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] 16 0.25 0.005 0.002 256 0.01 256 16 0.001 256
#> [11] 8 0.0625 1 16 0.01 0.005 0.25 0.0625 32 0.025
#> [21] 16 4 4 4 0.002
random_disk(25)
#> Class 'disk'
#> [1] 16 42 16 44 9 49 50 44 43 44 43 46 14 26 47 44 24 27 50 14 9 36 45 16 50
random_rsi(25)
#> Class 'rsi'
#> [1] S S I I I R S S R S I I R R S S I R I S I I I S 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] 0.025 0.005 0.0625 4 64 0.0625 2 0.01 16
#> [10] 0.005 64 128 0.25 <=0.002 0.025 <=0.002 0.01 1
#> [19] 64 0.5 128 0.01 16 4 16
random_mic(25, "Klebsiella pneumoniae", "meropenem") # range 0.0625-16
#> Class 'mic'
#> [1] 4 0.25 0.5 16 >=32 2 4 0.25 4 >=32 8 2 1 1 0.25
#> [16] 4 4 0.5 16 16 8 8 8 0.25 0.5
random_mic(25, "Streptococcus pneumoniae", "meropenem") # range 0.0625-4
#> Class 'mic'
#> [1] >=8 2 4 0.025 0.0625 2 0.5 0.25 4 >=8
#> [11] 4 0.025 2 1 0.0625 0.125 >=8 2 0.5 0.25
#> [21] 0.125 1 1 0.25 0.125
random_disk(25, "Klebsiella pneumoniae") # range 8-50
#> Class 'disk'
#> [1] 47 43 32 46 48 46 19 16 46 34 34 8 42 44 49 39 27 18 33 21 15 41 41 10 43
random_disk(25, "Klebsiella pneumoniae", "ampicillin") # range 11-17
#> Class 'disk'
#> [1] 12 11 16 17 15 16 16 11 15 17 17 11 13 16 14 15 17 15 13 11 13 14 15 15 17
random_disk(25, "Streptococcus pneumoniae", "ampicillin") # range 12-27
#> Class 'disk'
#> [1] 22 17 26 18 27 26 15 17 22 15 17 27 23 15 17 23 23 25 25 18 18 26 20 26 27
# }