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Plot Combined Cholera Surveillance Data

Source: R/plot_cholera_surveillance_data.R
plot_cholera_surveillance_data.Rd

This function generates a two-panel plot that visualizes daily cholera cases and deaths for a specific country, based on the combined downscaled surveillance data from WHO, JHU, and SUPP. The top panel shows reported cholera cases and the bottom panel shows reported cholera deaths. Both panels use a log-transformation (with log(count + 1)) while labeling the y-axis with raw counts. Daily data bars are colored by their original source (WHO, JHU, or SUPP), and weekly observations are shown as discrete points without connecting lines.

Usage

plot_cholera_surveillance_data(PATHS, iso)

Arguments

PATHS

A named list of file paths. Required elements include:

  • DATA_CHOLERA_WEEKLY - Directory containing the combined weekly data file "cholera_surveillance_weekly_combined.csv".

  • DATA_CHOLERA_DAILY - Directory containing the combined daily data file "cholera_surveillance_daily_combined.csv".

  • DOCS_FIGURES - Directory in which the output PNG file will be saved.

iso

A character string representing the ISO code of the target country (e.g., "ETH").

Value

Invisibly returns NULL. The function produces a combined two-panel plot, which is printed to the active graphics device and saved as a PNG file.

Details

The function reads input CSV files from the directories specified in PATHS and saves the resulting combined plot as a PNG file in the directory specified by PATHS$DOCS_FIGURES.