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] 0.0625 0.001 4 1 0.125 8 0.002 1 0.0625 0.5
#> [11] 1 1 0.001 1 16 0.005 0.005 256 1 16
#> [21] 1 0.0625 0.005 0.0625 0.25
random_disk(25)
#> Class 'disk'
#> [1] 40 10 46 9 7 28 11 25 18 37 33 20 46 26 47 23 41 32 38 37 40 26 28 23 42
random_rsi(25)
#> Class 'rsi'
#> [1] R I S R I I S S S I I R I S S S I S R I R I R 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 4 0.01 64 0.01 8 0.001 0.025 4 0.005
#> [11] 32 32 0.025 2 0.025 64 0.0625 0.001 0.125 0.025
#> [21] 256 0.0625 256 256 8
random_mic(25, "Klebsiella pneumoniae", "meropenem") # range 0.0625-16
#> Class 'mic'
#> [1] 0.25 4 >=16 2 1 4 4 0.25 0.25 0.25 4 1 8 0.5 0.25
#> [16] 8 4 2 0.5 1 0.5 8 0.5 >=16 8
random_mic(25, "Streptococcus pneumoniae", "meropenem") # range 0.0625-4
#> Class 'mic'
#> [1] 0.5 0.5 0.5 1 0.25 2 0.0625 0.125 1 0.0625
#> [11] 0.5 0.125 0.125 2 0.125 0.025 0.25 >=4 0.0625 0.0625
#> [21] 0.0625 0.25 0.5 2 2
random_disk(25, "Klebsiella pneumoniae") # range 8-50
#> Class 'disk'
#> [1] 36 27 44 26 43 42 49 42 46 41 41 12 32 35 20 21 8 43 8 45 50 47 45 50 37
random_disk(25, "Klebsiella pneumoniae", "ampicillin") # range 11-17
#> Class 'disk'
#> [1] 15 16 14 14 14 14 11 17 11 14 13 16 15 15 17 17 13 17 11 14 14 12 12 12 11
random_disk(25, "Streptococcus pneumoniae", "ampicillin") # range 12-27
#> Class 'disk'
#> [1] 16 27 27 17 18 15 17 25 15 22 23 22 26 24 15 15 16 24 16 19 20 26 25 21 15
# }