custom_data_process_wrapper — custom_data_process

Load, Process, and Optionally Override All Model Input Data

Usage

custom_data_process_wrapper(
  iso,
  disease,
  R0,
  cfr_off = T,
  year_start = "",
  year_end = "",
  WHO_seed_switch = TRUE,
  aggregate_age = TRUE,
  new_age_breaks = c(0, 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80,
    Inf),
  custom_migration = NA,
  custom_fertility = NA,
  custom_mortality = NA,
  custom_population = NA,
  custom_contact_matricies = NA,
  custom_routine_vaccination = NA,
  custom_sia_vaccination = NA,
  custom_disease_data = NA,
  custom_vaccination_schedule = NA,
  custom_disease_parameters = NA,
  custom_vaccine_parameters = NA
)

Arguments

iso: A 3-letter ISO country code identifying the country for analysis (e.g., "ETH" for Ethiopia).
disease: A character string specifying the disease of interest (e.g., "measles", "diphtheria", "pertussis").
R0: Numeric scalar or vector specifying the basic reproduction number, defining disease transmissibility.
cfr_off: Logical; Sets the CFR to zero. Used when calculating current susceptibility as prior mortality rates will already include disease specific mortality.
year_start: Optional numeric value specifying the first year of the simulation window. Default ("") uses the earliest available data year.
year_end: Optional numeric value specifying the last year of the simulation window. Default ("") uses the latest available data year.
WHO_seed_switch: Logical; use WHO-style seeding to replicate historical case-reporting patterns (default TRUE).
aggregate_age: Logical; aggregate data from single-year age groups into custom intervals (default TRUE).
new_age_breaks: Numeric vector; breakpoints for age group aggregation. Default is c(0, 5, ..., Inf).
custom_migration: Optional. Data frame to override default migration data.
custom_fertility: Optional. Data frame to override default fertility data.
custom_mortality: Optional. Data frame to override default mortality data.
custom_population: Optional. Data frame to override default population (total) data.
custom_contact_matricies: Optional. Data frame to override default contact matrix data.
custom_routine_vaccination: Optional. Data frame to override default routine vaccination data.
custom_sia_vaccination: Optional. Data frame to override default SIA vaccination data.
custom_disease_data: Optional. Data frame to override default disease surveillance data.
custom_vaccination_schedule: Optional. Data frame to override default vaccination schedule.
custom_disease_parameters: Optional. Data frame to override default disease parameter values.
custom_vaccine_parameters: Optional. Data frame to override default vaccine parameter values.

Value

A named list containing structured parameters ready for use in the PREVAIL dynamic transmission model.

Details

This wrapper function loads internal datasets and processes them into structured model input parameters for a specified country, disease, and vaccine. Compared to data_load_process_wrapper, this function allows users to override any internal demographic, vaccination, or disease dataset with a custom data frame provided through the custom_* arguments. All data are formatted appropriately for use in the dynamic transmission model within PREVAIL.

Any custom_* argument can be used to override the corresponding internal dataset with a user-supplied data frame. If provided (not NA), these inputs are reformatted as needed and replace the matching internal dataset for this model run.

If any custom_* argument is provided, it replaces the corresponding PREVAIL internal dataset for that run. Demographic custom data is reformatted with reformat_demographic_data before use.