as.sir_vectorised: Convert MIC or Disk Diffusion to SIR, vectorised over...

In MIC: Analysis of Antimicrobial Minimum Inhibitory Concentration Data

Convert MIC or Disk Diffusion to SIR, vectorised over antimicrobials

Description

The AMR::as.sir function is not vectorised over antimicrobials. This function provides vectorisation over antimicrobials. Due to the overhead of running AMR::as.sir, this function tries to be efficient by only running AMR::as.sir as little as necessary.

Usage

as.sir_vectorised(mic, mo, ab, accept_ecoff = FALSE, ...)

Arguments

mic	vector of MIC values
mo	vector of microorganism names
ab	vector of antibiotic names
accept_ecoff	if TRUE, ECOFFs will be used when no clinical breakpoints are available
...	additional arguments that are passed to AMR::as.sir

Value

S3 sir values

Examples

mic <- c("<0.25", "8", "64", ">64")
mo <- c("B_ESCHR_COLI", "B_ESCHR_COLI", "B_ESCHR_COLI", "B_ESCHR_COLI")
ab <- c("AMK", "AMK", "AMK", "AMK")
as.sir_vectorised(mic, mo, ab)
# using different microorganisms and antibiotics
mic <- c("<0.25", "8", "64", ">64")
mo <- c("B_ESCHR_COLI", "B_ESCHR_COLI", "B_PROTS_MRBL", "B_PROTS_MRBL")
ab <- c("AMK", "AMK", "CIP", "CIP")
as.sir_vectorised(mic, mo, ab)

MIC documentation built on June 10, 2025, 9:14 a.m.