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Compute Mortality Population Attributable Fraction per Resistance Profile

Source: R/daly_yll.R
daly_calc_paf_mortality.Rd

Computes PAF_kd_mortality for each pathogen k and resistance profile delta using the GBD multi-exposure Levin formula, substituting the mortality odds ratio (OR_death) from fit_mortality_rr_logistic() in place of the LOS relative risk used by compute_paf_los():

Usage

daly_calc_paf_mortality(
  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() called with rr_col = "OR_death". Each element is a profile data frame for one pathogen.

probability_col

Character. Profile probability column name. Default "probability".

rr_profile_col

Character. Profile-level OR column as produced by assign_rr_to_profiles(). Default "RR_LOS_profile".

profile_col

Character. Profile label column. Default "profile".

Value

Named list (one entry per pathogen) containing:

  • per_profile: profile data frame augmented with numerator_mort (= \(R'_{K\delta}(\text{OR}_{K\delta}-1)\)), PAF_mortality (= numerator / denominator), and denominator_mort (= \(1 + \sum_\delta\) numerator).

  • PAF_k_mort: overall mortality PAF for pathogen k.

  • denominator_mort: shared denominator \(E[\text{OR}_k]\).

Details

$$\text{PAF}_{kd,\text{mort}} = \frac{R'_{K\delta}\,(\text{OR}_{K\delta} - 1)} {1 + \sum_\delta R'_{K\delta}\,(\text{OR}_{K\delta} - 1)}$$

The all-susceptible profile carries OR = 1 and contributes 0. The denominator equals \(E[\text{OR}_k] = \sum_\delta R'_{K\delta} \cdot \text{OR}_{K\delta}\), numerically identical to the denominator produced by compute_paf_los().

Overall mortality PAF for pathogen k:

$$\text{PAF}_{k,\text{mort}} = \sum_\delta \text{PAF}_{kd,\text{mort}} = \frac{\sum_\delta R'_{K\delta}(\text{OR}_{K\delta}-1)} {1 + \sum_\delta R'_{K\delta}(\text{OR}_{K\delta}-1)}$$

Usage pipeline:


  # 1. Fit mortality OR per class
  mort_or <- fit_mortality_rr_logistic(data, ...)

  # 2. Assign OR to profiles via max rule (rr_col = "OR_death")
  profiles_with_or <- assign_rr_to_profiles(
      profiles_output,
      rr_table = mort_or,
      rr_col   = "OR_death"
  )

  # 3. Compute per-profile and overall mortality PAF
  paf_mort <- daly_calc_paf_mortality(profiles_with_or)