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Collapse to Class Level

Source: R/collapse.R
collapse_to_class_level.Rd

Aggregates resistance at antibiotic class level instead of individual drugs. Uses "any R in class -> class R" logic.

Usage

collapse_to_class_level(
  data,
  event_col = "event_id",
  organism_col = "organism_normalized",
  class_col = "antibiotic_class",
  susceptibility_col = "antibiotic_value",
  extra_cols = NULL
)

Arguments

data

Data frame with antibiotic class information

event_col

Character. Event ID column. Default "event_id".

organism_col

Character. Organism column. Default "organism_normalized".

class_col

Character. Antibiotic class column. Default "antibiotic_class".

susceptibility_col

Character. Susceptibility column. Default "antibiotic_value".

extra_cols

Character vector or NULL. Additional columns to carry through the aggregation. Default NULL.

Value

Aggregated data frame (one row per event-organism-class)

Examples

if (FALSE) { # \dontrun{
class_level <- collapse_to_class_level(data)
} # }