mic_censor: Censor MIC values

In MIC: Analysis of Antimicrobial Minimum Inhibitory Concentration Data

Censor MIC values

Description

MIC datasets often arise from different laboratories or experimental conditions. In practice, this means that there can be different levels of censoring (<= and >) within the data. This function can be used to harmonise the dataset to a single level of censoring. The function requires a set of rules that specify the censoring levels (see example).

Usage

mic_censor(mic, ab, mo, rules)

Arguments

mic	MIC (coercible to AMR::as.mic)
ab	antibiotic name (coercible to AMR::as.ab)
mo	microorganism name (coercible to AMR::as.mo)
rules	censor rules - named list of pathogen (in AMR::as.mo code) to antibiotic (in AMR::as.ab code) to censoring rules. The censoring rules should provide a min or max value to censor MICs to. See example for more.

Value

censored MIC values (S3 mic class)

Examples

example_rules <- list("B_ESCHR_COLI" = list(
  "AMK" = list(min = 2, max = 32),
  "CHL" = list(min = 4, max = 64),
  "GEN" = list(min = 1, max = 16),
  "CIP" = list(min = 0.015, max = 4),
  "MEM" = list(min = 0.016, max = 16),
  "AMX" = list(min = 2, max = 64),
  "AMC" = list(min = 2, max = 64),
  "FEP" = list(min = 0.5, max = 64),
  "CAZ" = list(min = 1, max = 128),
  "TGC" = list(min = 0.25, max = 1)
  ))

mic_censor(AMR::as.mic(512),
           "AMK",
           "B_ESCHR_COLI",
           example_rules) == AMR::as.mic(">32")

MIC documentation built on April 12, 2025, 2:26 a.m.