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 2022 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] 1 <=0.001 <=0.001 8 32 <=0.001 128 0.01 0.002
#> [10] 0.01 256 <=0.001 0.5 1 4 256 0.25 64
#> [19] 1 0.01 1 0.5 0.0625 2 0.005
random_disk(25)
#> Class 'disk'
#> [1] 44 35 30 50 38 41 6 45 36 25 28 45 43 9 15 22 46 12 45 22 37 25 12 50 43
random_sir(25)
#> Class 'sir'
#> [1] S I R S S R R R R R S S S R S I R S I S S 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 64 0.025 >=128 0.25 1 16 8 4 8
#> [11] 4 0.0625 0.25 2 0.01 8 32 >=128 1 0.002
#> [21] 16 0.025 0.002 0.01 0.0625
random_mic(25, "Klebsiella pneumoniae", "meropenem") # range 0.0625-16
#> Class 'mic'
#> [1] 32 16 2 32 4 8 4 0.5 0.5 4 1 0.5 0.5 16 4 16 2 1 0.5
#> [20] 2 0.5 0.5 1 1 16
random_mic(25, "Streptococcus pneumoniae", "meropenem") # range 0.0625-4
#> Class 'mic'
#> [1] 16 0.5 16 1 2 1 1 4 0.0625 0.025
#> [11] 16 0.0625 0.25 4 0.5 16 0.25 0.5 0.125 16
#> [21] 0.025 1 0.5 0.125 0.025
random_disk(25, "Klebsiella pneumoniae") # range 8-50
#> Class 'disk'
#> [1] 34 48 26 44 41 18 40 49 46 32 49 30 14 40 18 9 42 17 47 42 18 43 20 33 48
random_disk(25, "Klebsiella pneumoniae", "ampicillin") # range 11-17
#> Class 'disk'
#> [1] 13 17 13 14 15 14 11 14 12 16 17 17 15 11 16 13 15 11 14 15 13 17 14 17 17
random_disk(25, "Streptococcus pneumoniae", "ampicillin") # range 12-27
#> Class 'disk'
#> [1] 26 24 15 17 22 20 26 19 18 22 24 20 16 16 27 16 19 27 25 18 16 26 17 26 19
# }