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 2024 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] 64 4 0.25 0.125 0.125 4 0.001 0.0625 32 0.025
#> [11] 16 2 2 4 16 0.0625 0.001 0.5 0.25 >=256
#> [21] 32 0.25 2 2 0.125
random_disk(25)
#> Class 'disk'
#> [1] 6 44 14 31 8 38 41 16 35 39 22 46 25 47 11 44 26 20 17 35 37 22 32 43 14
random_sir(25)
#> Class 'sir'
#> [1] I R I I S S S R R I I S S R R I I I I I I S R I R
# \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] 16 0.25 >=64 32 2 4 0.01 1 1
#> [10] 0.0625 32 0.0625 0.025 <=0.001 1 4 >=64 0.25
#> [19] 0.5 4 0.005 8 1 4 0.002
random_mic(25, "Klebsiella pneumoniae", "meropenem") # range 0.0625-16
#> Class 'mic'
#> [1] 4 16 8 8 2 32 4 8 16 4 16 <=1 16 >=64 16
#> [16] >=64 8 >=64 4 >=64 <=1 4 4 >=64 4
random_mic(25, "Streptococcus pneumoniae", "meropenem") # range 0.0625-4
#> Class 'mic'
#> [1] 0.25 1 4 1 1 0.25 0.0625 0.25 0.0625
#> [10] 0.5 <=0.025 <=0.025 0.5 1 <=0.025 0.25 4 0.5
#> [19] 1 0.125 0.5 1 1 1 <=0.025
random_disk(25, "Klebsiella pneumoniae") # range 8-50
#> Class 'disk'
#> [1] 46 48 26 34 22 36 47 21 21 45 46 8 11 39 17 17 45 19 44 37 21 25 16 48 44
random_disk(25, "Klebsiella pneumoniae", "ampicillin") # range 11-17
#> Class 'disk'
#> [1] 13 13 14 14 12 12 12 15 17 11 11 15 17 16 15 15 16 12 11 12 15 17 13 14 11
random_disk(25, "Streptococcus pneumoniae", "ampicillin") # range 12-27
#> Class 'disk'
#> [1] 20 25 26 15 23 20 26 22 20 16 26 17 21 17 23 17 22 26 27 15 17 25 21 18 15
# }