https://github.com/theeconomist/hpv

https://github.com/theeconomist/hpv

Last synced: 18 days ago
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• Host: GitHub
• URL: https://github.com/theeconomist/hpv
• Owner: TheEconomist
• Created: 2023-06-01T14:18:45.000Z (over 1 year ago)
• Default Branch: main
• Last Pushed: 2023-06-01T14:37:30.000Z (over 1 year ago)
• Last Synced: 2024-11-14T21:14:06.257Z (3 months ago)
• Language: R
• Size: 10.2 MB
• Stars: 0
• Watchers: 5
• Forks: 1
• Open Issues: 0
• Metadata Files:
  • Readme: README.md

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README

        
## Cervical Cancer & HPV Vaccines

---- description ---- 

* This repo contains data and scripts to recreate the analysis and charts in the article "Cheap vaccines could prevent millions of deaths from cervical cancer. A turning-point looms in the campaign to eliminate the disease" 

* article:  

* author: Daniella Raz

---- source-data ---- 

* wuenic2021rev_hpv-estimates.xlsx 

* data.pop.rda 

* country_codes.csv 

* country-incomes.xlsx 

* cc_incidence_rates.csv 

* 2019_2021_all_vaccine_rates.csv

---- scripts ---- 

* main.r 

* analysis.r 

* combine_dfs.r

---- output-data ---- 

* hpv_2020s_results.csv 

* hpv_past_results.csv 

* mixed_results.csv 

* results_2021.csv 

* folder: yearly-results 

* folder: projections_with_gradual_90pct_rate 

* folder: projections_with_2021_rate 

* folder: case_and_death_estimates_without_vaccine

---- sources ---- 

* The World Health Organization / UNICEF 

* Papillomavirus Rapid Interface for Modelling and Economics (PRIME): London School of Hygiene & Tropical Medicine, Mark Jit, Marc Brisson, Kaja Abbas, and Han Fu

#### variable definitions

by age 15, first dose:

by age 15, last dose:

coverage, first dose, females:

coverage, last dose, females:

country = country code

cohort_size = total number of girls who are in the cohort that should be getting vaccinated

current_cov = coverage in X year

curr_vacc_cohort_size = number vaccinated in that cohort

future_cov = 90% coverage rate

future_vacc_cohort_size = number vaccinated in cohort under new coverage rate

curr_cc_prev: cervical cancer cases prevented under the current coverage

curr_mort_prev: deaths from cervical cancer prevented under the current coverage

curr_cost: current cost of the program

curr_cost_prev: current costs prevented by reducing cervical cancer

proj_cc_prev, proj_mort_prev, proj_cost, proj_cost_prev are the same as above but under the "projected" 90% coverage rate the WHO says is necessary for elimination of cervical cancer