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] 0.001 256 0.025 0.0625 0.125 0.25 2 0.001 32 0.01
#> [11] 0.0625 0.001 0.01 256 0.0625 32 0.001 0.25 128 256
#> [21] 1 0.002 0.5 0.01 0.002
random_disk(25)
#> Class 'disk'
#> [1] 41 43 23 17 19 28 14 38 18 30 42 11 37 40 39 16 41 43 49 45 44 28 36 14 10
random_sir(25)
#> Class 'sir'
#> [1] R S R I R R R I R S R I I S S R I I I S I R I 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 0.5 32 0.002 0.005 0.25 0.25 4 0.001 0.005 0.025 0.01
#> [13] 0.25 0.005 0.005 2 0.01 1 4 8 0.5 16 1 >=64
#> [25] 0.25
random_mic(25, "Klebsiella pneumoniae", "meropenem") # range 0.0625-16
#> Class 'mic'
#> [1] 1 1 1 4 16 8 1 16 4 16 8 16 4 2 16 4 4 1 2 4 4 1 16 16 2
random_mic(25, "Streptococcus pneumoniae", "meropenem") # range 0.0625-4
#> Class 'mic'
#> [1] 2 4 0.25 0.0625 2 4 0.25 4 1 0.0625
#> [11] 0.25 0.25 4 1 0.5 0.0625 4 0.5 2 0.5
#> [21] 0.5 0.0625 1 0.0625 0.125
random_disk(25, "Klebsiella pneumoniae") # range 8-50
#> Class 'disk'
#> [1] 25 11 13 40 46 37 44 42 10 41 50 39 39 40 33 19 48 39 20 11 32 20 50 38 46
random_disk(25, "Klebsiella pneumoniae", "ampicillin") # range 11-17
#> Class 'disk'
#> [1] 14 15 14 14 17 13 16 17 12 15 17 11 17 17 17 12 17 11 11 14 13 17 13 15 15
random_disk(25, "Streptococcus pneumoniae", "ampicillin") # range 12-27
#> Class 'disk'
#> [1] 26 16 22 23 19 22 19 18 19 23 23 24 22 16 17 15 17 16 18 17 26 16 16 20 22
# }