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Process Vaccination Data for MOSAIC Model

Source: R/process_WHO_vaccination_data.R
process_WHO_vaccination_data.Rd

This function processes raw vaccination data from WHO to create a clean, structured dataset for the MOSAIC model. It handles data cleaning, infers missing campaign dates, validates the dataset, and saves the output for use in modeling cholera vaccination efforts.

Usage

process_WHO_vaccination_data(PATHS)

Arguments

PATHS

A list containing file paths for input and output data. The list should include:

  • DATA_SCRAPE_WHO_VACCINATION: Path to the directory containing raw WHO vaccination data.

  • MODEL_INPUT: Path to the directory where processed vaccination data will be saved.

Value

The function saves the processed vaccination data to a CSV file in the directory specified by PATHS$MODEL_INPUT. It also returns the processed data as a data frame for further use in R.

Details

This function performs the following steps:

  1. Load and Clean Vaccination Data: - Reads raw WHO vaccination data. - Converts country names to ISO codes for consistency. - Filters the data to include only countries in the MOSAIC database.

  2. Infer Missing Campaign Dates: - Computes the delay between decision and campaign dates. - Infers missing campaign dates based on the mean delay where possible. - Fixes missing decision dates for grouped request numbers.

  3. Validate and Filter Data: - Ensures all rows have valid campaign dates. - Removes rows where doses_shipped is zero or missing.

  4. Save Processed Data: - Writes the cleaned and processed dataset to a CSV file for further modeling.

Examples

if (FALSE) { # \dontrun{
# Example usage
PATHS <- list(
  DATA_SCRAPE_WHO_VACCINATION = "path/to/who/vaccination",
  MODEL_INPUT = "path/to/model/input"
)

processed_data <- process_WHO_vaccination_data(PATHS)
} # }