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 agent, 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 agent 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] >=256 0.125 1 0.01 0.01 0.001 32 4 32 0.01 0.125 0.001
#> [13] 0.25 0.002 0.025 0.125 4 0.002 0.01 128 0.5 0.005 0.125 0.001
#> [25] 16
random_disk(25)
#> Class 'disk'
#> [1] 29 26 25 49 46 40 38 32 38 49 15 50 16 40 15 27 12 6 22 11 13 17 26 24 47
random_rsi(25)
#> Class 'rsi'
#> [1] R S S R I S S I R I S R I R I R R S S I R 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] 0.25 0.125 0.125 32 16 0.5 0.001 8 0.025 4
#> [11] 0.5 0.001 16 0.01 16 1 >=64 0.025 0.025 0.25
#> [21] 32 0.25 32 0.005 0.0625
random_mic(25, "Klebsiella pneumoniae", "meropenem") # range 0.0625-16
#> Class 'mic'
#> [1] <=1 16 16 4 2 <=1 <=1 8 8 2 <=1 16 <=1 2 <=1 4 16 16 8
#> [20] 8 16 16 4 2 4
random_mic(25, "Streptococcus pneumoniae", "meropenem") # range 0.0625-4
#> Class 'mic'
#> [1] 2 0.025 1 2 2 0.5 2 2 0.25 0.25
#> [11] 0.25 1 2 0.125 0.0625 0.125 0.25 0.025 2 >=4
#> [21] 0.025 0.025 >=4 0.025 0.25
random_disk(25, "Klebsiella pneumoniae") # range 8-50
#> Class 'disk'
#> [1] 22 21 48 15 14 28 48 36 43 24 14 42 41 43 8 10 31 9 47 41 26 41 19 50 35
random_disk(25, "Klebsiella pneumoniae", "ampicillin") # range 11-17
#> Class 'disk'
#> [1] 13 17 14 16 12 17 15 11 16 13 16 15 17 11 15 14 11 15 17 16 13 11 16 14 11
random_disk(25, "Streptococcus pneumoniae", "ampicillin") # range 12-27
#> Class 'disk'
#> [1] 15 20 26 20 21 21 24 19 21 20 17 27 21 20 17 20 23 15 21 17 17 24 16 17 16
# }