Vaccination coverage forecasting

Formerly known as Immunization Uptake Projections, or vcf.

Getting started

1. Read the docs at https://cdcgov.github.io/cfa-vaccination-coverage-forecasting, or build them locally with mkdocs serve
2. This project uses uv for environment and dependency management. Ensure you can uv sync. Use the uv-managed virtual environment (e.g., by prepending uv run).
3. Run the vignette.

Vignette

The vignette demonstrates an analytical pipeline:

1. Fit models to coverage data from past seasons
2. Use those trained models to forecast future coverage data in the latest season
3. Evaluate forecasts against observed values

Data source

The vignette uses monthly estimates of season flu vaccination coverage, from the 2009/2010 season through the 2022/2023 season, as reported by the National Immunization Survey and Behavioral Risk Factor Surveillance System and cleaned using nis-py-api in December 2025.

Running the vignette

1. Run the pipeline with make. (You can run steps in parallel with, e.g., make -j4.)
   • By default, make will use scripts/config_vignette.yaml for its configuration.
   • You can use different configs by running make CONFIG=/path/to/config.yaml.
2. Inspect output/vignette/:
   • config.yaml: a copy of the input config
   • data.parquet: the preprocessed, observed data
   • scores.parquet: model scores
   • fits/: pickled model fits, organized by forecast date
   • plots/: visualizations
   • pred/: model predictions, in Hive-partitioned parquet files

Analysis pipeline

flowchart TB;

data[output/RUN_ID/data.parquet];
pred[output/RUN_ID/pred/forecast_date=DATE/part-0.parquet];
scores[output/RUN_ID/scores.parquet];
preprocess[/scripts/preprocess.py/];
fit[/scripts/fit.py/];
predict[/scripts/predict.py/];
eval[/scripts/eval.py/];
viz[/scripts/plot_*.py/];
plots[/output/RUN_ID/plots/*.svg/]

data/raw.parquet --> preprocess --> data --> fit --> output/RUN_ID/fits/fit_DATE.pkl --> predict --> pred;

data --> eval;
pred--> eval -->scores;

data --> viz;
pred --> viz;
scores --> viz;
viz --> plots;

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