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] <=0.001 32 0.005 0.25 0.5 128 8 0.0625 2
#> [10] 0.0625 64 8 4 0.025 0.25 32 0.5 <=0.001
#> [19] 256 0.0625 4 0.01 0.01 0.025 1
random_disk(25)
#> Class 'disk'
#> [1] 29 20 39 43 38 39 11 22 49 47 44 14 10 36 7 14 44 7 24 6 32 47 28 7 27
random_rsi(25)
#> Class 'rsi'
#> [1] I S I R R R R S I R S S I R I I S S R I R S S I 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] 16 16 0.025 4 1 4 64 0.005 2 64
#> [11] 2 0.002 0.025 0.001 0.0625 64 0.5 8 0.025 8
#> [21] 2 0.01 16 4 0.025
random_mic(25, "Klebsiella pneumoniae", "meropenem") # range 0.0625-16
#> Class 'mic'
#> [1] 4 2 0.5 1 0.5 <=0.25 <=0.25 2 0.5 2
#> [11] 4 <=0.25 4 >=16 0.5 0.5 0.5 2 >=16 2
#> [21] <=0.25 <=0.25 <=0.25 >=16 2
random_mic(25, "Streptococcus pneumoniae", "meropenem") # range 0.0625-4
#> Class 'mic'
#> [1] 1 0.25 0.5 0.125 0.0625 0.125 2 >=4 0.5 0.0625
#> [11] >=4 >=4 0.025 0.025 0.025 2 0.0625 0.025 0.125 0.025
#> [21] 1 0.025 0.125 0.25 0.0625
random_disk(25, "Klebsiella pneumoniae") # range 8-50
#> Class 'disk'
#> [1] 43 40 12 49 41 42 44 39 47 30 11 33 9 45 36 30 50 19 50 33 40 18 50 45 38
random_disk(25, "Klebsiella pneumoniae", "ampicillin") # range 11-17
#> Class 'disk'
#> [1] 14 12 14 17 11 14 12 12 17 11 13 16 16 11 17 15 15 13 14 11 13 16 12 14 12
random_disk(25, "Streptococcus pneumoniae", "ampicillin") # range 12-27
#> Class 'disk'
#> [1] 26 25 22 25 21 25 20 16 21 17 26 24 24 22 24 21 17 16 15 25 20 22 18 16 27
# }