Files in epiforecasts/EpiNow2

Estimate Real-Time Case Counts and Time-Varying Epidemiological Parameters

.github/CONTRIBUTING.md .github/ISSUE_TEMPLATE/bug_report.md .github/ISSUE_TEMPLATE/documentation.md .github/ISSUE_TEMPLATE/feature_request.md .github/ISSUE_TEMPLATE/other_issue.md .github/PULL_REQUEST_TEMPLATE.md CODE_OF_CONDUCT.md LICENSE.md NEWS.md R/EpiNow2-package.R R/checks.R R/create.R R/data.R R/deprecated.R R/dist_spec.R R/epinow-internal.R R/epinow.R R/estimate_delay.R R/estimate_infections.R R/estimate_secondary.R R/estimate_truncation.R R/extract.R R/fit.R R/get.R R/opts.R R/plot.R R/preprocessing.R R/regional_epinow.R R/report.R R/setup.R R/simulate_infections.R R/simulate_secondary.R R/stan.R R/stanmodels.R R/summarise.R R/utilities.R README.Rmd README.md cran-comments.md data-raw/estimate-infections.R data-raw/generation-time.R data-raw/incubation-period.R data-raw/reporting-delay.R data-raw/truncated.R inst/dev/accumulation.Rmd inst/dev/accumulation.md inst/dev/benchmark-functions.R inst/dev/benchmark.R inst/dev/design_dist.md inst/dev/load-stan-functions.R inst/dev/recover-synthetic/eval_rt.R inst/dev/recover-synthetic/plot.R inst/dev/recover-synthetic/rt.R man/Distributions.Rd man/EpiNow2-package.Rd man/R_to_growth.Rd man/add_day_of_week.Rd man/adjust_infection_to_report.Rd man/allocate_delays.Rd man/allocate_empty.Rd man/apply_default_cdf_cutoff.Rd man/apply_tolerance.Rd man/backcalc_opts.Rd man/bootstrapped_dist_fit.Rd man/bound_dist.Rd man/c.dist_spec.Rd man/calc_CrI.Rd man/calc_CrIs.Rd man/calc_summary_measures.Rd man/calc_summary_stats.Rd man/check_generation_time.Rd man/check_na_setting_against_data.Rd man/check_reports_valid.Rd man/check_sparse_pmf_tail.Rd man/check_stan_delay.Rd man/clean_nowcasts.Rd man/clean_regions.Rd man/collapse.Rd man/construct_output.Rd man/convert_to_logmean.Rd man/convert_to_logsd.Rd man/convert_to_natural.Rd man/convolve_and_scale.Rd man/copy_results_to_latest.Rd man/create_backcalc_data.Rd man/create_clean_reported_cases.Rd man/create_complete_cases.Rd man/create_delay_inits.Rd man/create_future_rt.Rd man/create_gp_data.Rd man/create_initial_conditions.Rd man/create_obs_model.Rd man/create_rt_data.Rd man/create_shifted_cases.Rd man/create_stan_args.Rd man/create_stan_data.Rd man/create_stan_delays.Rd man/create_stan_params.Rd man/default_fill_missing_obs.Rd man/delay_opts.Rd man/discrete_pmf.Rd man/discretise.Rd man/dist_fit.Rd man/dist_skel.Rd man/dist_spec.Rd man/epinow.Rd man/epinow2_cmdstan_model.Rd man/epinow2_rstan_model.Rd man/epinow2_stan_model.Rd man/equals-.dist_spec.Rd man/estimate_delay.Rd man/estimate_infections.Rd man/estimate_secondary.Rd man/estimate_truncation.Rd man/estimates_by_report_date.Rd man/example_confirmed.Rd man/example_generation_time.Rd man/example_incubation_period.Rd man/example_reporting_delay.Rd man/example_truncated.Rd man/expose_stan_fns.Rd man/extract_CrIs.Rd man/extract_inits.Rd man/extract_parameter.Rd man/extract_parameter_samples.Rd man/extract_params.Rd man/extract_samples.Rd man/extract_single_dist.Rd man/extract_stan_param.Rd man/extract_static_parameter.Rd man/fill_missing.Rd man/filter_opts.Rd man/fit_model.Rd man/fit_model_approximate.Rd man/fit_model_with_nuts.Rd man/fix_dist.Rd man/fix_parameters.Rd man/forecast_infections.Rd man/forecast_secondary.Rd man/format_fit.Rd man/gamma_dist_def.Rd man/generation_time_opts.Rd man/generation_times.Rd man/get_dist.Rd man/get_distribution.Rd man/get_element.Rd man/get_generation_time.Rd man/get_incubation_period.Rd man/get_parameters.Rd man/get_pmf.Rd man/get_raw_result.Rd man/get_regional_results.Rd man/get_regions.Rd man/get_regions_with_most_reports.Rd man/get_seeding_time.Rd man/gp_opts.Rd man/growth_to_R.Rd man/incubation_periods.Rd man/init_cumulative_fit.Rd man/is_constrained.Rd