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] 0.5 >=256 1 128 0.25 0.002 0.01 0.001 0.0625 64
#> [11] 0.025 0.25 4 2 0.125 128 0.002 0.125 0.5 0.125
#> [21] 0.01 2 0.01 0.001 0.01
random_disk(25)
#> Class 'disk'
#> [1] 9 49 8 40 12 34 34 45 45 47 21 44 18 38 42 17 14 14 40 41 34 45 7 46 47
random_rsi(25)
#> Class 'rsi'
#> [1] R S R S R I S S R S S R R S R S S S S R I 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] 0.0625 >=64 0.125 1 0.5 >=64 0.002 32 0.0625 0.25
#> [11] 8 0.001 0.0625 8 4 >=64 1 0.025 0.0625 32
#> [21] 0.001 1 0.025 4 1
random_mic(25, "Klebsiella pneumoniae", "meropenem") # range 0.0625-16
#> Class 'mic'
#> [1] 2 4 2 16 <=1 8 4 8 2 16 16 <=1 <=1 <=1 8 16 16 16 8
#> [20] 2 4 2 4 8 8
random_mic(25, "Streptococcus pneumoniae", "meropenem") # range 0.0625-4
#> Class 'mic'
#> [1] 0.5 >=16 8 2 0.25 0.5 8 1 >=16
#> [10] 8 4 2 0.5 0.0625 >=16 <=0.025 0.0625 4
#> [19] 0.125 >=16 0.0625 0.0625 0.125 0.0625 0.25
random_disk(25, "Klebsiella pneumoniae") # range 8-50
#> Class 'disk'
#> [1] 49 43 15 49 11 42 31 22 13 10 9 50 50 30 13 14 33 22 36 27 18 40 31 44 46
random_disk(25, "Klebsiella pneumoniae", "ampicillin") # range 11-17
#> Class 'disk'
#> [1] 15 11 15 16 11 16 12 14 16 17 15 13 12 14 16 17 14 17 17 12 13 16 17 15 11
random_disk(25, "Streptococcus pneumoniae", "ampicillin") # range 12-27
#> Class 'disk'
#> [1] 15 25 25 20 26 23 27 23 23 27 24 27 25 25 16 21 25 26 15 17 26 19 18 18 17
# }