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] 0.005 0.025 16 0.002 1 1 8 2 64 1
#> [11] 0.125 8 256 0.001 0.0625 4 4 16 0.01 0.025
#> [21] 0.125 16 8 0.005 256
random_disk(25)
#> Class 'disk'
#> [1] 43 42 49 41 7 15 8 46 35 41 14 32 43 26 27 21 45 38 49 50 37 45 6 28 20
random_rsi(25)
#> Class 'rsi'
#> [1] I S S R S R I I I I I R I I S S S R R I S S I S 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] 8 0.0625 0.25 64 0.5 16 0.005 0.125 0.025
#> [10] 4 4 0.5 1 0.025 2 0.025 32 0.0625
#> [19] <=0.002 0.005 1 0.5 4 32 0.01
random_mic(25, "Klebsiella pneumoniae", "meropenem") # range 0.0625-16
#> Class 'mic'
#> [1] 8 4 16 16 2 8 16 16 8 16 16 2 <=1 16 4 <=1 16 <=1 8
#> [20] 16 2 16 <=1 8 4
random_mic(25, "Streptococcus pneumoniae", "meropenem") # range 0.0625-4
#> Class 'mic'
#> [1] <=0.125 0.25 >=4 1 1 0.5 <=0.125 0.25 >=4
#> [10] 0.25 1 0.25 >=4 0.5 2 >=4 >=4 0.5
#> [19] 2 <=0.125 1 0.25 2 <=0.125 >=4
random_disk(25, "Klebsiella pneumoniae") # range 8-50
#> Class 'disk'
#> [1] 27 23 48 33 20 30 48 15 19 46 27 14 27 39 10 50 23 50 11 37 29 35 33 12 18
random_disk(25, "Klebsiella pneumoniae", "ampicillin") # range 11-17
#> Class 'disk'
#> [1] 14 14 14 16 13 15 17 12 14 11 11 14 13 11 17 17 17 16 17 17 17 17 13 15 17
random_disk(25, "Streptococcus pneumoniae", "ampicillin") # range 12-27
#> Class 'disk'
#> [1] 25 16 20 15 23 26 16 22 15 22 15 15 25 20 20 20 15 24 15 25 15 21 20 18 25
# }