Export EBI Antibiogram — export_ebi

Convert AMRgen long-format AST data to an EBI antibiogram submission file (see EBI COMPARE-AMR).

Usage

export_ebi_antibiogram(
  data,
  file,
  overwrite = FALSE,
  pheno_col = "pheno_provided",
  sep = "\t"
)

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.
overwrite: Logical; overwrite an existing file? Default FALSE.
pheno_col: Character string naming the column that contains SIR interpretations (class sir). Default "pheno_provided".
sep: Field separator for the output file. Default "\t" (tab-delimited). Use "," for CSV.

The formatted data frame is returned invisibly. A file is written to file.

Antibiotic names are in Title Case with "/" separating combination agents (EBI convention, e.g. "Amoxicillin/clavulanic acid").

Species names are derived from the spp_pheno column via AMR::mo_name().