MIC (version 1.1.0)

mic_censor: 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 = NULL, mo = NULL, rules = NULL, max = Inf, min = -Inf)

Value

censored MIC values (S3 mic class)

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.

max

maximum concentration to censor to (default = Inf), will override any rules provided

min

minimum concentration to censor to (default = -Inf), will override any rules provided

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")