├── .github ├── actions │ └── pre-commit │ │ └── action.yaml └── workflows │ ├── pre-commit.yaml │ └── tests.yaml ├── .gitignore ├── .lintr ├── .pre-commit-config.yaml ├── .secrets.baseline ├── LICENSE ├── README.md ├── docs ├── api.md ├── architecture.md ├── index.md ├── javascript │ └── katex.js └── notation.md ├── exploration ├── README.md ├── clade_year_maps.py ├── priors.qmd ├── simulation-study │ ├── README.md │ ├── main.py │ └── visualize.R └── whole_hist_viz.py ├── linmod ├── data.py ├── eval.py ├── models │ ├── __init__.py │ ├── models.py │ └── utils.py ├── tests │ ├── test_eval.py │ ├── test_frames.py │ └── test_hhs_agg.py ├── utils.py └── visualize.py ├── mkdocs.yml ├── poetry.lock ├── pyproject.toml └── retrospective-forecasting ├── README.md ├── config ├── 2022-early-omicron.yaml ├── 2023-variant-soup.yaml └── 2024-nomenclature-shift.yaml ├── main.py ├── pop_sizes_nst_est_2023.csv ├── run_all.sh └── test ├── 2022 └── 06 │ └── 01 │ └── public-2022-06-01.metadata.tsv.gz ├── config.yaml ├── metadata.tsv.xz └── run.sh /.github/actions/pre-commit/action.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CDCgov/cfa-viral-lineage-model/HEAD/.github/actions/pre-commit/action.yaml -------------------------------------------------------------------------------- /.github/workflows/pre-commit.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CDCgov/cfa-viral-lineage-model/HEAD/.github/workflows/pre-commit.yaml -------------------------------------------------------------------------------- /.github/workflows/tests.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CDCgov/cfa-viral-lineage-model/HEAD/.github/workflows/tests.yaml -------------------------------------------------------------------------------- /.gitignore: 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