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] 1 8 8 8 0.25 0.25 0.025 0.01 0.002 0.01
#> [11] >=64 0.5 2 1 0.01 0.0625 1 0.5 >=64 0.025
#> [21] 0.005 0.001 >=64 1 16
random_disk(25)
#> Class 'disk'
#> [1] 23 48 36 18 46 48 41 40 42 42 46 8 45 50 32 37 50 22 20 34 25 9 8 30 45
random_rsi(25)
#> Class 'rsi'
#> [1] I R S R R R I S R R S R S I S S I S R S I I R 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] 0.002 64 0.125 64 1 0.125 0.002 >=256 4
#> [10] 4 0.125 64 >=256 1 1 32 <=0.001 1
#> [19] 0.5 0.01 0.002 <=0.001 0.01 0.25 0.5
random_mic(25, "Klebsiella pneumoniae", "meropenem") # range 0.0625-16
#> Class 'mic'
#> [1] 16 64 4 64 32 8 4 2 4 8 16 4
#> [13] 4 1 32 2 4 64 16 64 <=0.5 8 4 64
#> [25] 2
random_mic(25, "Streptococcus pneumoniae", "meropenem") # range 0.0625-4
#> Class 'mic'
#> [1] 2 0.125 0.5 0.25 0.25 0.125 2 <=0.0625
#> [9] 0.25 >=4 0.5 0.25 0.5 2 1 1
#> [17] 0.25 <=0.0625 0.125 <=0.0625 0.25 0.5 2 1
#> [25] 0.125
random_disk(25, "Klebsiella pneumoniae") # range 8-50
#> Class 'disk'
#> [1] 31 18 17 13 25 50 33 11 43 28 47 34 32 30 10 48 13 11 44 40 46 8 32 19 19
random_disk(25, "Klebsiella pneumoniae", "ampicillin") # range 11-17
#> Class 'disk'
#> [1] 15 16 11 12 11 16 12 11 11 11 14 17 12 14 14 16 16 16 16 17 13 17 15 11 14
random_disk(25, "Streptococcus pneumoniae", "ampicillin") # range 12-27
#> Class 'disk'
#> [1] 25 17 21 26 26 15 18 19 24 23 20 24 18 18 25 24 17 17 25 15 16 20 15 27 21
# }