├── .Rbuildignore ├── .gitattributes ├── .github ├── .gitignore ├── ISSUE_TEMPLATE │ ├── bug_report.md │ ├── feature_request.md │ ├── maintenance.md │ └── scientific-improvement.md ├── PULL_REQUEST_TEMPLATE │ ├── pull_request_template.md │ └── vulnerability.md ├── dependabot.yml ├── scripts │ ├── cleanup-on-pr-close.sh │ ├── create_pool.py │ ├── delete-container-tag.sh │ └── docker_build_and_push.sh └── workflows │ ├── block-fixup.yaml │ ├── check-news-md.yaml │ ├── cleanup-on-pr-close.yaml │ ├── containers-and-az-pool.yaml │ ├── delete-container-tag.yaml │ ├── format-suggest.yaml │ ├── gh-act │ ├── 2-dry.sh │ └── 2-full.sh │ ├── manual-docker-prune.yml │ ├── pkgdown.yaml │ ├── pr-commands.yaml │ ├── run-prod.yaml │ ├── test-coverage.yaml │ └── test-documentation.yaml ├── .gitignore ├── .lintr ├── .pre-commit-config.yaml ├── .secrets.baseline ├── CONTRIBUTING.md ├── DESCRIPTION ├── DISCLAIMER.md ├── Dockerfile ├── LICENSE.md ├── Makefile ├── NAMESPACE ├── NEWS.md ├── R ├── azure.R ├── config.R ├── data.R ├── diagnostics.R ├── exclusions.R ├── find_low_count_threshold.R ├── fit_model.R ├── parameters.R ├── pipeline.R ├── read_data.R ├── utils.R └── write_output.R ├── README.md ├── SOP.md ├── _pkgdown.yml ├── air.toml ├── azure ├── generate_configs.py ├── generate_rerun_configs.py ├── job.py └── run_container_app_job.py ├── code-of-conduct.md ├── codecov.yml ├── data-raw ├── convert_gostic_toy_rt_to_test_dataset.R └── sir_gt_pmf.R ├── data ├── gostic_toy_rt.rda └── sir_gt_pmf.rda ├── image.png ├── man ├── Config.Rd ├── Data.Rd ├── Interval.Rd ├── Parameters.Rd ├── apply_exclusions.Rd ├── check_returned_pmf.Rd ├── download_file_from_container.Rd ├── download_if_specified.Rd ├── extract_diagnostics.Rd ├── fetch_blob_container.Rd ├── fetch_credential_from_env_var.Rd ├── fit_model.Rd ├── format_stan_opts.Rd ├── gostic_toy_rt.Rd ├── low_case_count_diagnostic.Rd ├── low_case_count_threshold.Rd ├── opts_formatter.Rd ├── pipeline.Rd ├── read_data.Rd ├── read_disease_parameters.Rd ├── read_exclusions.Rd ├── read_interval_pmf.Rd ├── read_json_into_config.Rd ├── sample_processing_functions.Rd ├── sir_gt_pmf.Rd ├── write_model_outputs.Rd └── write_output_dir_structure.Rd ├── open_practices.md ├── rules_of_behavior.md ├── start.sh ├── tests ├── testthat.R └── testthat │ ├── _snaps │ ├── fit_model.md │ ├── parameters.md │ └── read_data.md │ ├── data │ ├── CA_COVID-19.json │ ├── CA_test.parquet │ ├── bad_config.json │ ├── sample_config_no_exclusion.json │ ├── sample_config_with_exclusion.json │ ├── test_big_exclusions.csv │ ├── test_data.parquet │ ├── test_exclusions.csv │ ├── test_parameters.parquet │ ├── us_overall_test_data.parquet │ └── v_bad_config.json │ ├── helper-expect_pipeline_files_written.R │ ├── helper-write_exclusion.R │ ├── helper-write_parameter_file.R │ ├── setup.R │ ├── test-diagnostics.R │ ├── test-exclusions.R │ ├── test-fit_model.R │ ├── test-parameters.R │ ├── test-pipeline.R │ ├── test-read_data.R │ └── 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