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] 0.005 1 0.001 0.025 64 1 16 8 8 64 0.002 4
#> [13] 8 32 0.001 1 16 0.025 0.125 0.125 2 1 0.025 0.25
#> [25] 8
random_disk(25)
#> Class 'disk'
#> [1] 37 44 22 48 24 19 46 27 48 14 15 42 48 37 44 10 45 14 38 37 42 16 50 45 46
random_rsi(25)
#> Class 'rsi'
#> [1] I R I S R I I S I S R R S S S R R R I R I S 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] 0.5 0.01 32 0.125 <=0.001 64 0.025 0.125 8
#> [10] 8 1 0.25 8 0.25 1 1 16 4
#> [19] 0.25 0.0625 0.025 0.025 0.5 0.025 64
random_mic(25, "Klebsiella pneumoniae", "meropenem") # range 0.0625-16
#> Class 'mic'
#> [1] 4 1 1 8 8 4 >=16 4 4 8
#> [11] 8 <=0.25 2 4 >=16 <=0.25 0.5 2 1 8
#> [21] 1 2 0.5 4 >=16
random_mic(25, "Streptococcus pneumoniae", "meropenem") # range 0.0625-4
#> Class 'mic'
#> [1] 1 0.25 2 0.125 2 2 2 4 0.25 2 1 0.5
#> [13] 4 8 2 8 0.5 1 8 4 4 0.25 2 1
#> [25] >=16
random_disk(25, "Klebsiella pneumoniae") # range 8-50
#> Class 'disk'
#> [1] 46 29 42 21 45 46 44 26 15 19 40 14 38 48 19 49 46 13 21 44 21 36 13 41 42
random_disk(25, "Klebsiella pneumoniae", "ampicillin") # range 11-17
#> Class 'disk'
#> [1] 14 13 11 11 12 15 14 13 15 11 15 17 16 13 13 13 11 11 16 17 15 17 16 13 14
random_disk(25, "Streptococcus pneumoniae", "ampicillin") # range 12-27
#> Class 'disk'
#> [1] 25 23 16 16 27 17 27 17 23 22 26 19 21 17 18 20 17 18 21 19 23 23 27 18 23
# }