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] 0.025 64 0.005 0.0625 32 0.001 0.5 0.002 4 4
#> [11] 0.5 0.5 1 0.25 4 8 16 128 128 >=256
#> [21] 0.025 0.025 2 0.25 128
random_disk(25)
#> Class 'disk'
#> [1] 41 19 42 25 27 35 32 49 6 50 36 32 43 44 36 43 11 41 38 25 44 25 47 29 45
random_rsi(25)
#> Class 'rsi'
#> [1] R I R I S S S I I I I R S S S S R S S R R 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] 0.125 0.0625 0.5 0.25 0.002 0.001 0.125 0.25 1 4
#> [11] 0.125 0.005 16 16 0.0625 0.125 32 2 8 32
#> [21] 0.25 0.25 0.01 0.0625 16
random_mic(25, "Klebsiella pneumoniae", "meropenem") # range 0.0625-16
#> Class 'mic'
#> [1] 2 <=1 4 4 2 8 8 2 8 4 2 4 8 2 4 <=1 4 16 16
#> [20] 32 4 2 2 <=1 16
random_mic(25, "Streptococcus pneumoniae", "meropenem") # range 0.0625-4
#> Class 'mic'
#> [1] 1 1 >=8 0.5 0.5 0.25 >=8 4 4 0.125 0.125 1
#> [13] >=8 >=8 1 1 1 1 >=8 1 0.5 >=8 0.125 4
#> [25] 0.5
random_disk(25, "Klebsiella pneumoniae") # range 8-50
#> Class 'disk'
#> [1] 25 22 41 22 49 44 48 36 14 33 41 48 11 11 12 39 14 47 18 16 28 38 16 26 47
random_disk(25, "Klebsiella pneumoniae", "ampicillin") # range 11-17
#> Class 'disk'
#> [1] 14 12 17 11 12 11 11 13 13 12 16 12 11 16 14 13 13 16 14 14 14 11 17 17 12
random_disk(25, "Streptococcus pneumoniae", "ampicillin") # range 12-27
#> Class 'disk'
#> [1] 27 20 26 18 19 16 23 18 26 20 16 15 16 20 17 19 16 23 16 22 15 20 18 27 23
# }