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] 16 16 0.125 0.0625 256 0.125 256 <=0.001 0.025
#> [10] 0.005 16 0.01 0.5 0.002 128 0.0625 0.025 0.5
#> [19] 0.01 0.125 128 1 128 0.005 4
random_disk(25)
#> Class 'disk'
#> [1] 49 27 35 49 28 36 14 43 14 22 36 45 40 39 42 16 25 31 44 21 43 28 17 21 47
random_rsi(25)
#> Class 'rsi'
#> [1] S S S S I R R R R S R I R I S R I S S R R I I 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] 0.0625 0.005 1 0.0625 4 0.5 2 8 2
#> [10] >=64 >=64 1 1 4 16 2 <=0.001 0.005
#> [19] 0.125 0.025 0.002 8 0.5 0.125 1
random_mic(25, "Klebsiella pneumoniae", "meropenem") # range 0.0625-16
#> Class 'mic'
#> [1] 16 16 2 2 8 >=32 4 <=0.5 <=0.5 16 <=0.5 8
#> [13] 2 2 1 2 1 <=0.5 2 2 1 1 16 4
#> [25] <=0.5
random_mic(25, "Streptococcus pneumoniae", "meropenem") # range 0.0625-4
#> Class 'mic'
#> [1] 1 8 16 4 0.25 1 4 2 0.125 4
#> [11] 2 8 0.0625 0.0625 16 8 0.0625 1 1 0.25
#> [21] 0.5 0.25 0.25 0.25 1
random_disk(25, "Klebsiella pneumoniae") # range 8-50
#> Class 'disk'
#> [1] 26 31 9 31 44 38 45 43 14 30 14 46 25 17 36 30 34 25 11 29 29 12 23 21 44
random_disk(25, "Klebsiella pneumoniae", "ampicillin") # range 11-17
#> Class 'disk'
#> [1] 17 13 13 13 17 13 17 14 15 11 12 15 16 16 11 12 14 11 11 11 17 15 16 11 11
random_disk(25, "Streptococcus pneumoniae", "ampicillin") # range 12-27
#> Class 'disk'
#> [1] 27 19 22 23 16 22 27 21 26 19 16 16 18 26 25 23 19 16 17 27 26 16 23 16 20
# }