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] 128 8 0.5 64 4 0.01 4 0.01 32
#> [10] 2 0.01 >=256 1 0.002 16 <=0.001 128 0.005
#> [19] 0.125 0.25 0.025 >=256 <=0.001 8 4
random_disk(25)
#> Class 'disk'
#> [1] 16 18 44 14 47 45 38 19 47 40 37 30 49 37 49 22 21 44 44 12 14 9 40 49 32
random_rsi(25)
#> Class 'rsi'
#> [1] I I R I S I I R R S I I S I I I R I S R S R S R 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] 0.001 1 0.025 0.5 0.025 4 0.005 8 0.025 0.025 0.01 16
#> [13] 0.001 32 2 0.005 0.001 0.002 32 0.125 16 0.25 128 1
#> [25] 0.025
random_mic(25, "Klebsiella pneumoniae", "meropenem") # range 0.0625-16
#> Class 'mic'
#> [1] 4 2 16 4 2 4 4 4 2 16 8 16 4 4 4 8 1 8 2 8 4 4 1 8 4
random_mic(25, "Streptococcus pneumoniae", "meropenem") # range 0.0625-4
#> Class 'mic'
#> [1] 0.125 1 0.125 2 <=0.0625 1 0.25 2
#> [9] 2 0.5 1 8 4 4 4 2
#> [17] 1 2 2 0.125 1 1 8 0.25
#> [25] 8
random_disk(25, "Klebsiella pneumoniae") # range 8-50
#> Class 'disk'
#> [1] 50 49 18 47 37 43 10 44 46 8 45 47 27 21 44 20 49 47 46 42 26 14 30 42 24
random_disk(25, "Klebsiella pneumoniae", "ampicillin") # range 11-17
#> Class 'disk'
#> [1] 14 11 17 11 13 13 13 11 14 13 17 11 14 15 13 15 17 17 17 12 17 13 12 17 16
random_disk(25, "Streptococcus pneumoniae", "ampicillin") # range 12-27
#> Class 'disk'
#> [1] 18 15 18 20 16 18 27 20 21 26 22 17 17 17 27 23 15 19 20 23 27 27 21 15 26
# }