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] 0.005 0.005 8 256 0.125 16 8 32 0.025
#> [10] 0.0625 0.0625 16 0.0625 0.005 4 <=0.001 256 4
#> [19] 0.5 8 <=0.001 32 0.025 0.002 0.5
random_disk(25)
#> Class 'disk'
#> [1] 39 32 46 15 26 43 36 23 7 12 6 19 47 14 12 23 19 41 49 12 41 34 23 49 11
random_sir(25)
#> Class 'sir'
#> [1] R S S I R I S S I I I I S R S S I R I R R S I R 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] 8 0.0625 0.001 16 4 0.0625 0.25 1 0.001 0.001
#> [11] 0.002 0.0625 2 0.5 0.005 0.01 0.5 64 0.025 0.5
#> [21] 4 0.0625 0.01 2 0.0625
random_mic(25, "Klebsiella pneumoniae", "meropenem") # range 0.0625-16
#> Class 'mic'
#> [1] 4 4 16 <=0.5 8 1 16 1 32 <=0.5 <=0.5 64
#> [13] 1 2 32 32 2 16 2 4 2 4 8 32
#> [25] 64
random_mic(25, "Streptococcus pneumoniae", "meropenem") # range 0.0625-4
#> Class 'mic'
#> [1] 8 0.125 2 0.125 >=16 0.0625 0.125 0.025 1 0.5
#> [11] 0.25 0.0625 0.125 4 0.5 >=16 2 1 8 0.25
#> [21] 8 4 0.5 1 0.125
random_disk(25, "Klebsiella pneumoniae") # range 8-50
#> Class 'disk'
#> [1] 30 40 48 47 38 29 22 40 44 40 29 28 38 48 50 34 13 41 40 50 43 33 34 19 43
random_disk(25, "Klebsiella pneumoniae", "ampicillin") # range 11-17
#> Class 'disk'
#> [1] 12 16 15 14 12 15 16 12 16 13 14 14 12 17 11 12 11 17 12 16 15 16 17 13 17
random_disk(25, "Streptococcus pneumoniae", "ampicillin") # range 12-27
#> Class 'disk'
#> [1] 21 26 27 24 18 18 22 23 18 19 24 15 27 25 22 27 20 17 16 26 16 15 25 20 18
# }