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] 64 16 2 64 0.005 2 0.0625 32 0.125
#> [10] 128 <=0.001 0.025 0.5 2 1 2 0.5 1
#> [19] 4 0.0625 1 0.25 >=256 8 1
random_disk(25)
#> Class 'disk'
#> [1] 38 33 42 7 18 50 44 28 17 8 35 37 48 17 43 41 46 41 36 22 43 50 8 40 7
random_sir(25)
#> Class 'sir'
#> [1] I I I I R R S S R I R S R I I R S I I S S I S R 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] >=128 0.002 0.01 0.025 >=128 0.025 4 0.01 4 0.0625
#> [11] 0.5 2 0.001 0.025 0.025 0.0625 0.25 4 1 32
#> [21] 0.025 0.125 0.5 1 2
random_mic(25, "Klebsiella pneumoniae", "meropenem") # range 0.0625-16
#> Class 'mic'
#> [1] 2 64 8 4 8 16 8 <=1 <=1 <=1 64 16 4 2 64 2 64 16 64
#> [20] 16 2 64 8 8 8
random_mic(25, "Streptococcus pneumoniae", "meropenem") # range 0.0625-4
#> Class 'mic'
#> [1] 0.025 0.025 2 0.025 2 0.025 >=8 1 0.0625 1
#> [11] 4 4 0.0625 >=8 4 0.025 2 1 >=8 0.025
#> [21] 1 4 0.25 0.5 0.5
random_disk(25, "Klebsiella pneumoniae") # range 8-50
#> Class 'disk'
#> [1] 40 32 29 24 30 25 28 46 35 17 16 45 35 30 48 17 45 20 39 41 18 24 48 22 41
random_disk(25, "Klebsiella pneumoniae", "ampicillin") # range 11-17
#> Class 'disk'
#> [1] 12 11 11 11 12 12 11 16 12 17 15 13 11 13 16 15 16 15 13 12 16 11 13 15 16
random_disk(25, "Streptococcus pneumoniae", "ampicillin") # range 12-27
#> Class 'disk'
#> [1] 26 20 25 26 22 18 24 23 23 23 26 21 25 16 17 24 26 22 22 20 18 27 23 25 26
# }