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] 16 0.025 >=256 >=256 4 64 0.25 1 0.01
#> [10] 0.005 0.5 0.0625 <=0.001 >=256 0.0625 4 16 >=256
#> [19] 16 <=0.001 32 32 0.005 32 0.025
random_disk(25)
#> Class 'disk'
#> [1] 21 47 36 47 30 34 46 18 26 41 27 14 21 44 41 44 24 47 27 46 49 43 21 6 15
random_rsi(25)
#> Class 'rsi'
#> [1] R S R R S I R I R R S I R R S R R S S S S I S I 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] 16 8 0.125 0.01 2 32 <=0.002 0.5 >=64
#> [10] 32 8 0.01 16 8 0.5 0.025 0.01 0.0625
#> [19] 0.5 0.005 0.125 32 16 8 0.125
random_mic(25, "Klebsiella pneumoniae", "meropenem") # range 0.0625-16
#> Class 'mic'
#> [1] >=64 4 2 >=64 1 32 8 <=0.5 4 16 8 16
#> [13] >=64 1 32 32 1 2 1 1 2 16 8 <=0.5
#> [25] <=0.5
random_mic(25, "Streptococcus pneumoniae", "meropenem") # range 0.0625-4
#> Class 'mic'
#> [1] 0.5 2 2 0.5 0.25 8 2 2 0.5
#> [10] 0.25 0.25 4 2 2 8 1 8 <=0.125
#> [19] 0.25 8 8 8 8 4 2
random_disk(25, "Klebsiella pneumoniae") # range 8-50
#> Class 'disk'
#> [1] 30 21 9 8 48 42 24 21 48 40 39 23 25 47 27 33 48 11 28 13 48 48 12 15 19
random_disk(25, "Klebsiella pneumoniae", "ampicillin") # range 11-17
#> Class 'disk'
#> [1] 12 13 16 13 17 11 11 17 16 16 17 13 13 11 17 16 17 14 16 12 11 16 12 17 11
random_disk(25, "Streptococcus pneumoniae", "ampicillin") # range 12-27
#> Class 'disk'
#> [1] 17 27 18 21 19 18 23 20 27 27 16 18 23 26 23 16 22 27 16 22 16 23 24 17 16
# }