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Plot Predicted Suitability and Reported Cholera Cases for a Specific Country

Source: R/plot_suitability_and_cases.R
plot_suitability_and_cases.Rd

This function plots the reported cholera cases and predicted environmental suitability for a specific country over time, with shaded regions indicating cholera outbreaks. Requires that est_suitability() has been run first to generate prediction files.

Usage

plot_suitability_and_cases(PATHS, plot_iso_code)

Arguments

PATHS

A list of paths to the directories where data is stored and plots will be saved. Must include MODEL_INPUT (for reading prediction files) and DOCS_FIGURES (for saving plots).

plot_iso_code

The ISO code of the country to plot (e.g., "AGO", "CMR").

Value

Invisibly, the combined plot showing both cholera case bars and the suitability series for the specified country.

Details

The function reads pred_psi_suitability_day.csv created by est_suitability() (columns date, cases, iso_code and psi) and plots the canonical psi column (smoothed and bias-corrected), the series that becomes the engine's psi_jt. A pre-v0.34 file without psi falls back to pred_smooth, with a message.