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Select Resistance Class for Burden Attribution

Source: R/daly_resistance_prevalence.R
select_resistance_class.Rd

Selects a single resistance class per event using beta-lactam hierarchy and relative risk (RR) values. Prevents double-counting in DALY burden estimation by choosing the most clinically relevant resistant class.

Usage

select_resistance_class(
  data,
  event_col = "event_id",
  class_col = "antibiotic_class",
  susceptibility_col = "antibiotic_value",
  rr_col = "rr_value",
  hierarchy = NULL,
  filter_resistant = TRUE
)

Arguments

data

Data frame with class-level resistance and RR columns.

event_col

Character. Event ID column. Default "event_id".

class_col

Character. Antibiotic class column. Default "antibiotic_class".

susceptibility_col

Character. Susceptibility column. Default "antibiotic_value".

rr_col

Character. RR value column. Default "rr_value". If missing, only hierarchy is used.

hierarchy

Named numeric vector. Custom hierarchy (class name -> rank). If NULL, uses get_beta_lactam_hierarchy().

filter_resistant

Logical. If TRUE, only consider resistant (R) classes. Default TRUE.

Value

Data frame filtered to one resistance class per event.

Details

Selection order: 1. Beta-lactam hierarchy rank (Carbapenems > 4GC > 3GC > ...) 2. RR value (higher relative risk = higher priority) 3. Alphabetical tie-breaker