├── .containerignore ├── .coveragerc ├── .env.example ├── .gitattributes ├── .github ├── .gitignore ├── CODEOWNERS ├── ISSUE_TEMPLATE │ ├── bug_report.md │ ├── feature_request.md │ └── scientific-improvement.md ├── actions │ ├── setup-hewr │ │ └── action.yaml │ └── setup-pyrenew-hew │ │ └── action.yaml ├── dependabot.yml ├── scripts │ └── docker_build_and_push.sh └── workflows │ ├── containers.yaml │ ├── delete-container-tag.yaml │ ├── format-suggest.yaml │ ├── pipeline-run-check.yaml │ ├── r-cmd-check.yaml │ └── test.yaml ├── .gitignore ├── .lintr ├── .pre-commit-config.yaml ├── .python-version ├── .secrets.baseline ├── Containerfile ├── LICENSE ├── Makefile ├── README.md ├── hewr ├── .Rbuildignore ├── DESCRIPTION ├── LICENSE.md ├── NAMESPACE ├── R │ ├── directory_utils.R │ ├── generate_exp_growth_process.R │ ├── hewr-package.R │ ├── make_forecast_figure.R │ ├── process_loc_forecast.R │ ├── timeseries_utils.R │ └── to_hub_quantile_table.R ├── man │ ├── disease_map_lower.Rd │ ├── epiweekly_samples_from_daily.Rd │ ├── format_timeseries_output.Rd │ ├── generate_exp_growth_pois.Rd │ ├── get_all_model_batch_dirs.Rd │ ├── hewr-package.Rd │ ├── load_training_data.Rd │ ├── make_forecast_figure.Rd │ ├── parse_model_batch_dir_path.Rd │ ├── parse_model_run_dir_path.Rd │ ├── parse_pyrenew_model_name.Rd │ ├── parse_variable_name.Rd │ ├── path_up_to.Rd │ ├── process_loc_forecast.Rd │ ├── prop_from_timeseries.Rd │ ├── read_and_combine_data.Rd │ ├── to_hub_quantile_table.Rd │ └── to_tidy_draws_timeseries.Rd └── tests │ ├── testthat.R │ └── testthat │ ├── helper.R │ ├── test_directory_utils.R │ ├── test_generate_exp_growth_process.R │ ├── test_process_loc_forecast.R │ └── test_to_hub_quantile_table.R ├── pipelines ├── README.md ├── __init__.py ├── azure_command_center.py ├── batch │ ├── __init__.py │ ├── setup_job.py │ └── setup_pool.py ├── cli_utils.py ├── collate_plots.py ├── combine_hubverse_tables.R ├── common_utils.py ├── fit_pyrenew_model.py ├── forecast_cdc_flat_baseline.R ├── forecast_pyrenew.py ├── forecast_timeseries.py ├── forecast_timeseries_ensemble.R ├── generate_epiweekly_data.R ├── generate_predictive.py ├── generate_test_data.py ├── generate_test_data_lib.py ├── plot_and_save_loc_forecast.R ├── postprocess_forecast_batches.py ├── prep_data.py ├── prep_eval_data.py ├── prep_ww_data.py ├── priors │ ├── eval_priors.py │ ├── parameter_inference_priors.py │ └── prod_priors.py ├── tests │ ├── README.md │ ├── __init__.py │ ├── test_common_utils.py │ ├── test_end_to_end.sh │ ├── test_generate_test_data_lib.py │ ├── test_prep_data.py │ ├── test_pyrenew_fit.sh │ └── test_ts_fit.sh └── utils.py ├── pyproject.toml ├── pyrenew_hew ├── __init__.py ├── pyrenew_hew_data.py ├── pyrenew_hew_model.py ├── pyrenew_hew_param.py └── utils.py ├── tests ├── __init__.py ├── test_hospital_admission_indices.py ├── test_latent_infection_process.py ├── test_pyrenew_hew_data.py ├── test_pyrenew_hew_param.py └── test_util.py └── uv.lock 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