Estimation of years of life lost according to age, sex and comorbidity. Code for pre-peer reviewed article posted at https://wellcomeopenresearch.org/articles/5-75.
Please see this link for the recent addendum
Please only include comments related to the code - eg errors, difficulty running the code etc on the issues here. Please discuss any issues related to the modelling assumptions, interpretation etc to the comments section of the paper which can be found at at https://wellcomeopenresearch.org/articles/5-75.
The following files are included in this repository:-
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Data/sail_outputs - model outputs from the SAIL repository alongside model diagnostics
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Data/Case_series_and_comorbidity.xlsx - original exploration of data sources indicating comorbidity distribution among people with COVID-19 who died
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Data/ - SimulatedProfilesConverged.Rds and SimulatedProfilesUnconverged.Rds - simulated patients based on earlier unconverged model and new converged model
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Data/age_distribution_italian_deaths.txt - age distribution of Italian people dying with COVID-19 from ISS report
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Data/ - files starting with "age_selection" show age distributions under different assumptions about relation of age and comorbidity
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Data/highest_cor_como.Rds - comorbidity dataframe assuming highly correlated comorbidities
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Data/independent_como.Rds - comorbidity dataframe assuming independent comorbidities
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Data/italy_update - aggregate comorbidity data from Italy
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Data/ - starting with "jags_model_age" - MCMC from model fitting age to comorbidity
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Data/ - starting with "men_" or "women_" - life expectancy estimates for men and women under different modelling assumptions
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Data/results_converged_cutdown.rds - MCMC output from comorbidity model
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Data/sensitivity_lifetables.txt - US and UK lifetables
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Data/who_mortality_table.txt - WHO GBD lifetable
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Output_rmd/ - Contains R objects created when run Scripts/simulation_combine.Rmd for different parameters
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Outputs/reports/ - Results in html format created by running Scripts/simulation_combine.Rmd for different parameters
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Outputs/ - Other files are YLL and other results under different assumptions
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Scripts/Estimating_age - Fit model to age data to obtain a simulated age distribution for calculations under different assumptions about association between age and comorbidity
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Scripts/Extracting_comorbidity_Distributions/ - Bayesian model for estimating comorbidity distributions as well as simple sensitivity analysis assuming high and low degree of correlation between comorbidities.
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Supporting/COVID_icd10_codes_for_sharing.csv - ICD-10 codes used to define comorbidities in SAIL dataset
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Supporting/COVID_readcodes_for_sharing.csv - Read codes used to define comorbidities in SAIL dataset
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Supporting/age_distribution_italian_deaths.xlsx - age distribution of deaths from ISS report
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run_report.R - meta-script to run analyses