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] 4 0.25 0.002 0.25 0.125 8 0.5 0.125 32 256
#> [11] 256 8 0.0625 2 0.5 8 0.001 128 256 0.005
#> [21] 0.01 128 0.002 0.01 0.001
random_disk(25)
#> Class 'disk'
#> [1] 28 47 9 12 25 45 46 47 21 41 31 50 48 49 30 37 42 41 35 28 48 40 44 44 29
random_sir(25)
#> Class 'sir'
#> [1] S S I R R I I I R R R R S S R R I I R S I R R 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] 0.01 1 4 0.025 16 0.0625 2 16 0.25
#> [10] 8 0.0625 1 4 16 32 0.125 4 16
#> [19] 0.5 1 32 16 <=0.001 0.005 >=64
random_mic(25, "Klebsiella pneumoniae", "meropenem") # range 0.0625-16
#> Class 'mic'
#> [1] 16 1 4 16 8 2 1 8 8 16 8 1 1 4 4 4 2 16 1 1 2 4 8 1 2
random_mic(25, "Streptococcus pneumoniae", "meropenem") # range 0.0625-4
#> Class 'mic'
#> [1] 8 1 0.25 0.0625 1 4 8 2 0.25 1
#> [11] 8 0.25 4 0.025 0.25 0.25 16 0.125 1 16
#> [21] 0.025 4 0.5 16 16
random_disk(25, "Klebsiella pneumoniae") # range 8-50
#> Class 'disk'
#> [1] 19 49 18 32 43 23 48 48 45 26 18 18 34 34 43 16 43 44 49 47 35 39 32 19 23
random_disk(25, "Klebsiella pneumoniae", "ampicillin") # range 11-17
#> Class 'disk'
#> [1] 16 12 16 11 14 12 13 11 13 15 17 16 14 12 12 16 15 14 13 15 17 16 15 17 14
random_disk(25, "Streptococcus pneumoniae", "ampicillin") # range 12-27
#> Class 'disk'
#> [1] 19 18 24 25 20 16 15 20 19 18 18 17 24 21 24 16 24 22 19 18 26 27 27 25 16
# }