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] 0.002 0.005 256 0.002 128 16 0.025 0.025 8 16
#> [11] 0.001 1 0.0625 0.01 0.5 0.001 256 16 64 0.0625
#> [21] 0.01 1 0.002 2 32
random_disk(25)
#> Class 'disk'
#> [1] 39 34 35 50 45 12 10 28 49 18 26 21 49 41 20 32 13 28 10 16 36 21 44 27 39
random_sir(25)
#> Class 'sir'
#> [1] S R I R I R I I I S R R S S R R S R R S I S I R 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] 16 128 0.005 8 1 8 0.25 2 4 1
#> [11] 0.002 0.125 0.25 2 1 0.0625 1 128 256 0.005
#> [21] 1 16 1 0.25 0.5
random_mic(25, "Klebsiella pneumoniae", "meropenem") # range 0.0625-16
#> Class 'mic'
#> [1] 2 <=1 4 16 <=1 8 8 4 8 2 <=1 8 8 8 16 2 2 16 4
#> [20] 2 4 4 16 16 <=1
random_mic(25, "Streptococcus pneumoniae", "meropenem") # range 0.0625-4
#> Class 'mic'
#> [1] 0.25 0.5 0.25 0.5 4 0.0625 8 8 4 4
#> [11] 0.0625 0.125 8 0.125 0.5 8 0.5 8 0.0625 2
#> [21] 0.25 1 8 0.0625 0.0625
random_disk(25, "Klebsiella pneumoniae") # range 8-50
#> Class 'disk'
#> [1] 47 33 27 16 18 9 27 18 41 23 46 27 46 32 43 33 49 47 24 25 50 50 47 26 13
random_disk(25, "Klebsiella pneumoniae", "ampicillin") # range 11-17
#> Class 'disk'
#> [1] 12 13 15 14 16 13 11 13 13 16 11 17 15 17 14 15 11 15 11 13 15 16 15 16 14
random_disk(25, "Streptococcus pneumoniae", "ampicillin") # range 12-27
#> Class 'disk'
#> [1] 17 27 20 17 25 23 24 20 24 25 17 20 24 15 18 22 20 21 22 27 22 16 21 21 17
# }