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] 4 16 1 1 128 0.125 0.5 32 8 2 0.005 >=256
#> [13] 0.005 32 0.025 >=256 >=256 16 64 2 0.001 16 16 0.025
#> [25] >=256
random_disk(25)
#> Class 'disk'
#> [1] 26 29 39 47 43 15 17 40 11 45 41 48 28 25 46 49 36 44 46 13 11 26 29 47 36
random_rsi(25)
#> Class 'rsi'
#> [1] R S I I R S I S R R I R R I R S R S R R R S I 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] 4 16 4 0.001 >=256 0.25 0.25 8 0.001 0.002
#> [11] 2 2 1 0.25 0.25 64 0.125 8 0.0625 64
#> [21] 4 0.5 0.5 0.01 0.5
random_mic(25, "Klebsiella pneumoniae", "meropenem") # range 0.0625-16
#> Class 'mic'
#> [1] 4 <=0.5 >=32 8 2 16 <=0.5 8 16 1 4 1
#> [13] 8 <=0.5 1 8 8 1 4 <=0.5 8 2 2 2
#> [25] 2
random_mic(25, "Streptococcus pneumoniae", "meropenem") # range 0.0625-4
#> Class 'mic'
#> [1] 4 0.0625 0.5 1 0.25 0.25 4 0.0625 2 4
#> [11] 0.0625 0.5 0.5 4 0.125 0.0625 1 0.25 1 0.5
#> [21] 0.25 1 0.125 1 1
random_disk(25, "Klebsiella pneumoniae") # range 8-50
#> Class 'disk'
#> [1] 12 47 48 45 12 36 36 14 49 39 42 38 45 47 47 42 46 50 25 50 9 42 50 41 28
random_disk(25, "Klebsiella pneumoniae", "ampicillin") # range 11-17
#> Class 'disk'
#> [1] 15 12 11 15 16 17 12 11 14 11 11 15 12 17 11 13 12 17 16 14 15 17 16 12 11
random_disk(25, "Streptococcus pneumoniae", "ampicillin") # range 12-27
#> Class 'disk'
#> [1] 25 18 23 25 25 21 19 15 24 20 19 24 20 18 17 26 20 17 21 16 15 25 27 25 22
# }