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] 2 0.0625 0.005 8 2 16 16 256 0.5 32
#> [11] 0.25 0.005 0.125 0.01 8 0.002 4 256 0.5 8
#> [21] 128 2 16 64 0.025
random_disk(25)
#> Class 'disk'
#> [1] 10 46 14 41 48 36 46 11 6 23 45 46 50 17 45 32 19 18 49 43 40 47 49 44 48
random_rsi(25)
#> Class 'rsi'
#> [1] S I I S I I I I R R I I I R I S R S I S I I R R 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] 1 0.001 0.25 0.005 0.002 0.005 4 1 0.01 4 256 0.25
#> [13] 16 128 2 0.25 0.001 8 0.25 8 0.005 256 0.5 1
#> [25] 8
random_mic(25, "Klebsiella pneumoniae", "meropenem") # range 0.0625-16
#> Class 'mic'
#> [1] >=16 2 4 4 2 >=16 1 4 >=16 8 1 8 2 >=16 >=16
#> [16] 2 4 8 2 2 >=16 4 4 4 8
random_mic(25, "Streptococcus pneumoniae", "meropenem") # range 0.0625-4
#> Class 'mic'
#> [1] <=0.025 0.5 0.25 >=16 <=0.025 <=0.025 0.5 >=16 <=0.025
#> [10] <=0.025 <=0.025 0.125 0.5 4 2 >=16 8 0.5
#> [19] 0.25 1 1 0.25 0.25 0.25 0.25
random_disk(25, "Klebsiella pneumoniae") # range 8-50
#> Class 'disk'
#> [1] 43 40 37 45 48 39 40 9 41 36 15 22 20 50 30 12 12 45 34 40 24 41 35 41 15
random_disk(25, "Klebsiella pneumoniae", "ampicillin") # range 11-17
#> Class 'disk'
#> [1] 13 15 14 17 17 12 16 11 13 12 17 13 11 12 17 11 12 14 14 13 15 16 13 16 12
random_disk(25, "Streptococcus pneumoniae", "ampicillin") # range 12-27
#> Class 'disk'
#> [1] 18 17 26 27 27 15 20 26 20 23 27 23 22 21 17 16 18 23 20 20 19 19 23 18 23
# }