Create Resistance Profile

Generates a resistance profile string for each event summarizing resistance patterns. Useful for identifying common resistance phenotypes.

Usage

create_resistance_profile(
  data,
  event_col = "event_id",
  antibiotic_col = "antibiotic_normalized",
  susceptibility_col = "antibiotic_value",
  format = "resistant_list",
  class_col = "antibiotic_class"
)

Arguments

data

Data frame with resistance data

event_col

Character. Event ID column. Default "event_id".

antibiotic_col

Character. Antibiotic column. Default "antibiotic_normalized".

susceptibility_col

Character. Susceptibility column. Default "antibiotic_value".

format

Character. Output format: - "resistant_list": List resistant drugs only (default) - "full_pattern": Full S/R pattern string - "class_summary": Resistant classes only

class_col

Character. Class column (required for format = "class_summary"). Default "antibiotic_class".

Value

Data frame with resistance_profile column added

Examples

if (FALSE) { # \dontrun{
# List resistant drugs
data_with_profile <- create_resistance_profile(data)

# Full S/R pattern
data_with_profile <- create_resistance_profile(
  data,
  format = "full_pattern"
)

# Resistant classes only
data_with_profile <- create_resistance_profile(
  data,
  format = "class_summary"
)
} # }