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] 128 2 0.25 256 8 0.025 2 0.5 0.01 0.001
#> [11] 0.0625 0.25 1 0.5 8 0.005 0.01 16 64 256
#> [21] 128 256 2 0.125 2
random_disk(25)
#> Class 'disk'
#> [1] 28 40 26 12 43 37 35 14 33 43 16 9 34 33 41 42 46 41 41 40 23 50 44 41 27
random_sir(25)
#> Class 'sir'
#> [1] I I R I S R R R R S S S R R S R I S I I S I I I I
# \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] 64 0.025 0.025 0.025 1 16 8 32 <=0.002
#> [10] 64 8 0.005 2 8 0.5 32 64 0.0625
#> [19] 0.025 0.025 0.125 0.125 1 16 32
random_mic(25, "Klebsiella pneumoniae", "meropenem") # range 0.0625-16
#> Class 'mic'
#> [1] 0.5 2 2 4 16 0.5 16 16 8 8 4 8 8 0.5 16 0.5 1 1 16
#> [20] 4 1 8 4 4 2
random_mic(25, "Streptococcus pneumoniae", "meropenem") # range 0.0625-4
#> Class 'mic'
#> [1] 0.25 1 2 0.125 0.25 >=4 1 2 0.5 2 0.125 0.5
#> [13] 0.5 0.125 >=4 2 1 2 2 0.5 0.125 >=4 1 1
#> [25] >=4
random_disk(25, "Klebsiella pneumoniae") # range 8-50
#> Class 'disk'
#> [1] 36 42 24 10 21 20 40 18 45 26 22 35 22 11 43 30 48 8 43 16 36 32 41 34 32
random_disk(25, "Klebsiella pneumoniae", "ampicillin") # range 11-17
#> Class 'disk'
#> [1] 15 12 14 16 12 12 12 13 14 16 12 11 13 12 12 15 12 12 17 17 14 17 15 13 15
random_disk(25, "Streptococcus pneumoniae", "ampicillin") # range 12-27
#> Class 'disk'
#> [1] 27 17 27 19 22 19 27 19 21 21 19 24 20 20 27 27 22 20 18 24 19 24 17 19 18
# }