Skip to contents

Plot Seasonal Transmission Example with Grid Points

Source: R/plot_seasonal_transmission_example.R
plot_seasonal_transmission_example.Rd

This function plots the map of a selected country with grid points used for climate data sampling, and visualizes the seasonal transmission dynamics using Fourier series for both precipitation and cholera cases.

Usage

plot_seasonal_transmission_example(PATHS, country_iso_code, n_points = 30)

Arguments

PATHS

A list containing paths where processed climate, cholera, and fitted data are stored. Typically generated by the get_paths() function and should include:

  • DATA_SHAPEFILES: Path to the directory containing shapefiles for African countries.

  • MODEL_INPUT: Path to the data_seasonal_precipitation.csv and pred_seasonal_dynamics_day.csv files written by est_seasonal_dynamics.

  • DOCS_FIGURES: Path to save the output plot.

country_iso_code

A character string representing the ISO3 code of the country to plot.

n_points

An integer specifying the number of grid points to generate within the country for sampling.

Value

The function generates and saves a PNG file showing the grid points on the country map and the seasonal transmission dynamics.

Details

The years in the legend labels of the precipitation and case points are the calendar years spanned by that country's points, read from the dates in data_seasonal_precipitation.csv (the window est_seasonal_dynamics was fit to). A country without case data in that window has no case points and its label carries no years.