requester: VIMC
author: Katy

displayname: VPD-COVID phase I figures

connection:
  con: source

data: ~

packages: 
 - jenner
 - R.utils
 - ggplot2
 - dplyr
 - tidyr
 - vimpact
 - cowplot

script: script.R

artefacts: 
 - staticgraph:
      description: All figures
      filenames: 
       - deaths_by_year_Measles-1.png
       - deaths_by_year_MeningitisA-1.png
       - deaths_by_year_YF-1.png
       
       - deaths_by_year_pop_Measles-1.png
       - deaths_by_year_pop_MeningitisA-1.png
       - deaths_by_year_pop_YF-1.png
       
       - dalys_by_year_pop_Measles-1.png
       - dalys_by_year_pop_MeningitisA-1.png
       - dalys_by_year_pop_YF-1.png
       
       - dalys_by_year_Measles-1.png
       - dalys_by_year_MeningitisA-1.png
       - dalys_by_year_YF-1.png
       - dalys_by_year_all.png
       
       - excess_deaths_per_pop_by_country-1.png
       - excess_dalys_per_pop_by_country-1.png
       
       - under_5s_deaths-1.png
       
       - deaths_by_year_all.png
       - deaths_by_year_pop_all.png
       - dalys_by_year_pop_all.png
       
       - excess_deaths_by_year_all.png
       - excess_deaths_by_year_Measles-1.png
       - excess_deaths_by_year_MeningitisA-1.png
       - excess_deaths_by_year_YF-1.png
       
       - survival_change_by_year_all.png
       - survival_change_by_year_Measles-1.png
       - survival_change_by_year_MeningitisA-1.png
       - survival_change_by_year_YF-1.png
       
       - deaths_by_year_all_under5.png
       - deaths_by_year_Measles_under5-1.png
       - deaths_by_year_MeningitisA_under5-1.png
       - deaths_by_year_YF_under5-1.png
       
       - excess_deaths_by_year_all_under5.png
       - excess_deaths_by_year_Measles_under5-1.png
       - excess_deaths_by_year_MeningitisA_under5-1.png
       - excess_deaths_by_year_YF_under5-1.png
       
       - norm_deaths_per_country.png
       - norm_deaths_per_country_Measles-1.png
       - norm_deaths_per_country_MenA-1.png
       - norm_deaths_per_country_YF-1.png
       
       - norm_dalys_per_country.png
       - norm_dalys_per_country_Measles-1.png
       - norm_dalys_per_country_MenA-1.png
       - norm_dalys_per_country_YF-1.png
       
       - excess_dalys_per_country_mod.png   
       - excess_dalys_per_country_mod_Measles-1.png   
       - excess_dalys_per_country_mod_MenA-1.png   
       - excess_dalys_per_country_mod_YF-1.png   
       - excess_deaths_per_country_mod.png   
       - excess_deaths_per_country_mod_Measles-1.png   
       - excess_deaths_per_country_mod_MenA-1.png   
       - excess_deaths_per_country_mod_YF-1.png
     
 - data:
      description: All tables
      filenames:
       - excess_deaths_2020_2030.csv
       - excess_dalys_2020_2030.csv
       - excess_deaths_under5_2020_2030.csv
       - excess_dalys_under5_2020_2030.csv
       - excess_dalys_per_pop_2020_2030.csv
       - excess_deaths_Measles_country_2000_2030.csv
       - excess_deaths_Measles_year_2000_2030.csv
       - excess_deaths_Meningitis A_country_2000_2030.csv
       - excess_deaths_Meningitis A_year_2000_2030.csv
       - excess_deaths_per_pop_2020_2030.csv
       - excess_deaths_per_pop_Measles_country_2000_2030.csv
       - excess_deaths_per_pop_Measles_year_2000_2030.csv
       - excess_deaths_per_pop_Meningitis A_country_2000_2030.csv
       - excess_deaths_per_pop_Meningitis A_year_2000_2030.csv
       - excess_deaths_per_pop_Yellow fever_country_2000_2030.csv
       - excess_deaths_per_pop_Yellow fever_year_2000_2030.csv
       - excess_deaths_Yellow fever_country_2000_2030.csv
       - excess_deaths_Yellow fever_year_2000_2030.csv
       - percent_change_deaths_2020_2030.csv
       - percent_change_dalys_2020_2030.csv
       - percent_change_deaths_all_2020_2030.csv
       - percent_change_dalys_all_2020_2030.csv
       
      
sources: 
  - R/figure_functions.R
  - R/table_functions.R
  
resources: 
  - country_names.csv
  
global_resources:
  R/disease_palette.R: disease_palette.R

depends: 
  - vpd-covid-phase-I-impact-estimates:
      id: latest
      use: 
        impact.rds: impact.rds