man/lapply_func.Rd man/lognorm_dist_def.Rd man/lower_bounds.Rd man/make_conf.Rd man/map_prob_change.Rd man/match_output_arguments.Rd man/max.dist_spec.Rd man/mean.dist_spec.Rd man/natural_params.Rd man/ndist.Rd man/new_dist_spec.Rd man/obs_opts.Rd man/opts_list.Rd man/plot.dist_spec.Rd man/plot.epinow.Rd man/plot.estimate_infections.Rd man/plot.estimate_secondary.Rd man/plot.estimate_truncation.Rd man/plot_CrIs.Rd man/plot_estimates.Rd man/plot_summary.Rd man/plus-.dist_spec.Rd man/print.dist_spec.Rd man/process_region.Rd man/process_regions.Rd man/regional_epinow.Rd man/regional_runtimes.Rd man/regional_summary.Rd man/report_cases.Rd man/report_plots.Rd man/report_summary.Rd man/rstan_opts.Rd man/rstan_sampling_opts.Rd man/rstan_vb_opts.Rd man/rt_opts.Rd man/run_region.Rd man/sample_approx_dist.Rd man/save_estimate_infections.Rd man/save_input.Rd man/sd.Rd man/secondary_opts.Rd man/set_dt_single_thread.Rd man/setup_default_logging.Rd man/setup_dt.Rd man/setup_future.Rd man/setup_logging.Rd man/setup_target_folder.Rd man/simulate_infections.Rd man/simulate_secondary.Rd man/stan_laplace_opts.Rd man/stan_opts.Rd man/stan_pathfinder_opts.Rd man/stan_sampling_opts.Rd man/stan_vb_opts.Rd man/summarise_key_measures.Rd man/summarise_results.Rd man/summary.epinow.Rd man/summary.estimate_infections.Rd man/test_data_complete.Rd man/trunc_opts.Rd man/update_horizon.Rd man/update_secondary_args.Rd tests/spelling.R tests/testthat.R tests/testthat/_snaps/calc_CrI.md tests/testthat/_snaps/calc_CrIs.md tests/testthat/_snaps/calc_summary_measures.md tests/testthat/_snaps/calc_summary_stats.md tests/testthat/_snaps/simulate-infections.md tests/testthat/_snaps/simulate-secondary.md tests/testthat/setup.R tests/testthat/test-calc_CrI.R tests/testthat/test-calc_CrIs.R tests/testthat/test-calc_summary_measures.R tests/testthat/test-calc_summary_stats.R tests/testthat/test-checks.R tests/testthat/test-create_clean_reported_cases.R tests/testthat/test-create_future-rt.R tests/testthat/test-create_gp_data.R tests/testthat/test-create_obs_model.R tests/testthat/test-create_rt_date.R tests/testthat/test-create_stan_args.R tests/testthat/test-create_stan_params.R tests/testthat/test-delays.R tests/testthat/test-dist.R tests/testthat/test-dist_spec.R tests/testthat/test-epinow.R tests/testthat/test-estimate_delay.R tests/testthat/test-estimate_infections.R tests/testthat/test-estimate_secondary.R tests/testthat/test-estimate_truncation.R tests/testthat/test-extract_CrIs.R tests/testthat/test-forecast-infections.R tests/testthat/test-gp_opts.R tests/testthat/test-match_output_arguments.R tests/testthat/test-obs_opts.R tests/testthat/test-plot_estimates.R tests/testthat/test-preprocessing.R tests/testthat/test-regional_epinow.R tests/testthat/test-regional_runtimes.R tests/testthat/test-regional_summary.R tests/testthat/test-report_plots.R tests/testthat/test-rt_opts.R tests/testthat/test-seeding-time.R tests/testthat/test-set_dt_single_thread.R tests/testthat/test-setup_future.R tests/testthat/test-simulate-infections.R tests/testthat/test-simulate-secondary.R tests/testthat/test-stan-convole.R tests/testthat/test-stan-generated_quantities.R tests/testthat/test-stan-guassian-process.R tests/testthat/test-stan-infections.R tests/testthat/test-stan-observation_model.R tests/testthat/test-stan-rt.R tests/testthat/test-stan-secondary.R tests/testthat/test-stan-truncate.R touchstone/footer.R touchstone/header.R touchstone/script.R touchstone/setup.R vignettes/EpiNow2.Rmd vignettes/case-studies.Rmd vignettes/epinow.Rmd vignettes/estimate_infections.Rmd vignettes/estimate_infections_options.Rmd vignettes/estimate_infections_workflow.Rmd vignettes/estimate_secondary.Rmd vignettes/estimate_truncation.Rmd vignettes/gaussian_process_implementation_details.Rmd vignettes/precompile.R