Generate target, fvps, coverage for a touchstone This function pulls vaccination and population data from Montagu database, and transform them into target, coverage and fvps. There are two modes of pulling population data: 1.) through touchstone_pop parameter 2.) through demographic_source parameter touchstone_pop is one of touchstone_demographic_dataset.touchstone; this parameter is null-able, when it is null, touchstone_cov is used demographic_source is one of demographic_source.code; by default it is null, when it is not null, it rulls out touchstone_pop parameter

extract_vaccination_history.Rd

Replace jenner:::fix_covreage_fvps() function

extract_vaccination_history(
  con,
  touchstone_cov = "201710gavi",
  touchstone_pop = NULL,
  year_min = 2000,
  year_max = 2100,
  vaccine_to_ignore = c("DTP3", "HepB_BD_home", "none"),
  disease_to_extract = NULL,
  countries_to_extract = NULL,
  gavi_support_levels = c("with", "bestminus"),
  scenario_type = "default",
  external_population_estimates = NULL,
  full_description = FALSE,
  demographic_source = NULL,
  coverage_scenario_type = NULL
)

Arguments

con: Datebase connection
touchstone_cov: Coverage touchstone
touchstone_pop: touchstone_demographic_dataset.touchstone
year_min: extract data from year_min
year_max: extract data to year_max
vaccine_to_ignore: Ignore defined vaccines
disease_to_extract: extract data for specific diseases
countries_to_extract: extract data for specific countries
gavi_support_levels: gavi support levels
scenario_type: scenario type
external_population_estimates: The rationales are 1. we can use external population estimates if any and if necessary; 2. demographic uncertainty not only affects models, but also FVPs. If we are to conduct sensitivity analysis on impact_by_year_of_vaccination, we need to vary population input for adjusting FVPs.
full_description: TRUE if including scenario_descriptions (coverage estimates will be duplicated for scenarios); and FALSE if only providing coverage estimates
demographic_source: Demographic_source.code
coverage_scenario_type: Coverage scenario type. This is particularly useful for a coverage touchstone. Montagu coverage.name follows <disease>:<vaccine>,<activity_type>,<gavi_support_level>:<coverage_scenario_type> It is NULL by default. When it is not null, only pulls coverage.name that contains specified pattern.