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 0.25 0.002 0.0625 128 256 1 4 1
#> [10] 128 <=0.001 0.0625 64 0.0625 0.125 0.025 0.25 0.002
#> [19] 0.5 8 64 128 0.025 8 256
random_disk(25)
#> Class 'disk'
#> [1] 50 37 18 41 39 28 16 24 31 40 13 12 46 25 6 27 21 45 13 43 15 21 36 27 21
random_rsi(25)
#> Class 'rsi'
#> [1] R S I R R R R S I S I S S S R S I I S S R R S 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] 4 64 0.025 0.025 64 0.01 128 >=256 0.5
#> [10] 2 0.125 0.0625 16 0.005 0.002 0.25 0.002 8
#> [19] 0.25 8 <=0.001 4 <=0.001 0.125 2
random_mic(25, "Klebsiella pneumoniae", "meropenem") # range 0.0625-16
#> Class 'mic'
#> [1] 4 2 4 <=1 <=1 8 8 16 4 4 2 <=1 <=1 16 4 <=1 16 16 4
#> [20] <=1 8 16 16 16 4
random_mic(25, "Streptococcus pneumoniae", "meropenem") # range 0.0625-4
#> Class 'mic'
#> [1] 0.5 1 0.5 0.5 0.0625 2 1 0.5 0.5 0.0625
#> [11] 1 0.25 0.125 2 0.25 2 0.125 1 0.0625 0.25
#> [21] >=4 1 0.125 1 0.0625
random_disk(25, "Klebsiella pneumoniae") # range 8-50
#> Class 'disk'
#> [1] 42 48 22 13 8 14 38 49 12 38 37 21 41 11 48 44 34 27 33 41 10 44 36 11 42
random_disk(25, "Klebsiella pneumoniae", "ampicillin") # range 11-17
#> Class 'disk'
#> [1] 11 17 12 17 17 14 15 17 16 16 16 15 16 12 13 12 15 12 12 11 13 14 17 13 16
random_disk(25, "Streptococcus pneumoniae", "ampicillin") # range 12-27
#> Class 'disk'
#> [1] 19 27 24 21 24 19 16 17 19 22 26 24 18 25 22 27 20 24 24 19 27 26 21 27 21
# }