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 0.005 0.01 0.25 0.25 16 0.01 32 0.125 32 64 0.001
#> [13] 0.002 16 1 0.002 32 32 0.5 0.001 128 128 0.001 0.5
#> [25] 0.001
random_disk(25)
#> Class 'disk'
#> [1] 21 32 24 30 24 6 44 26 46 8 27 18 45 44 42 39 24 34 8 37 34 15 17 48 17
random_rsi(25)
#> Class 'rsi'
#> [1] I R S S S I S I R R R I R I R I R R R S I R I 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] 4 0.005 0.025 32 8 0.025 8 16 64 0.125 4 0.005
#> [13] 0.5 2 0.025 4 0.001 0.5 2 1 0.001 32 4 1
#> [25] 1
random_mic(25, "Klebsiella pneumoniae", "meropenem") # range 0.0625-16
#> Class 'mic'
#> [1] 8 32 2 16 32 4 32 4 16 2 16 2 2 0.25 32
#> [16] 4 2 16 2 16 2 0.5 0.5 2 32
random_mic(25, "Streptococcus pneumoniae", "meropenem") # range 0.0625-4
#> Class 'mic'
#> [1] 1 0.125 4 0.125 1 0.0625 4 1 1 0.25
#> [11] 4 2 1 4 0.5 0.0625 0.125 1 0.0625 1
#> [21] 1 2 2 0.0625 2
random_disk(25, "Klebsiella pneumoniae") # range 8-50
#> Class 'disk'
#> [1] 9 44 40 35 36 40 30 17 25 18 9 14 24 14 30 41 38 16 27 50 12 11 44 46 20
random_disk(25, "Klebsiella pneumoniae", "ampicillin") # range 11-17
#> Class 'disk'
#> [1] 15 14 17 12 17 11 12 16 14 17 17 11 16 13 16 16 14 16 12 13 12 15 12 17 17
random_disk(25, "Streptococcus pneumoniae", "ampicillin") # range 12-27
#> Class 'disk'
#> [1] 24 22 25 16 17 16 20 16 19 15 24 16 24 23 16 16 25 23 15 26 20 22 24 25 20
# }