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] 32 0.125 128 8 128 0.25 0.025 0.005 4 1
#> [11] 0.25 64 2 0.005 32 0.005 8 128 0.01 0.002
#> [21] 0.0625 128 0.025 1 0.025
random_disk(25)
#> Class 'disk'
#> [1] 42 47 14 38 23 43 26 25 47 42 19 43 37 27 11 28 48 21 28 43 35 44 26 31 30
random_rsi(25)
#> Class 'rsi'
#> [1] R S R R S S R I S I S S I S R R I R S I S R I R 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] 32 32 0.002 0.002 0.5 0.01 1 0.5 128 128 0.005 0.005
#> [13] 4 1 4 16 8 0.002 >=256 0.01 128 1 0.025 64
#> [25] >=256
random_mic(25, "Klebsiella pneumoniae", "meropenem") # range 0.0625-16
#> Class 'mic'
#> [1] 4 16 8 2 4 0.5 4 2 >=32 >=32 0.5 0.5 8 1 >=32
#> [16] 16 >=32 16 1 16 0.5 8 >=32 1 >=32
random_mic(25, "Streptococcus pneumoniae", "meropenem") # range 0.0625-4
#> Class 'mic'
#> [1] 1 1 2 0.5 2 1 >=4 2 0.125 1
#> [11] 0.5 0.0625 0.0625 2 2 1 0.125 2 >=4 1
#> [21] 0.125 1 0.5 1 0.0625
random_disk(25, "Klebsiella pneumoniae") # range 8-50
#> Class 'disk'
#> [1] 11 46 50 15 25 18 23 38 45 50 22 25 50 42 13 47 9 45 26 43 17 10 45 45 13
random_disk(25, "Klebsiella pneumoniae", "ampicillin") # range 11-17
#> Class 'disk'
#> [1] 17 11 11 14 15 15 16 15 15 16 15 17 12 17 15 17 16 14 13 11 16 11 11 13 14
random_disk(25, "Streptococcus pneumoniae", "ampicillin") # range 12-27
#> Class 'disk'
#> [1] 17 27 21 15 25 19 18 21 16 16 23 16 23 15 16 24 20 27 17 17 19 22 24 17 22
# }