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Select Resistance Class

Source: R/select.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 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 resistance and RR information

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 default from 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 logic: 1. Filter to resistant classes only (R) 2. Apply beta-lactam hierarchy (Carbapenems > 4GC > 3GC > ...) 3. Within same hierarchy rank, prioritize by RR value (higher RR first) 4. If tied, select alphabetically for reproducibility

Examples

if (FALSE) { # \dontrun{
# Select single resistance class per event
selected <- select_resistance_class(data)

# Include susceptible classes too
selected <- select_resistance_class(data, filter_resistant = FALSE)
} # }