Extracts clean S/I/R values from messy antibiotic result columns.
Handles common patterns like "S (HIGH LEVEL)", "R Escherichia coli", etc.
Usage
prep_clean_ast_values(data, value_col = "antibiotic_value", strict = FALSE)
Arguments
- data
Data frame with antibiotic susceptibility data.
- value_col
Character. Column containing susceptibility values.
Default "antibiotic_value".
- strict
Logical. If TRUE, only accept S/I/R values. If FALSE, attempt
to parse from messy strings. Default FALSE.
Value
Data frame with cleaned antibiotic_value column.