flu_peak_prediction

Scripts for assembling ILI and hospitalization data used to explore flu-peak prediction.

Python scripts

data/download_FluID_dataset.py

Downloads the WHO FluMart VIW_FID_EPI dataset.

Inputs	Optional CLI args: --output (default ./data/who_viw_fid_epi.csv), --chunk-size-mb
Output	./data/who_viw_fid_epi.csv
Description	Raw WHO FluID epidemiology CSV (ILI/ARI/SARI cases and denominators by country and week).

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analysis_data/create_WWHO_ILI_Signal.py

Builds a seasonal ILI signal from WHO FluID data.

Inputs	./data/who_viw_fid_epi.csv
Output	./analysis_data/ILI_signal_by_season.csv
Description	Country–season summary with outpatient ILI proportion (ili_proportion / ili_percent) and population-based ILI rate per 100k person-weeks. Seasons run week 35 through week 20.

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analysis_data/from_FLUID_to_formmatted_data.py

Alternative FluID seasonal summarizer (older / parallel path).

Inputs	./data/who_viw_fid_epi.csv
Output	./analysis_data/summarized_fluid.csv
Description	Country–season aggregates of ILI/ARI/SARI counts and a crude outpatient ILI proportion (pILI). Season windows differ by hemisphere (NH vs SH).

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analysis_data/build_ili_data.py

Pulls US ILINet data from the Delphi Epidata API.

Inputs	None (queries Epidata FluView for all states, 2021–present)
Output	./analysis_data/ili_data_all_states_2021_present.csv
Description	Weekly state-level ILI metrics (wili, ili, case/patient counts, age groups) with epiweek and season labels.

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analysis_data/format_ili_data.py

Formats the Epidata ILI extract and adds a national series.

Inputs	./analysis_data/ili_data_all_states_2021_present.csv
Output	./analysis_data/ili_data_all_states_2021_present__formatted.csv
Description	State abbreviations, zero-padded FIPS codes, and a national (nat) row per epiweek computed from pooled ILI counts.

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analysis/predict_total_US_hosps_setup.py

Assembles a modeling table linking US hosps, US ILI, and Southern Hemisphere ILI.

Inputs	./analysis_data/ILI_signal_by_season.csv, ./data/target-data/target-hospital-admissions.csv
Output	./analysis/US_plus_SH_data.csv
Description	Season-level table with total US hospitalizations, US ILI proportion, and Southern Hemisphere country ILI proportions (from 2022 onward). Helper dataset for exploring peak prediction.