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] 0.005 8 1 0.005 0.025 0.5 2 0.25 1 0.005 256 0.01
#> [13] 128 1 64 256 2 0.01 0.002 0.025 16 128 0.005 1
#> [25] 256
random_disk(25)
#> Class 'disk'
#> [1] 47 46 41 50 25 23 41 13 13 22 41 39 22 31 34 43 20 42 8 13 45 44 34 10 40
random_sir(25)
#> Class 'sir'
#> [1] I R R S R I S S I R R S S I S R S I S S R R S S 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] 0.0625 0.025 0.002 4 64 1 32 0.0625 8 0.25
#> [11] 16 16 2 0.01 0.25 0.002 0.0625 0.0625 16 16
#> [21] 0.125 0.025 0.002 256 0.5
random_mic(25, "Klebsiella pneumoniae", "meropenem") # range 0.0625-16
#> Class 'mic'
#> [1] 2 8 2 1 1 8 0.5 2 4 1 4 0.5 8 1 16
#> [16] 0.5 16 16 8 2 8 0.25 4 0.5 1
random_mic(25, "Streptococcus pneumoniae", "meropenem") # range 0.0625-4
#> Class 'mic'
#> [1] 0.0625 4 8 2 4 0.5 0.0625 8 0.5
#> [10] 0.5 0.25 8 0.0625 8 0.125 0.125 2 4
#> [19] 0.25 2 0.25 8 0.25 2 <=0.025
random_disk(25, "Klebsiella pneumoniae") # range 8-50
#> Class 'disk'
#> [1] 21 40 47 36 48 49 42 26 12 46 42 47 39 44 17 30 14 50 9 35 49 22 24 40 31
random_disk(25, "Klebsiella pneumoniae", "ampicillin") # range 11-17
#> Class 'disk'
#> [1] 12 15 11 13 11 11 11 17 13 14 16 11 12 11 13 13 17 16 11 13 13 14 11 14 14
random_disk(25, "Streptococcus pneumoniae", "ampicillin") # range 12-27
#> Class 'disk'
#> [1] 26 20 25 16 25 27 18 17 16 15 20 18 19 16 20 26 27 16 19 24 16 21 18 20 19
# }