Import and process antimicrobial phenotype data from WHONET files

This function imports antimicrobial susceptibility testing (AST) data from WHONET software output files (wide CSV format) and converts it to the standardised long-format used by AMRgen.

Usage

import_whonet_ast(
  input,
  sample_col = "Identification number",
  source = NULL,
  species = NULL,
  ab = NULL,
  interpret_eucast = FALSE,
  interpret_clsi = FALSE,
  interpret_ecoff = FALSE,
  include_patient_info = FALSE
)

Arguments

input

A dataframe or path to a CSV file containing WHONET AST output data

sample_col

Column name for sample identifiers. Default: "Identification number"

source

Optional source value to record for all data points

species

Optional species override for phenotype interpretation

ab

Optional antibiotic override for phenotype interpretation

interpret_eucast

Interpret against EUCAST breakpoints

interpret_clsi

Interpret against CLSI breakpoints

interpret_ecoff

Interpret against ECOFF values

include_patient_info

Include patient demographic columns in output

Value

Standardised AST data frame