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Plot Vaccination Maps

Source: R/plot_vaccination_maps.R
plot_vaccination_maps.Rd

Generates choropleth maps and corresponding bar plots to visualize OCV vaccination data from WHO, GTFCC, or combined sources across African countries.

Usage

plot_vaccination_maps(PATHS, data_source = "WHO")

Arguments

PATHS

A named list containing file paths required for input and output operations. It should include:

MODEL_INPUT

Directory path where the processed vaccination data files are located.

DOCS_FIGURES

Directory path where the generated plots will be saved.

data_source

The source of the vaccination data. Must be one of "WHO", "GTFCC", or "BOTH". Default is "WHO".

Value

The function does not return any value. It generates and saves a PNG file containing the vaccination maps and barplots with annotations.

Details

The function performs the following steps:

  1. Data Loading and Processing: Reads the vaccination data from a CSV file, converts the date column to Date objects, and extracts the latest cumulative doses distributed and corresponding vaccination proportions for each country.

  2. Map Data Retrieval: Obtains map data for African countries using the rnaturalearth package.

  3. Data Merging: Merges the vaccination data with the map data, identifying Sub-Saharan African countries based on ISO codes provided by the MOSAIC::iso_codes_ssa dataset.

  4. Color Scale Definition: Defines distinct color scales for cumulative doses distributed (green gradient) and proportion vaccinated (purple gradient), including appropriate breaks and labels.

  5. Choropleth Map Creation: Creates two choropleth maps—one for cumulative doses distributed and another for the proportion vaccinated—using ggplot2 and layering map data accordingly.

  6. Barplot Generation: Constructs barplots for each metric, ordering countries by descending values and applying the corresponding color scales.

  7. Plot Arrangement: Utilizes the patchwork and cowplot packages to arrange the maps and barplots into a structured grid with panel labels "A" and "B" and adds a footnote.

  8. Saving the Plot: Saves the final combined plot as a PNG file in the specified DOCS_FIGURES directory.

Examples

if (FALSE) { # \dontrun{
# Define the PATHS list with appropriate directories
PATHS <- list(
  MODEL_INPUT = "path/to/model/input",
  DOCS_FIGURES = "path/to/docs/figures"
)

# Call the function to generate and save the vaccination maps
plot_vaccination_maps(PATHS)
plot_vaccination_maps(PATHS, data_source = "GTFCC")
plot_vaccination_maps(PATHS, data_source = "BOTH")
} # }