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 0.001 >=256 0.001 0.005 8 8 1 16 0.002 >=256 16
#> [13] 4 64 0.002 0.001 0.25 64 0.025 64 0.025 1 0.001 16
#> [25] 0.5
random_disk(25)
#> Class 'disk'
#> [1] 10 42 50 49 46 44 48 49 32 49 20 30 44 13 10 34 26 26 26 47 19 38 23 41 41
random_sir(25)
#> Class 'sir'
#> [1] R S S I I I I S S I S S R S S R S S R S R R R 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] 0.125 0.5 128 64 8 0.0625 0.125 >=256 4 8
#> [11] 0.125 2 32 2 0.0625 0.125 64 0.025 64 8
#> [21] 0.002 8 0.025 1 4
random_mic(25, "Klebsiella pneumoniae", "meropenem") # range 0.0625-16
#> Class 'mic'
#> [1] 8 16 4 8 2 16 16 2 0.5 1 8 8 16 1 1
#> [16] 4 2 8 8 2 8 0.25 2 0.5 0.5
random_mic(25, "Streptococcus pneumoniae", "meropenem") # range 0.0625-4
#> Class 'mic'
#> [1] <=0.0625 0.25 8 2 0.25 1 4 2
#> [9] 0.25 <=0.0625 0.5 8 0.25 0.5 4 0.125
#> [17] 2 0.25 4 4 0.25 <=0.0625 8 <=0.0625
#> [25] <=0.0625
random_disk(25, "Klebsiella pneumoniae") # range 8-50
#> Class 'disk'
#> [1] 40 43 38 39 15 49 39 10 47 43 30 38 15 26 16 24 32 16 36 47 35 11 45 42 41
random_disk(25, "Klebsiella pneumoniae", "ampicillin") # range 11-17
#> Class 'disk'
#> [1] 11 16 14 13 11 11 16 17 14 11 15 16 17 12 17 16 11 11 12 13 14 12 13 11 11
random_disk(25, "Streptococcus pneumoniae", "ampicillin") # range 12-27
#> Class 'disk'
#> [1] 19 25 18 20 25 16 15 25 19 25 27 19 25 20 23 21 17 19 25 25 22 24 17 22 21
# }