taoveloz / international-covid-ifr

Age-specific mortality and immunity patterns of SARS-CoV-2 https://www.nature.com/articles/s41586-020-2918-0

International-COVID-IFR

Code and data to reproduce the analysis in "Age-specific mortality and immunity patterns of SARS-CoV-2". https://doi.org/10.1038/s41586-020-2918-0

Code

• RunModel.R is the main RScript to call all data, functions & model fitting.
• IFRInternational_ensemble.stan contains the core ensemble model code.
• IFRInternational_singlesero.stan contains core model code for use when fitting individual serological studies in the model likelihood. For studies with only a single survey time point IFRInternational_singlesero_1.stan should be used.
• adjust-deaths.R estimates age-specific non-nursing home COVID-19 deaths aged 65+ for a subset of countries.

Data

• deaths_age.csv contains reported age-specific COVID-19 death data from 45 countries.
• deaths_location.csv contains the number of COVID-19 deaths associated with nursing home/long-term care facilities for a subset of countries.
• deaths_age_adjusted.csv is the estimated age-specific number of COVID-19 deaths for a subset of countries where nursing home/long-term care deaths could be excluded.
• time_series_covid19_deaths_global.csv is the daily time-series of COVID-19 deaths from the COVID-19 Data Repository by the Center for Systems Science and Engineering (CSSE) at Johns Hopkins University (https://github.com/CSSEGISandData/COVID-19).
• deathsT_region.csv contains daily time-series of COVID-19 deaths for a subset of locations, where unavailable from the Johns Hopkins repository.
• serostudies.csv are the results from each of the seroprevalence surveys included in the analysis.
• data_sources.csv contains URL links to sources of age-specific death data for each country.
• France_NursingHomePop.csv is the nursing home population demographics for France.