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] 128 0.0625 32 4 128 0.0625 0.5 0.025 256 4
#> [11] 16 0.025 0.025 4 256 0.5 8 4 0.005 4
#> [21] 0.01 0.0625 0.025 64 4
random_disk(25)
#> Class 'disk'
#> [1] 35 45 37 36 16 17 25 47 47 40 50 10 6 31 33 37 29 14 33 41 31 7 13 46 42
random_sir(25)
#> Class 'sir'
#> [1] S R S I S I S S I S I S R S R R R I S S I S S R 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] 4 0.0625 0.25 0.0625 16 4 1 4 1
#> [10] 8 0.5 <=0.001 8 16 <=0.001 4 0.25 0.025
#> [19] 16 0.005 0.025 16 0.0625 0.0625 <=0.001
random_mic(25, "Klebsiella pneumoniae", "meropenem") # range 0.0625-16
#> Class 'mic'
#> [1] 2 2 2 32 8 >=64 1 16 16 16 16 1 0.5 4 >=64
#> [16] 1 8 >=64 1 0.5 32 4 16 0.5 16
random_mic(25, "Streptococcus pneumoniae", "meropenem") # range 0.0625-4
#> Class 'mic'
#> [1] 4 0.5 0.5 0.5 0.025 2 1 0.5 0.025 0.5
#> [11] 0.125 0.125 4 0.25 0.25 0.0625 0.0625 0.0625 0.5 2
#> [21] 0.025 0.025 0.5 2 1
random_disk(25, "Klebsiella pneumoniae") # range 8-50
#> Class 'disk'
#> [1] 42 21 25 17 47 14 34 35 40 45 18 35 24 40 48 45 19 31 45 9 35 26 30 26 48
random_disk(25, "Klebsiella pneumoniae", "ampicillin") # range 11-17
#> Class 'disk'
#> [1] 16 13 13 17 14 11 14 14 14 17 17 17 14 17 15 12 12 12 15 16 17 14 16 14 13
random_disk(25, "Streptococcus pneumoniae", "ampicillin") # range 12-27
#> Class 'disk'
#> [1] 24 20 26 20 18 27 18 15 18 17 16 20 24 21 25 21 25 18 23 25 17 24 17 16 20
# }