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 2023 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] 128 <=0.001 0.25 <=0.001 2 0.0625 64 1 8
#> [10] 0.25 128 <=0.001 128 64 0.025 <=0.001 0.005 4
#> [19] <=0.001 0.125 <=0.001 16 0.0625 <=0.001 4
random_disk(25)
#> Class 'disk'
#> [1] 49 37 48 24 40 25 46 28 29 48 32 22 42 41 42 27 36 11 42 28 50 16 41 8 43
random_sir(25)
#> Class 'sir'
#> [1] R S S I S S S R R S S R S R R R S I S I R S R S 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] 0.001 4 0.5 16 0.002 32 0.01 64 1 0.002
#> [11] 32 0.025 0.0625 0.25 16 2 0.002 8 0.5 0.001
#> [21] 8 16 0.25 0.002 0.001
random_mic(25, "Klebsiella pneumoniae", "meropenem") # range 0.0625-16
#> Class 'mic'
#> [1] 0.5 2 0.5 4 1 1 1 16 1 0.5 0.25 16 1 4 0.25
#> [16] 2 2 0.5 16 1 0.5 2 4 1 1
random_mic(25, "Streptococcus pneumoniae", "meropenem") # range 0.0625-4
#> Class 'mic'
#> [1] 8 0.025 0.5 2 0.125 0.25 4 0.5 0.125 0.0625
#> [11] 0.0625 1 0.5 >=16 0.025 0.0625 0.5 1 4 4
#> [21] 8 0.125 1 0.25 0.025
random_disk(25, "Klebsiella pneumoniae") # range 8-50
#> Class 'disk'
#> [1] 20 36 50 50 46 42 47 48 43 31 42 50 44 49 39 29 46 44 47 20 48 12 10 47 12
random_disk(25, "Klebsiella pneumoniae", "ampicillin") # range 11-17
#> Class 'disk'
#> [1] 14 13 12 14 11 12 15 16 13 14 13 17 15 14 15 13 15 16 16 15 11 11 16 11 15
random_disk(25, "Streptococcus pneumoniae", "ampicillin") # range 12-27
#> Class 'disk'
#> [1] 17 16 22 26 23 26 20 19 15 15 24 23 23 18 16 17 23 27 21 26 22 24 23 26 23
# }