Wrapper that applies the full AST cleaning pipeline in sequence:
prep_clean_ast_values()- extract clean S/I/R from raw strings (handles exact matches, regex patterns, and keyword scanning in one pass)prep_recode_intermediate_ast()- resolve I values
Retains the original ast_col column as ast_value_raw and adds
ast_value_harmonized and intermediate_recoded.
Usage
prep_harmonize_ast(
data,
antibiotic_col = "antibiotic_name_std",
ast_col = "ast_value_raw",
colistin_to_s = TRUE,
others_to_r = TRUE
)Arguments
- data
Data frame with AST data.
- antibiotic_col
Character. Standardized antibiotic name column. Default "antibiotic_name_std".
- ast_col
Character. Raw AST value column. Default "ast_value_raw".
- colistin_to_s
Logical. Recode Colistin I -> S. Default TRUE.
- others_to_r
Logical. Recode non-Colistin I -> R. Default TRUE.