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] <=0.001 0.125 0.002 0.25 0.5 128 0.002 16 4
#> [10] 0.125 0.005 2 1 0.125 0.005 >=256 >=256 >=256
#> [19] <=0.001 0.125 4 0.0625 0.002 32 0.025
random_disk(25)
#> Class 'disk'
#> [1] 18 16 49 48 27 18 45 13 7 40 27 50 41 29 45 31 23 18 25 46 40 20 34 20 34
random_sir(25)
#> Class 'sir'
#> [1] S I R I S I R R R R S R I R R S S S I I R I R R R
# \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 0.001 >=128 2 0.5 4 1 8 0.5 1 0.001 0.125
#> [13] 2 2 0.002 64 16 0.002 8 0.002 4 >=128 0.025 0.125
#> [25] >=128
random_mic(25, "Klebsiella pneumoniae", "meropenem") # range 0.0625-16
#> Class 'mic'
#> [1] 32 2 1 1 4 1 32 4 4 8 2 16 4 16 8 16 4 2 16 1 16 8 2 1 8
random_mic(25, "Streptococcus pneumoniae", "meropenem") # range 0.0625-4
#> Class 'mic'
#> [1] >=4 >=4 0.5 >=4 0.0625 2 0.0625 1 0.25 0.125
#> [11] 0.125 1 >=4 1 0.25 1 >=4 0.25 >=4 0.5
#> [21] 0.125 0.5 0.125 0.5 >=4
random_disk(25, "Klebsiella pneumoniae") # range 8-50
#> Class 'disk'
#> [1] 45 40 47 40 41 48 35 45 42 27 44 17 17 30 8 8 44 30 26 49 50 35 44 37 43
random_disk(25, "Klebsiella pneumoniae", "ampicillin") # range 11-17
#> Class 'disk'
#> [1] 17 17 11 11 17 16 15 13 13 11 15 12 15 12 14 13 14 14 14 14 15 17 12 15 17
random_disk(25, "Streptococcus pneumoniae", "ampicillin") # range 12-27
#> Class 'disk'
#> [1] 20 21 27 15 26 21 25 23 27 25 15 19 26 20 25 20 25 22 19 16 25 20 24 17 22
# }