Generate_diagnostic_plots: Generate diagnostic plots of vaccine coverage and burden...

In lshtm-vimc/prime: PRIME -- Papillomavirus Rapid Interface for Modelling and Economics

Generate diagnostic plots of vaccine coverage and burden estimates

Description

Generate diagnostic plots of vaccine coverage and burden estimates (cases, deaths, dalys)

Usage

Generate_diagnostic_plots(
  vaccine_coverage_folder,
  coverage_prefix,
  touchstone,
  scenarios,
  no_vaccine_scenario,
  plot_no_vaccine_scenario = TRUE,
  burden_estimate_folder,
  plot_folder,
  plot_file,
  plot_type,
  countries,
  start_year = -1,
  end_year = -1,
  compare_plots = FALSE,
  vaccine_prefix,
  no_vaccine_prefix
)

Arguments

vaccine_coverage_folder	character, folder to read vaccine coverage of different scenarios
coverage_prefix	character, prefix of coverage file
touchstone	character, touchstone (VIMC)
scenarios	character, names of vaccination scenarios
no_vaccine_scenario	character, name of no vaccination scenario
plot_no_vaccine_scenario	logical, if TRUE then also generate plots for no vaccine scenario
burden_estimate_folder	character, folder to read burden estimates of different scenarios
plot_folder	character, diagnostic plot folder
plot_file	character, diagnostic plot file
plot_type	character, diagnostic plot type (central or stochastic)
countries	character, "all" countries or specific countries (iso3 codes)
start_year	numeric, start year of plot
end_year	numeric, end year of plot
compare_plots	logical, if TRUE then generate comparative plots
vaccine_prefix	character, prefix of burden estimates file (vaccination scenarios)
no_vaccine_prefix	character, prefix of burden estimates file (no vaccination scenario)

Details

Diagnostic plots of vaccine coverage and burden estimates (cases, deaths, dalys) are generated for each country and scenario. Optionally, comparative plots across all scenarios can be generated.

Value

Null return value; diagnostic plots are saved to file

Examples

Generate_diagnostic_plots (
    vaccine_coverage_folder    = "vaccine_coverage",
    coverage_prefix            = "coverage_",
    touchstone                 = "touchstone",
    scenarios                  = c ("hpv-routine-default", "hpv-routine-best"),
    no_vaccine_scenario        = "hpv-no-vaccination",
    plot_no_vaccine_scenario   = TRUE,
    burden_estimate_folder     = "output_all",
    plot_folder                = "plots"
    plot_file                  = "plot_file.pdf",
    plot_type                  = "central"
    countries                  = "all",
    start_year                 = 2000,
    end_year                   = 2100,
    compare_plots              = TRUE,
    vaccine_prefix             = "central-burden-vaccination_all_",
    no_vaccine_prefix          = "central-burden-novaccination_all_" )

lshtm-vimc/prime documentation built on April 21, 2024, 3:21 a.m.