Computes the fraction of total expected YLD burden that *occurs in* infections with each resistance profile delta (YLDs associated with resistance). This is a **burden partition**, not a counterfactual.

Usage

compute_fraction_associated(
  profiles_with_rr,
  probability_col = "probability",
  rr_profile_col = "RR_LOS_profile"
)

Arguments

profiles_with_rr: Named list from assign_rr_to_profiles() or filter_profiles_to_rr_classes(). Each entry is a profile data frame.
probability_col: Character. Profile probability column. Default "probability".
rr_profile_col: Character. Profile-level RR column. Default "RR_LOS_profile".

Value

Named list (one entry per pathogen) containing:

per_profile: profile data frame augmented with numerator_assoc (= p * rr) and fraction_assoc (= p * rr / E_RR_k).
Fraction_k: overall associated fraction for the pathogen (sum of fraction_assoc over all resistant profiles).
E_RR_k: expected RR = sum_delta R'_K_delta * RR_K_delta.

Details

For a single drug-class d the formula simplifies to:

Fraction_assoc_Kd = R'_Kd * RR_Kd / [(1 - R'_Kd) + R'_Kd * RR_Kd]

With resistance profiles the denominator becomes the expected RR across ALL profiles (including the all-susceptible profile with RR = 1):

E_RR_k = sum_delta R'_K_delta * RR_K_delta = 1 + sum_delta R'_K_delta * (RR_K_delta - 1) [equivalent]

Per-profile associated fraction: fraction_K_delta = R'_K_delta * RR_K_delta / E_RR_k

Overall associated fraction (all resistant profiles combined): Fraction_k = sum_{delta != 0} fraction_K_delta

where delta != 0 denotes profiles with at least one resistant class.

Note: E_RR_k is numerically identical to the `denominator` produced by compute_paf_los() – both equal 1 + sum_d R'_kd*(RR_kd - 1).

Compute Associated-Burden Fractions per Resistance Profile

Usage

Arguments

Value

Details