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Plot Binary Environmental Suitability Indicator with Case Data

Source: R/plot_cases_binary.R
plot_cases_binary.Rd

This function creates a visualization showing cholera case counts over time with shaded regions indicating periods identified as environmentally suitable for cholera transmission. The environmental suitability is determined using sophisticated temporal logic that considers not only outbreak periods but also lead-up weeks when conditions become favorable.

Usage

plot_cases_binary(PATHS)

Arguments

PATHS

A list containing paths where the data is stored. Must include:

  • DATA_CHOLERA_WEEKLY: Path to combined weekly cholera surveillance data (WHO+JHU+SUPP)

  • DOCS_FIGURES: Path where the generated plot will be saved

Value

Invisibly returns the ggplot object after displaying and saving it.

Details

The function performs the following steps:

  • Loads processed suitability data containing pre-computed cases_binary indicators

  • Uses the existing binary environmental suitability indicators from the main pipeline

  • Generates a multi-panel plot showing case counts as bars with shaded regions indicating environmentally suitable periods

  • Saves the plot as a PNG file to the figures directory

The shaded regions represent periods identified as environmentally suitable by the compile_suitability_data() pipeline, including both outbreak periods and lead-up weeks when conditions become favorable.

See also

compile_suitability_data for the main pipeline that creates the processed data with cases_binary. get_cases_binary for details on how the environmental suitability indicator is created.

Examples

if (FALSE) { # \dontrun{
PATHS <- get_paths()
plot_cases_binary(PATHS)
} # }