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] 2 0.002 0.5 0.5 0.125 0.25 32 0.0625 0.002 0.025
#> [11] 16 0.125 8 0.002 4 8 0.0625 8 8 1
#> [21] 0.001 0.002 0.01 4 64
random_disk(25)
#> Class 'disk'
#> [1] 24 44 41 19 45 23 10 41 41 41 44 35 33 48 10 19 33 28 22 17 41 32 49 45 10
random_rsi(25)
#> Class 'rsi'
#> [1] S I R S S S I I R I S S I I R I R S S R I I R R 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] 0.01 32 8 2 0.005 0.002 0.005 0.025 1 0.5
#> [11] 0.125 1 0.01 1 4 0.0625 0.025 0.5 0.125 >=64
#> [21] 16 0.5 1 4 0.001
random_mic(25, "Klebsiella pneumoniae", "meropenem") # range 0.0625-16
#> Class 'mic'
#> [1] <=1 <=1 <=1 4 4 16 16 4 <=1 8 4 16 <=1 2 2 16 8 16 2
#> [20] 4 2 4 4 4 4
random_mic(25, "Streptococcus pneumoniae", "meropenem") # range 0.0625-4
#> Class 'mic'
#> [1] 8 >=16 0.125 0.0625 1 0.0625 0.125 2 >=16
#> [10] 2 <=0.025 1 2 8 1 0.25 0.0625 >=16
#> [19] 8 1 0.5 >=16 0.125 >=16 8
random_disk(25, "Klebsiella pneumoniae") # range 8-50
#> Class 'disk'
#> [1] 28 26 38 49 10 27 11 35 47 12 8 45 33 18 8 44 43 21 23 28 48 47 47 24 11
random_disk(25, "Klebsiella pneumoniae", "ampicillin") # range 11-17
#> Class 'disk'
#> [1] 13 16 16 15 14 13 12 15 12 16 14 15 17 11 13 13 14 17 13 14 17 12 14 11 17
random_disk(25, "Streptococcus pneumoniae", "ampicillin") # range 12-27
#> Class 'disk'
#> [1] 17 21 25 24 22 27 15 21 15 26 16 27 26 27 20 17 15 18 17 19 16 20 16 17 19
# }