── plus-.dist_spec.Rd ├── print.dist_spec.Rd ├── print.epinowfit.Rd ├── process_region.Rd ├── process_regions.Rd ├── regional_epinow.Rd ├── regional_runtimes.Rd ├── regional_summary.Rd ├── report_plots.Rd ├── report_summary.Rd ├── rt_opts.Rd ├── run_region.Rd ├── save_estimate_infections.Rd ├── save_input.Rd ├── sd.Rd ├── secondary_opts.Rd ├── select_plots.Rd ├── set_dt_single_thread.Rd ├── setup_default_logging.Rd ├── setup_dt.Rd ├── setup_future.Rd ├── setup_logging.Rd ├── setup_target_folder.Rd ├── simulate_infections.Rd ├── simulate_secondary.Rd ├── stable_convolve.Rd ├── stan_laplace_opts.Rd ├── stan_opts.Rd ├── stan_pathfinder_opts.Rd ├── stan_sampling_opts.Rd ├── stan_vb_opts.Rd ├── summarise_key_measures.Rd ├── summarise_results.Rd ├── summary.epinow.Rd ├── summary.estimate_infections.Rd ├── summary.estimate_secondary.Rd ├── summary.forecast_infections.Rd ├── trunc_opts.Rd ├── update_horizon.Rd └── update_secondary_args.Rd ├── pkgdown └── favicon │ ├── apple-touch-icon.png │ ├── favicon-96x96.png │ ├── favicon.ico │ ├── favicon.svg │ ├── site.webmanifest │ ├── web-app-manifest-192x192.png │ └── web-app-manifest-512x512.png ├── tests ├── spelling.R ├── testthat.R └── testthat │ ├── _snaps │ ├── calc_CrI.md │ ├── calc_CrIs.md │ ├── calc_summary_measures.md │ ├── calc_summary_stats.md │ ├── simulate-infections.md │ └── simulate-secondary.md │ ├── setup.R │ ├── test-calc_CrI.R │ ├── test-calc_CrIs.R │ ├── test-calc_summary_measures.R │ ├── test-calc_summary_stats.R │ ├── test-checks.R │ ├── test-create_future-rt.R │ ├── test-create_gp_data.R │ ├── test-create_obs_model.R │ ├── test-create_rt_date.R │ ├── test-create_shifted_cases.R │ ├── test-create_stan_args.R │ ├── test-create_stan_params.R │ ├── test-delays.R │ ├── test-dist.R │ ├── test-dist_spec.R │ ├── test-epinow.R │ ├── test-estimate_delay.R │ ├── test-estimate_infections.R │ ├── test-estimate_secondary.R │ ├── test-estimate_truncation.R │ ├── test-extract_CrIs.R │ ├── test-fit.R │ ├── test-forecast-infections.R │ ├── test-forecast-opts.R │ ├── test-gp_opts.R │ ├── test-match_output_arguments.R │ ├── test-obs_opts.R │ ├── test-plot_estimates.R │ ├── test-preprocessing.R │ ├── test-regional_epinow.R │ ├── test-regional_runtimes.R │ ├── test-regional_summary.R │ ├── test-report_plots.R │ ├── test-rt_opts.R │ ├── test-seeding-time.R │ ├── test-set_dt_single_thread.R │ ├── test-setup_future.R │ ├── test-simulate-infections.R │ ├── test-simulate-secondary.R │ ├── test-stan-convole.R │ ├── test-stan-delays.R │ ├── test-stan-generated_quantities.R │ ├── test-stan-guassian-process.R │ ├── test-stan-infections.R │ ├── test-stan-observation_model.R │ ├── test-stan-pmfs.R │ ├── test-stan-rt.R │ ├── test-stan-secondary.R │ └── test-stan-truncate.R ├── touchstone ├── .gitignore ├── config.json ├── footer.R ├── header.R ├── script.R └── setup.R └── vignettes ├── .gitignore ├── EpiNow2-plot_estimates-1.png ├── EpiNow2-plot_reg_epinow_opts_list_eg-1.png ├── EpiNow2-plot_regional_epinow_summary-1.png ├── EpiNow2.Rmd ├── EpiNow2.Rmd.orig ├── case-studies.Rmd ├── epinow-epinow-1.png ├── epinow-regional_epinow-1.png ├── epinow-regional_epinow_multiple-1.png ├── epinow.Rmd ├── epinow.Rmd.orig ├── estimate_infections.Rmd ├── estimate_infections_options-bp-1.png ├── estimate_infections_options-data-1.png ├── estimate_infections_options-default-1.png ├── estimate_infections_options-fixed-1.png ├── estimate_infections_options-gp_projection-1.png ├── estimate_infections_options-lower_accuracy-1.png ├── estimate_infections_options-no_delays-1.png ├── estimate_infections_options-nonparametric-1.png ├── 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