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] 0.005 256 256 0.0625 64 0.5 0.25 <=0.002 0.025
#> [10] 0.0625 0.0625 32 0.5 0.01 32 0.005 0.0625 <=0.002
#> [19] 0.5 0.025 4 16 128 1 4
random_disk(25)
#> Class 'disk'
#> [1] 30 46 46 42 24 26 25 45 42 43 21 40 13 48 44 6 50 31 27 11 9 20 46 11 47
random_sir(25)
#> Class 'sir'
#> [1] R I R I S I S R I I R R S S R S R R I S S I I S 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] 2 8 0.025 4 8 0.002 0.01 0.5 1 128 8 0.01
#> [13] 0.025 >=256 >=256 0.125 >=256 8 16 0.01 64 32 16 0.001
#> [25] 8
random_mic(25, "Klebsiella pneumoniae", "meropenem") # range 0.0625-16
#> Class 'mic'
#> [1] 0.5 16 1 0.5 8 8 1 1 8 2 8 2 0.5 16 0.5 16 4 4 0.5
#> [20] 4 8 8 8 1 1
random_mic(25, "Streptococcus pneumoniae", "meropenem") # range 0.0625-4
#> Class 'mic'
#> [1] 0.5 <=0.125 2 0.5 0.25 2 0.25 0.5 <=0.125
#> [10] <=0.125 1 1 4 1 <=0.125 0.25 4 0.5
#> [19] 4 <=0.125 4 <=0.125 1 1 <=0.125
random_disk(25, "Klebsiella pneumoniae") # range 8-50
#> Class 'disk'
#> [1] 25 10 45 47 8 43 46 45 43 28 9 46 19 15 46 13 50 35 44 46 25 9 11 50 33
random_disk(25, "Klebsiella pneumoniae", "ampicillin") # range 11-17
#> Class 'disk'
#> [1] 16 13 17 14 12 13 14 13 11 14 17 12 12 17 16 16 13 12 12 11 14 13 17 15 17
random_disk(25, "Streptococcus pneumoniae", "ampicillin") # range 12-27
#> Class 'disk'
#> [1] 20 18 19 21 20 22 19 17 23 23 15 24 24 25 21 15 19 19 27 27 25 19 16 22 16
# }