Process supplementary cholera outbreak data from raw SUPP directory

This function reads the first CSV line-list file in the raw SUPP directory (e.g., Aceng et al. 2025 S1 Data), cleans and standardizes the data, and returns a data.frame of weekly counts in the standard MOSAIC surveillance format.

Usage

process_SUPP_weekly_data(PATHS)

Arguments

PATHS

A list of file paths used by the MOSAIC pipeline. Must include:

DATA_RAW

Root data directory (e.g., root/MOSAIC-data/raw).

Value

A data.frame with columns:

country

Country name (fixed to "Uganda").

iso_code

ISO3 country code (fixed to "UGA").

year

Calendar year of week.

month

Calendar month (1–12) of week start.

week

Epidemiological week number (1–52).

date_start

Start date of week (Monday).

date_stop

End date of week (Sunday).

cases

Number of onset dates in that week.

deaths

Number of outcomes coded as death in that week.

cases_binary

Indicator (0/1) if any cases >0.