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] 0.002 0.005 32 32 >=256 0.025 8 0.001 64 0.0625
#> [11] >=256 8 1 64 0.025 128 0.01 64 0.025 0.5
#> [21] 4 0.002 0.5 0.001 0.5
random_disk(25)
#> Class 'disk'
#> [1] 32 43 22 35 41 40 26 6 34 37 42 11 50 10 41 8 7 44 31 19 44 26 16 46 33
random_rsi(25)
#> Class 'rsi'
#> [1] R S S S I R S R S R R R R R S R S S R R I R I R S
# \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] 0.01 0.125 2 <=0.001 0.025 0.125 0.5 0.5 1
#> [10] 16 2 0.25 1 64 0.0625 0.5 0.002 0.01
#> [19] 0.5 0.01 0.5 0.025 0.0625 1 0.025
random_mic(25, "Klebsiella pneumoniae", "meropenem") # range 0.0625-16
#> Class 'mic'
#> [1] 2 4 8 4 16 2 8 16 16 2 1 1 4 8 1 16 8 1 2 2 4 1 8 1 8
random_mic(25, "Streptococcus pneumoniae", "meropenem") # range 0.0625-4
#> Class 'mic'
#> [1] 8 0.0625 4 4 0.0625 8 8 0.25 0.25 0.125
#> [11] 4 0.25 0.125 0.125 8 4 2 0.0625 1 4
#> [21] 0.0625 1 0.5 16 1
random_disk(25, "Klebsiella pneumoniae") # range 8-50
#> Class 'disk'
#> [1] 44 19 39 43 28 43 13 43 29 8 33 45 19 20 10 32 9 30 35 37 23 40 18 27 22
random_disk(25, "Klebsiella pneumoniae", "ampicillin") # range 11-17
#> Class 'disk'
#> [1] 14 12 11 16 16 13 15 14 15 13 16 15 13 15 12 16 13 11 17 17 14 15 12 13 15
random_disk(25, "Streptococcus pneumoniae", "ampicillin") # range 12-27
#> Class 'disk'
#> [1] 15 15 27 18 26 16 23 18 18 27 23 15 21 26 15 16 23 25 18 18 18 17 24 25 21
# }