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] 0.001 0.0625 0.002 0.005 0.01 0.25 128 0.125 0.002 0.0625
#> [11] 0.025 0.25 >=256 64 0.002 0.0625 1 0.25 0.01 4
#> [21] 4 1 0.5 0.002 0.025
random_disk(25)
#> Class 'disk'
#> [1] 43 6 16 49 45 14 26 43 40 22 38 32 15 38 8 47 17 22 50 50 37 32 36 18 14
random_rsi(25)
#> Class 'rsi'
#> [1] S R I S R S I S R R I I R S I S I R R I R S R S 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] 0.0625 0.01 0.01 1 64 1 64 64 2
#> [10] 0.002 <=0.001 4 2 1 <=0.001 0.25 0.005 0.125
#> [19] 0.025 2 16 0.5 0.5 64 2
random_mic(25, "Klebsiella pneumoniae", "meropenem") # range 0.0625-16
#> Class 'mic'
#> [1] 8 8 <=0.5 >=16 <=0.5 <=0.5 8 <=0.5 <=0.5 8 1 >=16
#> [13] >=16 4 4 1 1 8 >=16 8 4 4 >=16 2
#> [25] 2
random_mic(25, "Streptococcus pneumoniae", "meropenem") # range 0.0625-4
#> Class 'mic'
#> [1] 1 0.25 1 2 2 1 1 1 8
#> [10] 2 2 8 1 0.25 2 0.5 0.25 0.25
#> [19] 2 0.25 0.25 0.0625 1 <=0.025 0.125
random_disk(25, "Klebsiella pneumoniae") # range 8-50
#> Class 'disk'
#> [1] 13 40 38 28 44 48 11 44 45 45 24 49 41 50 8 42 40 47 41 50 45 40 31 17 21
random_disk(25, "Klebsiella pneumoniae", "ampicillin") # range 11-17
#> Class 'disk'
#> [1] 15 17 15 13 12 13 12 14 12 17 17 17 13 12 15 12 17 11 11 15 14 14 14 17 14
random_disk(25, "Streptococcus pneumoniae", "ampicillin") # range 12-27
#> Class 'disk'
#> [1] 23 16 15 25 26 17 26 18 18 19 20 16 17 20 23 16 19 15 26 15 24 17 27 22 20
# }