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, ...)
random_disk(size = NULL, mo = NULL, ab = NULL, ...)
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
dplyrverb, will get the current (group) size if left blank.- mo
Any character that can be coerced to a valid microorganism code with
as.mo().- ab
Any character that can be coerced to a valid antimicrobial drug code with
as.ab().- ...
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
The base R function sample() is used for generating values.
Generated values are based on the EUCAST 2025 guideline as implemented in the clinical_breakpoints data set. To create specific generated values per bug or drug, set the mo and/or ab argument.
Examples
random_mic(25)
#> Class 'mic'
#> [1] 0.125 8 1 4 0.01 0.002 64 <=0.001 0.01
#> [10] 1 >=256 >=256 2 0.025 0.01 64 4 0.5
#> [19] 0.025 8 0.005 >=256 8 <=0.001 8
random_disk(25)
#> Class 'disk'
#> [1] 7 45 30 48 23 12 45 40 47 9 20 20 23 9 32 20 50 26 42 30 47 11 24 34 46
random_sir(25)
#> Class 'sir'
#> [1] I R I S S I S S I S S R I S I I R S R S R R S I I
# \donttest{
# make the random generation more realistic by setting a bug and/or drug:
random_mic(25, "Klebsiella pneumoniae") # range 0.0625-64
#> Class 'mic'
#> [1] 32 0.0625 16 0.005 0.01 0.25 0.5 4 0.5
#> [10] 0.125 0.125 0.25 >=64 >=64 2 0.025 0.0625 0.025
#> [19] 2 0.125 0.01 8 <=0.001 0.0625 0.5
random_mic(25, "Klebsiella pneumoniae", "meropenem") # range 0.0625-16
#> Class 'mic'
#> [1] 1 8 1 0.5 4 4 2 4 8 2
#> [11] 8 <=0.25 16 2 2 2 16 4 0.5 8
#> [21] 8 <=0.25 2 8 1
random_mic(25, "Streptococcus pneumoniae", "meropenem") # range 0.0625-4
#> Class 'mic'
#> [1] 0.25 1 0.25 >=8 2 1 <=0.125 0.25 2
#> [10] 2 1 4 0.5 <=0.125 2 2 <=0.125 0.5
#> [19] 0.5 >=8 2 0.5 2 >=8 >=8
random_disk(25, "Klebsiella pneumoniae") # range 8-50
#> Class 'disk'
#> [1] 39 14 27 41 44 37 46 17 16 13 23 31 19 22 42 15 40 44 40 40 30 34 34 43 16
random_disk(25, "Klebsiella pneumoniae", "ampicillin") # range 11-17
#> Class 'disk'
#> [1] 12 15 17 17 12 13 16 14 15 12 15 16 11 15 11 17 15 13 14 11 13 17 11 17 16
random_disk(25, "Streptococcus pneumoniae", "ampicillin") # range 12-27
#> Class 'disk'
#> [1] 16 26 21 26 20 22 25 18 26 27 18 25 17 23 21 16 20 23 21 15 21 22 20 19 17
# }