Import and process antimicrobial phenotype data exported from Vitek instruments
Source:R/import_pheno.R
import_vitek_ast.RdThis function imports antimicrobial susceptibility testing (AST) data from Vitek instrument output files (wide CSV format) and converts it to the standardised long-format used by AMRgen.
Usage
import_vitek_ast(
input,
sample_col = "Lab ID",
source = NULL,
species = NULL,
ab = NULL,
instrument_guideline = NULL,
use_expertized = TRUE,
interpret_eucast = FALSE,
interpret_clsi = FALSE,
interpret_ecoff = FALSE,
include_dates = TRUE
)Arguments
- input
A dataframe or path to a CSV file containing Vitek AST output data
- sample_col
Column name for sample identifiers. Default: "Lab ID"
- source
Optional source value to record for all data points (e.g., dataset name or study identifier)
- species
Optional species override for phenotype interpretation
- ab
Optional antibiotic override for phenotype interpretation
- instrument_guideline
Optional guideline used by the Vitek instrument for SIR interpretation (e.g., "EUCAST 2025", "CLSI 2025"). Default: NULL
- use_expertized
Use expertized SIR (TRUE, default) or instrument SIR (FALSE)
- interpret_eucast
Interpret against EUCAST breakpoints
- interpret_clsi
Interpret against CLSI breakpoints
- interpret_ecoff
Interpret against ECOFF values
- include_dates
Include collection_date and testing_date in output