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] 0.0625 0.125 0.005 0.01 0.125 1 0.5 0.005 8
#> [10] 0.002 0.25 <=0.001 8 128 8 1 0.002 0.025
#> [19] 0.002 0.0625 >=256 128 16 0.125 4
random_disk(25)
#> Class 'disk'
#> [1] 42 13 15 41 49 27 45 44 25 40 42 27 12 47 33 46 43 47 8 29 50 30 46 10 47
random_rsi(25)
#> Class 'rsi'
#> [1] R I S I S S S R I S R I S R I S S S R I I R I R S
# \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] 128 <=0.001 128 0.002 32 0.025 0.5 2 16
#> [10] 0.002 0.25 0.005 16 32 8 0.0625 64 0.5
#> [19] 0.002 4 0.125 64 16 0.01 0.002
random_mic(25, "Klebsiella pneumoniae", "meropenem") # range 0.0625-16
#> Class 'mic'
#> [1] 0.5 16 2 16 4 16 0.5 2 0.25 2 8 4 2 4 0.5
#> [16] 4 0.25 0.25 1 1 1 4 2 16 4
random_mic(25, "Streptococcus pneumoniae", "meropenem") # range 0.0625-4
#> Class 'mic'
#> [1] <=0.025 1 0.5 0.5 0.0625 0.0625 <=0.025 1 0.5
#> [10] <=0.025 2 2 0.5 4 <=0.025 1 4 0.25
#> [19] 0.25 0.0625 4 0.125 2 0.125 0.0625
random_disk(25, "Klebsiella pneumoniae") # range 8-50
#> Class 'disk'
#> [1] 17 10 48 50 9 49 47 33 25 47 24 45 18 10 46 20 48 10 36 48 38 40 28 17 50
random_disk(25, "Klebsiella pneumoniae", "ampicillin") # range 11-17
#> Class 'disk'
#> [1] 17 13 12 11 16 15 15 16 17 14 14 15 15 16 17 15 15 14 13 13 16 11 17 15 14
random_disk(25, "Streptococcus pneumoniae", "ampicillin") # range 12-27
#> Class 'disk'
#> [1] 16 17 20 17 20 16 26 19 20 16 18 22 27 24 16 24 26 26 18 20 18 17 16 15 23
# }