Collapse to Antibiotic Level (OPTIONAL - Run When YOU Decide)

**IMPORTANT**: This function removes duplicate tests. Only run this when you have reviewed your data and decided to collapse duplicates.

Usage

collapse_to_antibiotic_level(
  data,
  event_col = "event_id",
  organism_col = "organism_normalized",
  antibiotic_col = "antibiotic_normalized",
  susceptibility_col = "antibiotic_value",
  aggregation_rule = "any_R"
)

Arguments

data

Data frame with susceptibility results

event_col

Character. Event ID column. Default "event_id".

organism_col

Character. Organism column. Default "organism_normalized".

antibiotic_col

Character. Antibiotic column. Default "antibiotic_normalized".

susceptibility_col

Character. Susceptibility column (S/I/R). Default "antibiotic_value".

aggregation_rule

Character. Rule for aggregation: "any_R" (default, any R -> R), "most_resistant" (R > I > S), "most_common" (mode).

Value

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

Details

Aggregates multiple test results for the same organism-antibiotic combination within an event. Uses "any R -> R" logic where resistance in any test results in resistant classification.

**When to use**: After you've cleaned and normalized data, if you have multiple tests for the same patient-organism-antibiotic and want one result per combination.

**What it removes**: Duplicate rows based on event_id + organism + antibiotic

Examples

if (FALSE) { # \dontrun{
# Check for duplicates first
data %>%
  group_by(event_id, organism_normalized, antibiotic_normalized) %>%
  filter(n() > 1)

# Then decide to collapse using any R -> R
collapsed <- collapse_to_antibiotic_level(data)

# Or use most common result
collapsed <- collapse_to_antibiotic_level(
  data,
  aggregation_rule = "most_common"
)
} # }