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] 8 64 1 128 0.25 <=0.001 0.25 0.01 0.025
#> [10] 128 <=0.001 128 >=256 2 0.025 8 >=256 0.002
#> [19] 1 0.5 0.25 2 <=0.001 1 2
random_disk(25)
#> Class 'disk'
#> [1] 7 18 38 42 43 47 45 10 45 24 17 15 24 45 26 23 44 50 45 50 19 28 25 47 11
random_rsi(25)
#> Class 'rsi'
#> [1] R S R I I R I R R R I R I I S I I S I R I R R I 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] 0.025 0.001 2 0.5 8 0.01 0.005 32 256 4
#> [11] 0.025 0.025 0.025 0.002 0.25 4 1 0.0625 0.025 0.0625
#> [21] 2 8 0.002 0.5 16
random_mic(25, "Klebsiella pneumoniae", "meropenem") # range 0.0625-16
#> Class 'mic'
#> [1] >=64 32 1 <=0.5 16 1 16 2 1 1 32 2
#> [13] <=0.5 2 32 2 8 4 16 32 2 1 4 1
#> [25] 8
random_mic(25, "Streptococcus pneumoniae", "meropenem") # range 0.0625-4
#> Class 'mic'
#> [1] 0.125 >=4 0.5 1 1 0.5 1 0.125 0.125 0.25 0.125 1
#> [13] 0.25 0.125 0.5 0.5 0.125 >=4 >=4 2 >=4 0.5 2 1
#> [25] 2
random_disk(25, "Klebsiella pneumoniae") # range 8-50
#> Class 'disk'
#> [1] 42 28 19 47 45 39 48 47 43 30 43 37 43 34 16 45 36 22 26 25 11 28 17 11 41
random_disk(25, "Klebsiella pneumoniae", "ampicillin") # range 11-17
#> Class 'disk'
#> [1] 13 16 12 16 14 12 15 14 12 11 13 16 12 14 16 12 13 12 17 16 11 14 12 13 15
random_disk(25, "Streptococcus pneumoniae", "ampicillin") # range 12-27
#> Class 'disk'
#> [1] 25 18 19 19 27 25 18 24 27 23 18 17 16 27 26 15 25 26 24 26 15 17 26 20 16
# }