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 drug, 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 drug 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 16 0.005 128 >=256 >=256 1 1 32
#> [11] 32 0.002 0.01 0.125 0.0625 32 0.001 128 0.001 0.005
#> [21] 0.25 1 2 32 4
random_disk(25)
#> Class 'disk'
#> [1] 34 41 31 43 38 34 43 31 11 44 49 9 45 6 36 43 48 43 34 47 16 35 41 40 20
random_rsi(25)
#> Class 'rsi'
#> [1] R R I I S S I S I I S S S R I I R I S S I R R S 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] <=0.002 16 0.5 0.005 4 0.0625 16 0.005 0.25
#> [10] >=64 0.25 0.005 >=64 2 16 0.0625 0.25 4
#> [19] >=64 0.5 32 16 4 1 8
random_mic(25, "Klebsiella pneumoniae", "meropenem") # range 0.0625-16
#> Class 'mic'
#> [1] 32 1 1 2 32 16 2 0.25 0.25 0.25 1 16 8 4 32
#> [16] 2 2 16 >=64 0.25 >=64 0.25 16 8 1
random_mic(25, "Streptococcus pneumoniae", "meropenem") # range 0.0625-4
#> Class 'mic'
#> [1] 0.25 0.25 16 0.25 2 2 0.25 8 0.125 0.0625
#> [11] 0.0625 8 0.5 2 2 0.5 0.125 4 1 0.0625
#> [21] 0.025 0.025 8 0.025 16
random_disk(25, "Klebsiella pneumoniae") # range 8-50
#> Class 'disk'
#> [1] 49 12 30 41 48 26 42 39 50 38 47 25 46 30 45 40 18 50 10 41 16 40 28 15 43
random_disk(25, "Klebsiella pneumoniae", "ampicillin") # range 11-17
#> Class 'disk'
#> [1] 17 11 14 14 12 17 17 14 12 11 15 16 15 16 11 17 12 11 13 17 12 12 14 15 15
random_disk(25, "Streptococcus pneumoniae", "ampicillin") # range 12-27
#> Class 'disk'
#> [1] 25 17 21 16 18 24 16 17 18 21 20 22 19 19 19 26 24 17 26 15 24 23 24 20 23
# }