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_rsi(size = NULL, prob_RSI = 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_RSI
a vector of length 3: the probabilities for "R" (1st value), "S" (2nd value) and "I" (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 rsi_translation 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] 32 4 0.001 8 2 0.025 4 128 128 0.5 0.025 8
#> [13] 0.025 16 64 1 64 8 0.125 128 0.25 >=256 2 0.025
#> [25] 16
random_disk(25)
#> Class 'disk'
#> [1] 29 13 31 34 33 32 7 8 18 32 46 16 14 41 10 26 10 45 41 39 40 13 18 13 35
random_rsi(25)
#> Class 'rsi'
#> [1] S I R S I R S R I R S R S I I I I I R R R R S I 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] 32 128 0.025 0.125 1 64 0.5 16 0.025
#> [10] 0.25 0.25 0.25 0.25 0.0625 <=0.001 0.005 0.25 0.0625
#> [19] 0.0625 0.025 <=0.001 16 2 32 0.0625
random_mic(25, "Klebsiella pneumoniae", "meropenem") # range 0.0625-16
#> Class 'mic'
#> [1] 0.5 1 8 2 2 16 8 8 16 0.5 4 8 4 8 0.5 2 16 0.5 8
#> [20] 8 0.5 16 2 8 0.5
random_mic(25, "Streptococcus pneumoniae", "meropenem") # range 0.0625-4
#> Class 'mic'
#> [1] 0.125 0.0625 0.125 0.25 2 0.25 0.0625 2 0.125 0.125
#> [11] 0.125 >=4 >=4 0.5 0.125 >=4 0.25 0.125 1 0.5
#> [21] 0.0625 1 >=4 0.0625 >=4
random_disk(25, "Klebsiella pneumoniae") # range 8-50
#> Class 'disk'
#> [1] 17 36 40 30 8 48 50 21 28 8 12 20 34 17 20 47 46 49 25 20 47 42 36 25 47
random_disk(25, "Klebsiella pneumoniae", "ampicillin") # range 11-17
#> Class 'disk'
#> [1] 12 14 14 13 14 14 17 14 14 14 12 17 13 11 14 11 13 11 14 13 11 12 16 14 14
random_disk(25, "Streptococcus pneumoniae", "ampicillin") # range 12-27
#> Class 'disk'
#> [1] 23 23 16 26 18 20 22 15 18 19 27 15 16 21 21 21 25 23 22 18 17 17 25 18 16
# }