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 0.25 8 0.025 0.01 2 0.025 8 64 256
#> [11] 256 0.0625 128 0.005 64 1 256 4 16 8
#> [21] 256 8 0.001 4 32
random_disk(25)
#> Class 'disk'
#> [1] 41 32 18 50 41 40 44 26 32 22 48 24 42 49 7 16 19 15 39 9 50 46 27 41 19
random_rsi(25)
#> Class 'rsi'
#> [1] R R I I S I R I I R I I S I R S R S R R I R I I 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] <=0.005 8 0.0625 1 0.125 0.025 0.125 0.025 0.025
#> [10] 0.01 0.5 0.125 16 2 64 16 0.0625 0.5
#> [19] 32 0.0625 4 64 0.0625 >=128 <=0.005
random_mic(25, "Klebsiella pneumoniae", "meropenem") # range 0.0625-16
#> Class 'mic'
#> [1] 0.25 4 4 8 4 0.5 32 8 32 8 64 4 2 8 64
#> [16] 16 0.25 4 0.5 2 8 2 16 4 4
random_mic(25, "Streptococcus pneumoniae", "meropenem") # range 0.0625-4
#> Class 'mic'
#> [1] 0.125 0.5 4 8 1 1 0.5 8 0.25 0.25 0.125 2
#> [13] 0.5 8 0.5 0.125 0.125 2 0.25 8 4 2 0.125 0.25
#> [25] 8
random_disk(25, "Klebsiella pneumoniae") # range 8-50
#> Class 'disk'
#> [1] 33 38 45 45 16 20 31 36 34 30 44 26 18 37 31 48 8 38 50 35 9 22 49 46 23
random_disk(25, "Klebsiella pneumoniae", "ampicillin") # range 11-17
#> Class 'disk'
#> [1] 16 13 12 16 14 17 16 17 11 12 14 17 12 12 14 13 16 15 13 12 12 12 16 15 17
random_disk(25, "Streptococcus pneumoniae", "ampicillin") # range 12-27
#> Class 'disk'
#> [1] 26 15 18 19 17 15 26 25 18 19 23 16 16 15 24 15 21 22 26 25 24 22 24 21 25
# }