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] 64 0.0625 0.025 0.25 0.025 0.01 0.005 128 64
#> [10] 64 64 32 0.125 0.002 0.005 64 0.0625 0.025
#> [19] 0.125 128 0.0625 <=0.001 0.002 0.0625 0.25
random_disk(25)
#> Class 'disk'
#> [1] 15 47 11 44 36 21 24 31 13 40 21 42 33 36 18 41 40 15 19 26 48 8 11 37 46
random_rsi(25)
#> Class 'rsi'
#> [1] S I S R R I S R I R I R R R I R I R S R R R I S 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] 0.025 0.5 0.01 16 8 0.0625 <=0.001 0.0625 0.025
#> [10] 4 8 <=0.001 0.002 4 <=0.001 0.0625 8 1
#> [19] 0.01 0.01 <=0.001 0.002 0.025 2 0.5
random_mic(25, "Klebsiella pneumoniae", "meropenem") # range 0.0625-16
#> Class 'mic'
#> [1] 4 16 16 8 16 1 8 8 4 16 4 16
#> [13] 1 <=0.5 4 <=0.5 16 1 2 8 16 <=0.5 2 4
#> [25] 2
random_mic(25, "Streptococcus pneumoniae", "meropenem") # range 0.0625-4
#> Class 'mic'
#> [1] 1 2 4 0.25 <=0.0625 16 <=0.0625 4
#> [9] 0.5 0.125 8 1 0.25 0.5 8 0.125
#> [17] <=0.0625 0.125 0.25 0.25 0.5 16 0.125 0.125
#> [25] <=0.0625
random_disk(25, "Klebsiella pneumoniae") # range 8-50
#> Class 'disk'
#> [1] 47 26 37 31 35 32 48 43 11 17 25 20 47 27 30 44 48 41 47 46 45 37 41 13 28
random_disk(25, "Klebsiella pneumoniae", "ampicillin") # range 11-17
#> Class 'disk'
#> [1] 13 16 14 12 17 11 14 11 12 11 16 12 16 11 16 12 14 17 12 13 14 15 17 15 11
random_disk(25, "Streptococcus pneumoniae", "ampicillin") # range 12-27
#> Class 'disk'
#> [1] 17 22 20 23 18 16 19 27 17 16 24 16 27 16 17 17 15 19 15 15 20 22 24 21 20
# }