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] 16 0.001 0.001 0.5 0.002 0.001 2 0.5 64 2
#> [11] 0.0625 0.25 128 0.025 128 128 8 0.001 32 64
#> [21] 64 16 0.01 0.125 64
random_disk(25)
#> Class 'disk'
#> [1] 41 30 7 30 50 25 9 50 38 41 12 20 13 16 40 25 25 23 32 46 47 37 20 13 44
random_sir(25)
#> Class 'sir'
#> [1] S S R R S S I S I R I S R S I R R S R S R S R I S
# \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] 0.25 128 2 0.001 0.01 0.5 32 8 64 1
#> [11] 64 1 0.5 0.0625 1 0.025 0.5 0.002 2 0.5
#> [21] 4 0.025 0.5 0.125 32
random_mic(25, "Klebsiella pneumoniae", "meropenem") # range 0.0625-16
#> Class 'mic'
#> [1] 16 2 16 8 2 4 32 16 2 <=1 16 8 8 <=1 8 <=1 <=1 2 8
#> [20] 32 8 2 32 32 32
random_mic(25, "Streptococcus pneumoniae", "meropenem") # range 0.0625-4
#> Class 'mic'
#> [1] 2 2 >=8 0.0625 4 1 4 0.25 0.125 4
#> [11] >=8 0.125 0.25 0.125 0.5 0.5 4 1 0.5 0.5
#> [21] 0.0625 1 4 4 0.5
random_disk(25, "Klebsiella pneumoniae") # range 8-50
#> Class 'disk'
#> [1] 46 49 42 41 41 17 46 32 45 13 47 43 47 34 43 20 28 40 15 46 26 14 45 41 23
random_disk(25, "Klebsiella pneumoniae", "ampicillin") # range 11-17
#> Class 'disk'
#> [1] 12 16 14 17 14 17 12 14 17 12 11 16 16 11 12 14 15 11 17 17 13 13 13 16 13
random_disk(25, "Streptococcus pneumoniae", "ampicillin") # range 12-27
#> Class 'disk'
#> [1] 22 25 16 23 20 25 24 17 23 18 26 16 21 16 25 17 23 23 20 20 27 20 18 24 15
# }