Normalize Organism Names

Normalizes organism names using organisms.csv reference file. Automatically handles abbreviations (E. coli), case variations, and typos.

Usage

normalize_organism(
  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 from CSV. Default TRUE.

add_resistance_flags

Logical. Add resistance flag columns (0/1). Default TRUE. Creates: is_MRSA, is_MSSA, is_MRCONS, is_MSCONS

Value

Data frame with organism_normalized, organism_group, and optionally resistance flag columns

Examples

if (FALSE) { # \dontrun{
data <- data.frame(organism = c("E. coli", "S. aureus", "MRSA"))
result <- normalize_organism(data, organism_col = "organism")
} # }