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Compute LOS Population Attributable Fraction per Resistance Profile

Source: R/burden.R
compute_paf_los.Rd

Computes PAF_kd_LOS for each pathogen k and profile d using the GBD multi-exposure Levin formula:

Usage

compute_paf_los(
  profiles_with_rr,
  probability_col = "probability",
  rr_profile_col = "RR_LOS_profile",
  profile_col = "profile"
)

Arguments

profiles_with_rr

Named list from assign_rr_to_profiles().

probability_col

Character. Profile probability column. Default "probability".

rr_profile_col

Character. Profile-level RR column. Default "RR_LOS_profile".

profile_col

Character. Profile label column. Default "profile".

Value

Named list (one entry per pathogen): per_profile: profiles data frame augmented with numerator, PAF_LOS, denominator. PAF_k: overall PAF for pathogen k. denominator: 1 + sum_d R'_kd(RR_kd-1).

Details

PAF_kd_LOS = R'_kd * (RR_kd - 1) / [1 + sum_d R'_kd * (RR_kd - 1)]

where R'_kd is the profile probability from compute_resistance_profiles() and RR_kd is from assign_rr_to_profiles(). The denominator equals E_d[RR_kd] (expected RR over all profiles) and is shared across profiles for pathogen k. The all-susceptible profile contributes 0 (RR = 1).

Overall PAF for pathogen k: PAF_k = sum_d PAF_kd_LOS = [sum_d R'_kd(RR_kd-1)] / [1 + sum_d R'_kd(RR_kd-1)]