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] 2 1 0.025 0.002 64 0.005 1 <=0.001 0.125
#> [10] 0.5 0.5 >=256 128 0.01 0.002 0.005 64 0.002
#> [19] 1 32 <=0.001 >=256 32 0.5 0.5
random_disk(25)
#> Class 'disk'
#> [1] 40 50 26 30 33 38 49 50 44 43 44 44 23 48 16 23 10 16 44 22 15 45 40 22 42
random_rsi(25)
#> Class 'rsi'
#> [1] I I S I R S R S R I I R S I R R R I I R I S I I R
# \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] 0.125 >=256 0.25 0.002 4 16 0.125 0.5 8 0.002
#> [11] 0.01 16 0.0625 128 2 0.5 0.0625 8 2 0.025
#> [21] 16 32 1 >=256 0.01
random_mic(25, "Klebsiella pneumoniae", "meropenem") # range 0.0625-16
#> Class 'mic'
#> [1] 8 16 16 4 4 1 16 2 1 1 8 <=0.5
#> [13] 32 2 1 <=0.5 1 4 4 1 2 2 8 <=0.5
#> [25] 8
random_mic(25, "Streptococcus pneumoniae", "meropenem") # range 0.0625-4
#> Class 'mic'
#> [1] 16 0.5 0.5 0.25 <=0.125 8 4 2 8
#> [10] 2 4 8 2 1 8 4 0.25 2
#> [19] <=0.125 <=0.125 0.25 8 0.25 0.5 <=0.125
random_disk(25, "Klebsiella pneumoniae") # range 8-50
#> Class 'disk'
#> [1] 44 47 50 45 9 46 47 39 36 41 45 22 49 50 28 50 28 13 16 44 17 10 15 44 23
random_disk(25, "Klebsiella pneumoniae", "ampicillin") # range 11-17
#> Class 'disk'
#> [1] 11 14 11 11 14 16 16 11 11 12 14 15 13 14 16 12 17 15 11 12 15 14 11 16 12
random_disk(25, "Streptococcus pneumoniae", "ampicillin") # range 12-27
#> Class 'disk'
#> [1] 23 25 15 17 25 18 22 20 24 17 15 24 22 23 15 16 27 19 24 21 25 15 15 23 23
# }