Check if Organism is a Contaminant

Checks if a given organism name matches any known contaminant for a specific syndrome or specimen type using flexible pattern matching.

Usage

is_contaminant(organism_name, syndrome = NULL, specimen_type = NULL)

Arguments

organism_name

Character vector. Organism name(s) to check.

syndrome

Character. Optional syndrome name to filter contaminants.

specimen_type

Character. Optional specimen type to filter contaminants.

Value

Logical vector indicating if each organism is a contaminant

Examples

# Check if organism is a blood culture contaminant
is_contaminant("Staph epidermidis", syndrome = "Bloodstream infections")
#> [1] TRUE
is_contaminant("E. coli", syndrome = "Bloodstream infections")
#> [1] FALSE

# Check multiple organisms
is_contaminant(c("Staph", "Klebsiella"), specimen_type = "Blood culture")
#> [1] FALSE FALSE