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Compute health burden

Source: R/health_burden.R
health_burden.Rd

Compute health burden for population in scenarios given relative risks for diseases

Usage

health_burden(ind_ap_pa, conf_int = F, combined_AP_PA = T)

Arguments

ind_ap_pa

dataframe of all individuals' relative risks for diseases

conf_int=F

logic: whether to include confidence interval from dose response relationships or not

combined_AP_PA=T

logic: whether to combine the two exposure pathways (AP and PA) or to compute them independently

Value

list of dataframes: one for deaths per disease per demographic group and scenario, and likewise for YLLs

Details

This function performs the following steps:

  • get the demographic and disease burden (subset of Global Burden of Disease dataset) data into the correct formats and join the two datasets

  • scale the burden data by the CHRONIC_DISEASE_SCALAR to account for bias in the data

  • split the above dataframe into two dataframes, one for deaths and one for years of life lost (YLLs)

  • add a demographic index (by age and sex category) to the dataframe containing the individual relative risk for different diseases

  • set the reference and the other scenarios

  • iterate over all disease outcomes:

    • define column names

    • loop either over 1 or 2 pathways depending on whether both PA and AP are affecting the disease and whether the AP and PA pathways are combined or not:

      • extract the relevant burden of disease for the specific scenario both for YLLs and deaths

      • find the sum of the relative risks (RR) for the specific disease for each age and sex category for the reference scenario

      • loop through the non-reference scenarios:

        • define column names

        • find the sum of the relative risks (RR) for the specific disease for each age and sex category for the non-reference scenario

        • calculate the PIF (potential impact fraction), i.e the proportional change in the sum of relative risks between the reference and the non-reference scenario for each age and sex category

        • calculate the health burden (deaths and ylls) for the non-reference scenario compared to the reference scenario by multiplying the current burden of disease by the PIF (combine_health_and_pif.R)

      • if confidence intervals are required, loop through the upper and lower confidence interval limits and calculate the health burden for deaths and YLLs using the upper and lower confidence relative risks. If no upper and lower relative risk values exist, use the median value instead