Handle Duplicate AST Results

Detects and optionally resolves conflicting AST records for the same patient + organism + antibiotic + date combination.

Usage

prep_deduplicate_ast(
  data,
  mode = c("detect", "remove"),
  strategy = c("resistant_wins", "susceptible_wins", "first"),
  patient_col = "patient_id",
  organism_col = "organism_normalized",
  antibiotic_col = "antibiotic_normalized",
  date_col = "culture_date",
  ast_col = "ast_value_harmonized"
)

Arguments

data

Data frame with AST data in long format.

mode

Character. "detect" (flag only) or "remove" (flag then resolve). Default "detect".

strategy

Character. Resolution strategy used only when mode = "remove". One of "resistant_wins" (default), "susceptible_wins", or "first".

patient_col

Character. Patient ID column. Default "patient_id".

organism_col

Character. Organism column. Default "organism_normalized".

antibiotic_col

Character. Antibiotic column. Default "antibiotic_normalized".

date_col

Character. Culture date column. Default "culture_date".

ast_col

Character. Harmonized AST value column. Default "ast_value_harmonized".

Value

• mode = "detect": original data with is_ast_duplicate logical column added.

• mode = "remove": data with conflicts resolved (one row per key) and no flag column.

Details

"detect"

Flags conflicting rows with is_ast_duplicate = TRUE and prints a QC summary of all conflict groups. Returns the full data frame with the flag column so you can inspect or filter before deciding how to resolve.

"remove"

Runs the detect step first (flag + QC summary), then applies strategy to keep one row per key combination and drops the flag column from the returned data.