Export AST Data — export

Generic dispatcher that exports AMRgen long-format AST data to a submission-ready file. Currently supports NCBI BioSample Antibiogram and EBI Antibiogram formats.

Usage

export_ast(
  data,
  file,
  format = "ncbi",
  overwrite = FALSE,
  pheno_col = "pheno_provided",
  ...
)

Arguments

data: A data frame in AMRgen long format (e.g. output of import_ast() or format_ast()). Expected columns: id, drug_agent, spp_pheno, and at least one phenotype column (see pheno_col). Optional columns: mic, disk, method, guideline, platform.
file: File path for the output file.
format: Target format: "ncbi" (default) or "ebi".
overwrite: Logical; overwrite an existing file? Default FALSE.
pheno_col: Character string naming the column that contains SIR interpretations. Default "pheno_provided".
...: Additional arguments passed to the format-specific export function.

Value

The formatted data frame is returned invisibly.