Loads contaminant organisms from common_commensals.csv and filters
by syndrome and/or specimen type.
Usage
prep_get_contaminant_list(
syndrome = NULL,
specimen_type = NULL,
return_all = FALSE
)
Arguments
- syndrome
Character. Syndrome name to filter (e.g., "Bloodstream infections").
- specimen_type
Character. Specimen type to filter (e.g., "Blood culture").
- return_all
Logical. If TRUE, returns all contaminants across syndromes.
Default FALSE.
Value
A list with names (character vector) and patterns
(list of pattern information for flexible matching).