E. coli NCBI AST example data, re-interpreted with AMR package

A subset of E. coli phenotype data from the NCBI AST browser

Usage

ecoli_ast

A data frame with 15320 rows and 24 columns representing reinterpreted data from NCBI AST Browser:

id: sample identifier, imported from BioSample column in raw input
spp_pheno: species identifier, interpreted from Scientific name using as.mo, used to interpret ecoff and pheno columns
drug_agent: antibiotic code, interpreted from Antibiotic using as.ab, used to interpret ecoff and pheno columns
ecoff: WT/NWT classification, interpreted using as.sir
pheno: S/I/R classification, interpreted using as.sir
mic: minimum inhibitory concentration, formated using as.mic, used to interpret ecoff and pheno columns
disk: disk diffusion zone, formated using as.disk, used to interpret ecoff and pheno columns
guideline: interpretation guidelines used to interpret ecoff and pheno columns
Scientific name: species identifier, from input file
Antibiotic: antibiotic name, from input file
Testing standard: interpretation standard (EUCAST or CLSI), from input file
Measurement sign: measurement sign (>, <, =, etc) relating to MIC measurement, from input file
MIC (mg/L): minimum inhibitory concentration, from input file
Disk diffusion (mm): disk diffusion zone, from input file
Resistance phenotype: resistance call (SIR), from input file