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] 0.025 2 0.25 8 4 >=256 64 0.125 1
#> [10] 16 2 0.025 8 32 <=0.001 4 2 128
#> [19] 0.125 4 0.01 >=256 0.25 0.25 1
random_disk(25)
#> Class 'disk'
#> [1] 48 8 6 21 6 34 30 30 42 26 10 41 26 22 46 19 16 38 34 12 50 42 45 42 44
random_sir(25)
#> Class 'sir'
#> [1] I R R S R I I R R R R R R I R S S S I I S S R 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] 1 16 0.025 0.001 4 4 0.125 0.002 2 0.25 0.25 64
#> [13] 0.5 0.005 256 8 0.125 16 0.005 0.001 64 0.5 8 64
#> [25] 0.001
random_mic(25, "Klebsiella pneumoniae", "meropenem") # range 0.0625-16
#> Class 'mic'
#> [1] 4 8 2 >=16 <=0.25 <=0.25 >=16 1 1 0.5
#> [11] 8 <=0.25 2 0.5 2 <=0.25 1 4 1 <=0.25
#> [21] >=16 4 2 1 <=0.25
random_mic(25, "Streptococcus pneumoniae", "meropenem") # range 0.0625-4
#> Class 'mic'
#> [1] 2 8 0.0625 0.0625 0.0625 4 <=0.025 0.125 8
#> [10] 8 0.25 0.25 0.125 <=0.025 0.25 <=0.025 0.0625 2
#> [19] <=0.025 8 4 4 <=0.025 8 8
random_disk(25, "Klebsiella pneumoniae") # range 8-50
#> Class 'disk'
#> [1] 8 24 46 50 48 11 23 30 47 33 21 43 17 16 48 16 39 38 16 49 33 47 14 18 42
random_disk(25, "Klebsiella pneumoniae", "ampicillin") # range 11-17
#> Class 'disk'
#> [1] 12 13 15 14 12 16 15 16 13 13 12 13 12 11 16 17 11 17 11 14 12 14 11 12 12
random_disk(25, "Streptococcus pneumoniae", "ampicillin") # range 12-27
#> Class 'disk'
#> [1] 20 18 24 24 17 18 26 24 26 24 20 20 26 24 19 15 17 17 24 20 17 22 22 19 15
# }