Standardizes organism names using organisms.csv reference file.
Automatically handles abbreviations (E. coli), case variations, and typos.
Usage
prep_standardize_organisms(
data,
organism_col = "organism_name",
add_organism_group = TRUE,
add_resistance_flags = TRUE
)
Arguments
- data
Data frame with organism column.
- organism_col
Character. Organism column name. Default "organism_name".
- add_organism_group
Logical. Add organism_group column. Default TRUE.
- add_resistance_flags
Logical. Add MRSA/MRCONS flags. Default TRUE.
Value
Data frame with organism_normalized, organism_group, and optionally
resistance flag columns.