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] 256 128 1 1 256 1 4 0.025 1 0.125 0.002 256
#> [13] 32 0.001 0.001 0.002 16 0.025 0.002 16 8 4 4 8
#> [25] 0.001
random_disk(25)
#> Class 'disk'
#> [1] 47 47 17 39 50 23 19 41 43 35 22 45 23 45 15 48 22 36 12 33 39 47 8 14 45
random_rsi(25)
#> Class 'rsi'
#> [1] R S I I S R S S I S R R S S S I R I S S S I 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] 0.25 0.01 0.005 8 1 128 0.125 32 0.5 0.01 0.005 64
#> [13] 4 0.125 0.125 8 16 128 8 256 0.001 0.125 128 0.025
#> [25] 16
random_mic(25, "Klebsiella pneumoniae", "meropenem") # range 0.0625-16
#> Class 'mic'
#> [1] 32 4 0.5 4 2 16 1 8 1 0.5 4 0.5 4 32 16 32 0.5 8 8
#> [20] 16 4 1 8 1 16
random_mic(25, "Streptococcus pneumoniae", "meropenem") # range 0.0625-4
#> Class 'mic'
#> [1] 16 8 16 16 8 16 8 <=0.0625
#> [9] 1 <=0.0625 0.25 0.25 16 8 1 16
#> [17] 0.125 <=0.0625 1 0.25 16 <=0.0625 2 1
#> [25] 2
random_disk(25, "Klebsiella pneumoniae") # range 8-50
#> Class 'disk'
#> [1] 46 39 20 40 25 36 19 24 44 49 13 35 23 12 25 18 30 26 48 37 50 35 15 35 42
random_disk(25, "Klebsiella pneumoniae", "ampicillin") # range 11-17
#> Class 'disk'
#> [1] 13 13 14 16 14 12 12 12 13 11 11 17 16 15 13 14 11 11 15 15 13 13 13 13 14
random_disk(25, "Streptococcus pneumoniae", "ampicillin") # range 12-27
#> Class 'disk'
#> [1] 21 16 23 24 22 19 15 24 17 24 16 19 15 17 15 26 15 26 21 22 15 20 20 23 18
# }