AMR: Antimicrobial Resistance Data Analysis

random

R Documentation

Random MIC Values/Disk Zones/SIR Generation

Description

These functions can be used for generating random MIC values and disk diffusion diameters, for AMR data analysis practice. By providing a microorganism and antimicrobial drug, the generated results will reflect reality as much as possible.

Usage

random_mic(size = NULL, mo = NULL, ab = NULL, skew = "right",
  severity = 1, ...)

random_disk(size = NULL, mo = NULL, ab = NULL, skew = "left",
  severity = 1, ...)

random_sir(size = NULL, prob_SIR = c(0.33, 0.33, 0.33), ...)

Arguments

`size`	Desired size of the returned vector. If used in a data.frame call or `dplyr` verb, will get the current (group) size if left blank.
`mo`	Any character that can be coerced to a valid microorganism code with `as.mo()`. Can be the same length as `size`.
`ab`	Any character that can be coerced to a valid antimicrobial drug code with `as.ab()`.
`skew`	Direction of skew for MIC or disk values, either `"right"` or `"left"`. A left-skewed distribution has the majority of the data on the right.
`severity`	Skew severity; higher values will increase the skewedness. Default is `2`; use `0` to prevent skewedness.
`...`	Ignored, only in place to allow future extensions.
`prob_SIR`	A vector of length 3: the probabilities for "S" (1st value), "I" (2nd value) and "R" (3rd value).

Details

Internally, MIC and disk zone values are sampled based on clinical breakpoints defined in the clinical_breakpoints data set. To create specific generated values per bug or drug, set the mo and/or ab argument. The MICs are sampled on a log2 scale and disks linearly, using weighted probabilities. The weights are based on the skew and severity arguments:

skew = "right" places more emphasis on lower MIC or higher disk values.
skew = "left" places more emphasis on higher MIC or lower disk values.
severity controls the exponential bias applied.

Value

class mic for random_mic() (see as.mic()) and class disk for random_disk() (see as.disk())

Examples

random_mic(25)
random_disk(25)
random_sir(25)

# add more skewedness, make more realistic by setting a bug and/or drug:
disks <- random_disk(100, severity = 2, mo = "Escherichia coli", ab = "CIP")
plot(disks)
# `plot()` and `ggplot2::autoplot()` allow for coloured bars if `mo` and `ab` are set
plot(disks, mo = "Escherichia coli", ab = "CIP", guideline = "CLSI 2025")


random_mic(25, "Klebsiella pneumoniae") # range 0.0625-64
random_mic(25, "Klebsiella pneumoniae", "meropenem") # range 0.0625-16
random_mic(25, "Streptococcus pneumoniae", "meropenem") # range 0.0625-4

random_disk(25, "Klebsiella pneumoniae") # range 8-50
random_disk(25, "Klebsiella pneumoniae", "ampicillin") # range 11-17
random_disk(25, "Streptococcus pneumoniae", "ampicillin") # range 12-27

msberends/AMR documentation built on June 14, 2025, 7:58 a.m.