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] 0.01 0.025 0.025 32 128 0.125 <=0.002 0.0625 0.01
#> [10] 0.0625 16 0.005 0.025 >=256 4 16 0.005 0.5
#> [19] 0.025 128 128 <=0.002 0.005 <=0.002 0.5
random_disk(25)
#> Class 'disk'
#> [1] 23 27 46 28 15 9 37 30 20 26 29 16 40 45 16 36 12 50 15 50 21 6 26 48 49
random_rsi(25)
#> Class 'rsi'
#> [1] R R R R S R S R S R S I R I I I R S R R S S S 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] 0.002 0.5 4 1 1 0.002 0.0625 0.01 0.025 4
#> [11] 0.025 0.0625 0.25 0.125 0.025 0.002 0.002 0.01 0.01 0.001
#> [21] 0.0625 0.002 8 64 0.125
random_mic(25, "Klebsiella pneumoniae", "meropenem") # range 0.0625-16
#> Class 'mic'
#> [1] 8 1 4 1 32 32 4 16 <=0.5 8 16 2
#> [13] <=0.5 1 2 2 1 1 1 1 16 1 2 8
#> [25] 1
random_mic(25, "Streptococcus pneumoniae", "meropenem") # range 0.0625-4
#> Class 'mic'
#> [1] 0.5 1 1 0.0625 0.125 0.5 0.25 4 2 1
#> [11] 0.5 0.25 1 0.5 4 0.25 0.0625 0.25 1 0.25
#> [21] 4 1 0.25 1 2
random_disk(25, "Klebsiella pneumoniae") # range 8-50
#> Class 'disk'
#> [1] 31 41 17 26 46 32 8 44 42 45 41 43 43 19 13 30 50 40 28 39 28 40 8 17 20
random_disk(25, "Klebsiella pneumoniae", "ampicillin") # range 11-17
#> Class 'disk'
#> [1] 16 17 14 12 12 17 12 14 14 13 12 14 12 16 16 12 12 13 16 14 13 16 11 15 13
random_disk(25, "Streptococcus pneumoniae", "ampicillin") # range 12-27
#> Class 'disk'
#> [1] 22 27 18 27 22 23 25 19 27 22 23 22 16 20 16 17 27 17 27 23 19 19 18 18 15
# }