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 2023 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] 64 1 1 1 0.025 0.025 0.5 <=0.002 0.25
#> [10] >=256 8 0.005 64 64 128 4 4 16
#> [19] 2 0.005 <=0.002 4 0.25 64 1
random_disk(25)
#> Class 'disk'
#> [1] 19 13 8 13 40 16 7 20 14 47 19 26 41 25 14 41 47 40 49 40 46 30 46 32 11
random_sir(25)
#> Class 'sir'
#> [1] S I S I I R I S I S S R I I R S S I R I R R I I 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] 0.025 4 0.25 0.001 4 0.125 0.002 0.125 1 0.025
#> [11] 0.002 2 0.002 0.0625 0.001 1 0.001 8 4 2
#> [21] 0.5 0.25 128 64 0.25
random_mic(25, "Klebsiella pneumoniae", "meropenem") # range 0.0625-16
#> Class 'mic'
#> [1] 4 8 16 64 4 1 4 64 0.5 16 32 16 32 4 8 1 2 32 4
#> [20] 8 0.5 32 64 32 32
random_mic(25, "Streptococcus pneumoniae", "meropenem") # range 0.0625-4
#> Class 'mic'
#> [1] 1 1 2 0.5 0.5 2 >=4 1 0.5
#> [10] 0.25 0.25 1 0.5 >=4 2 0.25 <=0.125 0.25
#> [19] 1 <=0.125 0.25 >=4 0.25 0.25 2
random_disk(25, "Klebsiella pneumoniae") # range 8-50
#> Class 'disk'
#> [1] 49 43 10 16 28 42 41 41 48 21 20 46 23 24 41 13 46 46 17 27 48 47 41 20 44
random_disk(25, "Klebsiella pneumoniae", "ampicillin") # range 11-17
#> Class 'disk'
#> [1] 14 16 13 13 17 11 17 13 15 17 17 11 15 14 14 17 16 17 15 16 13 14 16 11 12
random_disk(25, "Streptococcus pneumoniae", "ampicillin") # range 12-27
#> Class 'disk'
#> [1] 24 23 23 15 26 16 21 25 23 22 22 21 16 19 27 23 25 18 26 17 24 25 22 18 15
# }