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] 4 4 4 128 8 4 0.0625 0.25 0.5 2
#> [11] 4 64 0.0625 32 0.25 0.001 0.001 0.025 0.001 >=256
#> [21] 4 0.025 0.5 4 0.025
random_disk(25)
#> Class 'disk'
#> [1] 32 46 50 35 15 7 42 27 21 15 8 36 30 46 47 43 42 50 32 34 21 43 21 28 43
random_rsi(25)
#> Class 'rsi'
#> [1] R I I S S R S I S R R S I S S I R I R I S S S S 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] 128 32 0.025 0.25 0.125 0.01 <=0.001 1 0.25
#> [10] 1 0.005 0.025 0.0625 128 0.5 0.005 0.0625 0.005
#> [19] <=0.001 128 4 0.5 0.002 0.25 0.01
random_mic(25, "Klebsiella pneumoniae", "meropenem") # range 0.0625-16
#> Class 'mic'
#> [1] 0.5 8 8 0.5 0.5 2 4 >=16 0.5 4 8 >=16 0.5 >=16 2
#> [16] >=16 1 8 1 4 4 >=16 >=16 >=16 0.5
random_mic(25, "Streptococcus pneumoniae", "meropenem") # range 0.0625-4
#> Class 'mic'
#> [1] 1 2 0.125 0.5 0.5 0.25 2 0.125 2 1
#> [11] 0.125 0.125 4 8 0.25 0.125 4 0.5 2 0.0625
#> [21] 4 0.5 1 >=16 1
random_disk(25, "Klebsiella pneumoniae") # range 8-50
#> Class 'disk'
#> [1] 11 41 18 50 12 39 48 47 25 23 19 14 14 36 46 21 46 18 17 50 26 20 33 12 44
random_disk(25, "Klebsiella pneumoniae", "ampicillin") # range 11-17
#> Class 'disk'
#> [1] 11 16 14 13 11 17 16 12 14 12 13 13 17 13 15 15 16 13 11 15 11 16 11 16 11
random_disk(25, "Streptococcus pneumoniae", "ampicillin") # range 12-27
#> Class 'disk'
#> [1] 24 22 18 26 22 20 27 27 20 18 24 26 25 20 20 25 19 19 25 20 18 25 16 20 17
# }