antibiotic_specific_susceptibility: Determine susceptibility to vancomycin

In tuv292/abx_idx: Modeling the Susceptibility of a Bacterial Community to Antibiotics

Determine susceptibility to vancomycin

Description

Determine susceptibility to vancomycin

Usage

antibiotic_susceptibility_vancomycin(
  lineage,
  antibiotic_db = taxon_susceptibility,
  phenotype_db = taxon_phenotypes
)

antibiotic_susceptibility_tetracycline(
  lineage,
  antibiotic_db = taxon_susceptibility
)

antibiotic_susceptibility_penicillin(
  lineage,
  antibiotic_db = taxon_susceptibility
)

antibiotic_susceptibility_aminoglycoside(
  lineage,
  antibiotic_db = taxon_susceptibility,
  phenotype_db = taxon_phenotypes
)

Arguments

lineage	A character vector of taxonomic assignments or lineages
antibiotic_db	A data frame with columns named "taxon", "rank", "antibiotic", and "value"
phenotype_db	A data frame with columns named "taxon", "rank", and "gram_stain"

Value

A vector of assigned susceptibility values, which should be either "susceptible", "resistant", or NA

tuv292/abx_idx documentation built on Jan. 12, 2023, 12:48 a.m.