antibiotic_specific_susceptibility | R Documentation |
Determine susceptibility to vancomycin
antibiotic_susceptibility_vancomycin(
lineage,
antibiotic_db = whatbacteria::taxon_susceptibility,
phenotype_db = whatbacteria::taxon_phenotypes
)
antibiotic_susceptibility_tetracycline(
lineage,
antibiotic_db = whatbacteria::taxon_susceptibility
)
antibiotic_susceptibility_penicillin(
lineage,
antibiotic_db = whatbacteria::taxon_susceptibility
)
antibiotic_susceptibility_aminoglycoside(
lineage,
antibiotic_db = whatbacteria::taxon_susceptibility,
phenotype_db = whatbacteria::taxon_phenotypes
)
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" |
A vector of assigned susceptibility values, which should be either
"susceptible", "resistant", or NA
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