├── .ContainerBuildRprofile ├── .containerignore ├── .gitattributes ├── .github ├── .gitignore ├── ISSUE_TEMPLATE │ ├── bug_report.md │ ├── feature_request.md │ └── maintenance.md ├── PULL_REQUEST_TEMPLATE │ ├── pull_request_template.md │ └── vulnerability.md ├── scripts │ └── docker_build_and_push.sh └── workflows │ ├── air-format-suggest.yaml │ ├── container-build-push.yaml │ ├── pkgdown.yaml │ └── r-cmd-check.yaml ├── .gitignore ├── .lintr ├── .pre-commit-config.yaml ├── .python-version ├── .secrets.baseline ├── CONTRIBUTING.md ├── Containerfile ├── DISCLAIMER.md ├── LICENSE ├── Makefile ├── README.md ├── _targets.R ├── _targets_benchmark.R ├── air.toml ├── archive ├── _targets_local_eval.R └── _targets_production.R ├── batch ├── .gitignore ├── README.md ├── setup_job.py ├── setup_pool.py └── upload_data.py ├── code-of-conduct.md ├── compute_diff.R ├── docs └── evaluation_plan.md ├── fit_trend.R ├── input ├── config │ └── eval │ │ └── example_eval_config.yaml ├── locations.csv ├── params.toml └── saved_pmfs │ ├── generation_interval.csv │ └── inf_to_hosp.csv ├── model_diagnostics └── diagnostic_report.Rmd ├── output ├── benchmarking │ ├── all_forecasts_by_forecast_date.tsv │ ├── all_forecasts_by_location.tsv │ ├── latest_all_forecasts_by_forecast_date.tsv │ ├── latest_all_forecasts_by_location.tsv │ ├── latest_subset_forecasts_by_forecast_date.tsv │ ├── latest_subset_forecasts_by_location.tsv │ ├── plots │ │ ├── all_forecasts_by_forecast_date.png │ │ ├── all_forecasts_by_location.png │ │ ├── all_forecasts_overall.png │ │ ├── subset_forecasts_by_forecast_date.png │ │ ├── subset_forecasts_by_location.png │ │ └── subset_forecasts_overall.png │ ├── subset_forecasts_by_forecast_date.tsv │ └── subset_forecasts_by_location.tsv └── forecasts │ ├── 2024-02-05 │ ├── 2024-02-05.tsv │ ├── metadata.yaml │ └── wastewater_metadata_table.tsv │ ├── 2024-02-12 │ ├── 2024-02-12.tsv │ ├── metadata.yaml │ └── wastewater_metadata_table.tsv │ ├── 2024-02-19 │ ├── 2024-02-19.tsv │ ├── metadata.yaml │ └── wastewater_metadata_table.tsv │ ├── 2024-02-26 │ ├── 2024-02-26.tsv │ ├── metadata.yaml │ └── wastewater_metadata_table.tsv │ ├── 2024-03-04 │ ├── 2024-03-04.tsv │ ├── metadata.yaml │ └── wastewater_metadata_table.tsv │ ├── 2024-03-11 │ ├── 2024-03-11.tsv │ ├── metadata.yaml │ └── wastewater_metadata_table.tsv │ ├── 2024-03-18 │ ├── 2024-03-18.tsv │ ├── metadata.yaml │ └── wastewater_metadata_table.tsv │ ├── 2024-03-25 │ ├── 2024-03-25.tsv │ ├── metadata.yaml │ └── wastewater_metadata_table.tsv │ ├── 2024-04-01 │ ├── 2024-04-01.tsv │ ├── metadata.yaml │ └── wastewater_metadata_table.tsv │ ├── 2024-04-08 │ ├── 2024-04-08.tsv │ ├── metadata.yaml │ └── wastewater_metadata_table.tsv │ ├── 2024-04-15 │ ├── 2024-04-15.tsv │ ├── metadata.yaml │ └── wastewater_metadata_table.tsv │ ├── 2024-04-22 │ ├── 2024-04-22.tsv │ ├── metadata.yaml │ └── wastewater_metadata_table.tsv │ └── 2024-04-29 │ ├── 2024-04-29.tsv │ ├── metadata.yaml │ └── wastewater_metadata_table.tsv ├── pyproject.toml ├── ruff.toml ├── run_eval.R ├── scratch ├── ar1_example.R ├── debug_ww_data.R ├── get_config_for_failed_postprocess.R ├── get_empirical_posterior_vals.R ├── quicker_way_to_make_figs.R ├── scratch_hub_api.R ├── site_level_inf_dynamics.Rmd ├── sites_sum_to_states_test.Rmd ├── state_level_model.Rmd ├── test_check_calibration_metrics.R ├── test_epi_class.R ├── toy_example_ind_variation.Rmd └── ww_data_quick_figs.R ├── src ├── create_scenarios.R ├── pull_nhsn.R ├── setup_eval.R ├── setup_subset_benchmarking.R ├── site_maps.R ├── test_pipeline.R └── tests │ └── test_end_to_end.R ├── uv.lock └── wweval ├── .Rbuildignore ├── DESCRIPTION ├── NAMESPACE ├── R ├── add_horizons.R ├── additional_figures.R ├── benchmarking.R ├── combine_and_summarize_ww_data.R ├── combine_outputs.R ├── composite_figures.R ├── compute_forecast_differences.R ├── compute_ww_data_quality_table.R ├── constants.R ├── create_hub_submissions.R ├── create_mock_submissions.R ├── data.R ├── eval_fit.R ├── exclude_hosp_outliers.R ├── filepath_mapping.R ├── fit_recent_trends.R ├── get_input_data.R ├── hub.R ├── model_run_diagnostic_flags.R ├── order_elements.R ├── parse_real_time_exclusions.R ├── plot_absolute_scores.R ├── plot_admissions.R ├── plot_bias.R ├── plot_calibration.R ├── plot_example_scores.R ├── plot_generic.R ├── plot_hub_comparison.R ├── plot_metadata.R ├── plot_predictive.R ├── plot_relative_scores.R ├── plot_trend_versus_diff.R ├── plotting_style.R ├── postprocess.R ├── process_recent_trend_fits.R ├── pull_data.R ├── score.R ├── summarize_ww_data_quality.R ├── utils.R └── wweval-package.R ├── _pkgdown.yml ├── data-raw └── flusight_location_table.R ├── data └── flusight_location_table.rda ├── man ├── add_horizons.Rd ├── assert_needed_env_vars.Rd ├── benchmark_performance.Rd ├── check_any_flags.Rd ├── clean_and_filter_nwss_data.Rd ├── clean_flag_df.Rd ├── clean_ww_data.Rd ├── combine_and_summarize_ww_data.Rd ├── combine_outputs.Rd ├── combine_ww_and_run_metadata.Rd ├── compose_example_scores_fig.Rd ├── compose_hub_fig.Rd ├── compose_pred_actual_fig.Rd ├── compose_rel_performance_fig.Rd ├── compute_flags.Rd ├── compute_forecast_differences.Rd ├── compute_retro_exclusions.Rd ├── compute_ww_data_quality_table.Rd ├── create_hub_submissions.Rd ├── create_mock_submission_scores.Rd ├── date_of_ww_data.Rd ├── dot-path_with_suffix.Rd ├── dot-relative_metric_display_abbr.Rd ├── dot-relative_metric_display_name.Rd ├── dot-target_model_relative_scores.Rd ├── eval_fit.Rd ├── eval_postprocess.Rd ├── exclude_hosp_outliers.Rd ├── file_exists_object_with_suffix.Rd ├── fit_hosp_trend.Rd ├── fit_recent_trends.Rd ├── fit_ww_trend.Rd ├── flusight_location_table.Rd ├── forecast_interval_coverage_plot.Rd ├── forecast_output_path.Rd ├── forecast_qq_plot.Rd ├── format_for_hub.Rd ├── format_scores_for_comparison.Rd ├── geom_decomposed_scores.Rd ├── get_convergence_df.Rd ├── get_diagnostic_flags.Rd ├── get_filepath.Rd ├── get_ind_forecast_score.Rd ├── get_input_hosp_data.Rd ├── get_input_ww_data.Rd ├── get_last_hosp_data_date.Rd ├── get_last_hosp_data_date_map.Rd ├── get_model_draws_w_data.Rd ├── get_model_path.Rd ├── get_object_existence_checker.Rd ├── get_object_loader.Rd ├── get_object_saver.Rd ├── get_plot_scores_and_forecasts.Rd ├── get_plot_theme.Rd ├── get_plot_xy_raw_limits.Rd ├── get_raw_output_suffix.Rd ├── get_scenario_site_ids.Rd ├── get_score_summary_tables.Rd ├── get_shared_xy_raw_limits.Rd ├── get_state_level_quantiles.Rd ├── get_state_level_ww_quantiles.Rd ├── get_stats_improved_forecasts.Rd ├── get_summary_metadata.Rd ├── get_summary_ww_table.Rd ├── heatmap_scores_by_loc_date.Rd ├── load_data_and_summarize.Rd ├── load_real_time_forecast.Rd ├── load_real_time_quantile_fcsts.Rd ├── make_baseline_score_table.Rd ├── nhsn_soda_query.Rd ├── order_col.Rd ├── order_horizons.Rd ├── order_locations.Rd ├── order_periods.Rd ├── order_phases.Rd ├── parse_real_time_exclusions.Rd ├── plot_benchmarks.Rd ├── plot_bias_t.Rd ├── plot_components.Rd ├── plot_crps_underlay.Rd ├── plot_forecast_comparison_t.Rd ├── plot_heatmap_metadata_retro.Rd ├── plot_hub_heatmap_relative_wis.Rd ├── plot_hub_performance_by_period.Rd ├── plot_hub_submit_info_real_time.Rd ├── plot_hub_submit_info_retro.Rd ├── plot_pointinterval_scatter.Rd ├── plot_rel_crps_by_horizon.Rd ├── plot_rel_score_dists.Rd ├── plot_rel_score_dists_by_horizon.Rd ├── plot_rel_score_heatmap.Rd ├── plot_rel_score_t.Rd ├── plot_ribbon_hosp_quantiles.Rd ├── plot_ribbon_ww_quantiles.Rd ├── plot_score_by_horizon_t.Rd ├── plot_score_decomposed_bars.Rd ├── plot_score_model_loc.Rd ├── plot_score_scatter.Rd ├── plot_score_t.Rd ├── plot_spaghetti_hosp_draws.Rd ├── plot_spaghetti_ww_draws.Rd ├── plot_std_rank_distribution.Rd ├── plot_total_admissions.Rd ├── plot_trend_versus_diff.Rd ├── postprocess_successful_fit.Rd ├── process_recent_trend_fits.Rd ├── pull_and_write_hosp_data.Rd ├── pull_daily_nhsn.Rd ├── pull_hub_forecasts.Rd ├── quantile_metrics.Rd ├── read_rds_with_suffix.Rd ├── relative_wis_histogram.Rd ├── sample_metrics.Rd ├── save_rds_with_suffix.Rd ├── save_table.Rd ├── scale_alpha_score_component.Rd ├── scale_fill_horizon.Rd ├── scale_fill_model.Rd ├── scale_fill_score_ratio.Rd ├── scale_x_weekly_iso_date.Rd ├── score_hub_forecasts.Rd ├── score_quantiles.Rd ├── score_real_time_outputs.Rd ├── score_samples.Rd ├── select_hub_models.Rd ├── select_like.Rd ├── soql_is_in.Rd ├── summarize_std_rank.Rd ├── summarize_ww_data_quality.Rd ├── with_dependencies.Rd └── wweval-package.Rd └── tests ├── testthat.R └── testthat ├── test_benchmarking.R ├── test_create_mock_submissions.R ├── test_filepath_mapping.R ├── test_fit_recent_trends.R ├── test_get_input_data.R ├── test_get_state_level_quantiles.R └── test_utils.R /.ContainerBuildRprofile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CDCgov/wastewater-informed-covid-forecasting/HEAD/.ContainerBuildRprofile 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