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Compute Mortality Population Attributable Fraction per Resistance Profile

Source: R/burden.R, R/yll.R
compute_paf_rr_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():

Computes PAF_kd_mortality for each pathogen x resistance profile using the GBD multi-exposure Levin formula with mortality OR substituted for LOS RR:

Usage

compute_paf_rr_mortality(
  profiles_with_rr,
  probability_col = "probability",
  rr_profile_col = "RR_LOS_profile",
  profile_col = "profile",
  facility_col = NULL,
  facility_name = NULL
)

compute_paf_rr_mortality(
  profiles_with_rr,
  probability_col = "probability",
  rr_profile_col = "RR_LOS_profile",
  profile_col = "profile",
  facility_col = NULL,
  facility_name = NULL
)

Arguments

profiles_with_rr

Named list from assign_rr_to_profiles() called with rr_col = "OR_death".

probability_col

Character. Default "probability".

rr_profile_col

Character. Default "RR_LOS_profile".

profile_col

Character. Default "profile".

facility_col

Character or NULL. Facility identifier column. Default NULL.

facility_name

Character or NULL. If provided, stored in the output for provenance tracking. Default NULL.

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 \(E[\text{OR}_k]\).

Named list (one per pathogen) with per_profile, PAF_k_mort, and denominator_mort.

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 <- compute_paf_rr_mortality(profiles_with_or)

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

Pipeline:


  or_table          <- fit_mortality_rr_logistic(data, ...)
  p0_res            <- compute_p0(data, ...)
  rr_table          <- convert_or_to_rr(or_table, p0 = p0_res$p0)
  profiles_with_or  <- assign_rr_to_profiles(profiles_output,
                           rr_table = or_table, rr_col = "OR_death")
  paf_mort          <- compute_paf_rr_mortality(profiles_with_or)