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 agent, 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 agent 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] 0.125 0.01 2 0.5 8 1 2 2 0.5 0.5 0.001 4
#> [13] 0.002 0.25 1 0.005 64 64 0.5 4 128 0.002 0.01 64
#> [25] 32
random_disk(25)
#> Class 'disk'
#> [1] 21 40 49 45 11 23 49 42 12 7 44 50 23 47 41 27 47 50 33 18 18 38 21 40 12
random_rsi(25)
#> Class 'rsi'
#> [1] R R I R R I I R I S I R S S R S I I R S S I R R 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] 16 0.025 128 0.5 0.002 4 0.125 0.125 0.5 8 0.01 0.001
#> [13] 8 2 64 0.5 0.5 0.025 0.01 8 0.125 0.5 0.5 2
#> [25] 4
random_mic(25, "Klebsiella pneumoniae", "meropenem") # range 0.0625-16
#> Class 'mic'
#> [1] 4 16 2 2 2 8 8 2 4 1 2 1 1 4 1 1 16 8 16 4 2 8 1 2 4
random_mic(25, "Streptococcus pneumoniae", "meropenem") # range 0.0625-4
#> Class 'mic'
#> [1] 4 0.25 0.125 0.0625 0.125 0.125 4 1 2
#> [10] 0.25 0.125 0.5 <=0.025 0.25 2 <=0.025 0.125 4
#> [19] 0.0625 4 0.25 2 <=0.025 0.25 0.25
random_disk(25, "Klebsiella pneumoniae") # range 8-50
#> Class 'disk'
#> [1] 8 31 45 32 40 26 48 46 43 10 41 45 33 23 41 25 26 18 16 16 49 26 14 21 10
random_disk(25, "Klebsiella pneumoniae", "ampicillin") # range 11-17
#> Class 'disk'
#> [1] 13 15 13 13 17 14 11 15 11 12 15 15 15 12 14 13 16 16 15 14 15 16 16 16 16
random_disk(25, "Streptococcus pneumoniae", "ampicillin") # range 12-27
#> Class 'disk'
#> [1] 19 22 23 20 25 24 26 24 27 18 22 21 22 26 25 24 15 15 22 20 22 22 20 25 21
# }