MIC (version 1.1.0)

tidy_patric_meta_data: Tidy PATRIC data

Description

Tidy PATRIC data

Usage

tidy_patric_meta_data(
  x,
  prefer_more_resistant = TRUE,
  as_ab = TRUE,
  filter_abx = NULL
)

Value

Tidy data, with antimicrobials in wide format, column names describing methodology ("mic_", "disk_", "pheno_"). S3 class "tidy_patric_db".

Arguments

x

PATRIC database loaded using MIC::load_patric_db

prefer_more_resistant

High MICs, narrow zones, or resistant phenotypes will be preferred where multiple reported for the same isolate

as_ab

convert antibiotics to AMR::ab class (column names are antibiotic codes)

filter_abx

filter antibiotics of interest, provided as a vector of antibiotics character names/codes, or ideally, as AMR::ab classes, created using AMR::as.ab

Examples

db <- data.frame(genome_id = 1,
                genome_name = "E. coli",
                antibiotic = "amoxicillin",
                measurement = 2.0,
                measurement_unit = "mg/L",
                laboratory_typing_method = "Agar dilution",
                resistant_phenotype = "R")
db <- load_patric_db(db)
tidy_patric_meta_data(db)