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 >=128 0.025 2 4 0.01 1 1 0.125 0.002 0.005 0.005
#> [13] 16 0.001 0.025 2 0.25 0.5 0.025 1 4 32 0.125 8
#> [25] 64
random_disk(25)
#> Class 'disk'
#> [1] 44 7 42 29 31 9 22 11 14 45 33 7 45 44 6 46 6 14 48 7 41 34 44 6 43
random_rsi(25)
#> Class 'rsi'
#> [1] S S S R I S R S I R R I I R R S I R S R R 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] 2 0.25 2 0.5 256 2 1 16 0.0625
#> [10] 0.005 <=0.001 32 16 256 4 0.005 0.0625 2
#> [19] 4 128 1 8 0.0625 0.125 0.0625
random_mic(25, "Klebsiella pneumoniae", "meropenem") # range 0.0625-16
#> Class 'mic'
#> [1] 0.5 4 16 0.5 0.5 1 16 16 2 32 16 4 0.5 1 1 1 4 16 1
#> [20] 16 8 8 0.5 16 8
random_mic(25, "Streptococcus pneumoniae", "meropenem") # range 0.0625-4
#> Class 'mic'
#> [1] >=16 >=16 2 <=0.125 >=16 2 1 <=0.125 1
#> [10] 8 4 4 0.25 0.5 2 2 4 8
#> [19] 0.25 8 1 8 2 0.25 0.25
random_disk(25, "Klebsiella pneumoniae") # range 8-50
#> Class 'disk'
#> [1] 38 45 43 20 45 28 12 21 15 46 35 46 45 25 18 16 47 40 35 36 14 21 24 25 8
random_disk(25, "Klebsiella pneumoniae", "ampicillin") # range 11-17
#> Class 'disk'
#> [1] 15 13 16 17 17 13 15 17 11 17 16 15 11 13 15 11 11 13 13 11 13 11 15 16 17
random_disk(25, "Streptococcus pneumoniae", "ampicillin") # range 12-27
#> Class 'disk'
#> [1] 24 24 17 16 26 16 22 20 26 19 24 15 22 21 23 15 17 21 22 16 21 24 20 17 18
# }