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] 0.125 0.01 32 1 16 256 32 0.01 64 0.005
#> [11] 1 32 256 0.0625 0.0625 1 32 1 0.125 1
#> [21] 0.0625 0.005 32 1 0.0625
random_disk(25)
#> Class 'disk'
#> [1] 38 34 36 19 43 49 42 38 43 49 28 27 13 35 50 21 42 48 13 46 13 7 45 18 42
random_rsi(25)
#> Class 'rsi'
#> [1] I R R I R I I I S I I R R R R R R I R S R R S I 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 0.25 2 >=128 0.025 0.025 32 0.5 0.002
#> [10] 2 0.0625 32 0.005 0.005 64 0.25 2 64
#> [19] 8 <=0.001 <=0.001 16 0.5 0.005 0.025
random_mic(25, "Klebsiella pneumoniae", "meropenem") # range 0.0625-16
#> Class 'mic'
#> [1] <=1 2 32 2 32 2 8 16 16 4 32 16 4 32 16 4 2 8 <=1
#> [20] 32 4 2 16 4 2
random_mic(25, "Streptococcus pneumoniae", "meropenem") # range 0.0625-4
#> Class 'mic'
#> [1] 1 >=8 1 4 4 1 0.025 0.125 0.5 >=8
#> [11] 0.0625 0.025 4 0.25 0.25 0.5 0.125 0.0625 1 0.0625
#> [21] 2 0.5 0.5 0.0625 1
random_disk(25, "Klebsiella pneumoniae") # range 8-50
#> Class 'disk'
#> [1] 40 27 35 42 49 47 43 26 29 28 14 8 24 40 23 49 40 26 10 37 15 8 36 40 42
random_disk(25, "Klebsiella pneumoniae", "ampicillin") # range 11-17
#> Class 'disk'
#> [1] 11 14 17 14 16 17 13 14 17 13 13 13 16 16 11 13 16 11 12 14 15 11 14 13 17
random_disk(25, "Streptococcus pneumoniae", "ampicillin") # range 12-27
#> Class 'disk'
#> [1] 25 22 20 23 18 22 15 16 24 20 23 21 15 18 17 16 23 19 19 18 20 21 20 24 25
# }