Converts "I" (Intermediate) values to either "S" or "R" based on antibiotic. For Colistin: I -> S (clinical guideline). For all other antibiotics: I -> R (conservative surveillance approach).
Usage
prep_recode_intermediate_ast(
data,
antibiotic_col = "antibiotic_name",
value_col = "antibiotic_value",
colistin_to_s = TRUE,
others_to_r = TRUE
)Arguments
- data
Data frame with antibiotic susceptibility data.
- antibiotic_col
Character. Column with antibiotic names. Default "antibiotic_name".
- value_col
Character. Column with S/I/R values. Default "antibiotic_value".
- colistin_to_s
Logical. Convert Colistin I to S. Default TRUE.
- others_to_r
Logical. Convert other antibiotics' I to R. Default TRUE.