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Decode Antibiotic Short Codes to Full Names

Source: R/prep_standardize_antibiotics.R
prep_decode_antibiotic_code.Rd

Converts antibiotic short codes (e.g. AMK, AMP, AMPSUL) to full antibiotic names using a caller-supplied code map CSV.

Usage

prep_decode_antibiotic_code(
  data,
  code_col = "antibiotic_name_raw",
  map_path = NULL,
  output_col = "antibiotic_name_std"
)

Arguments

data

Data frame with a column of antibiotic codes.

code_col

Character. Column containing antibiotic codes. Default "antibiotic_name_raw".

map_path

Character. Path to the code map CSV file. Must have columns code and antibiotic_name_full. If NULL, falls back to inst/extdata/antibiotic_code_map.csv if it exists.

output_col

Character. Name of the output column for decoded names. Default "antibiotic_name_std".

Value

Data frame with output_col column added.

Details

The code map must have columns code and antibiotic_name_full. This function is dataset-agnostic: the code map and the column containing the codes are supplied by the caller (typically from the analysis layer).