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] 0.5 32 8 0.25 0.0625 128 16 0.0625 0.01 0.5
#> [11] 0.002 2 0.5 0.01 0.001 1 2 0.025 128 64
#> [21] 64 2 8 0.25 >=256
random_disk(25)
#> Class 'disk'
#> [1] 45 47 24 47 50 23 36 10 30 50 39 19 46 42 47 49 11 22 12 33 18 22 41 19 40
random_rsi(25)
#> Class 'rsi'
#> [1] R R I I R I S I R I I R I S S S I S S R S 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] 0.0625 0.5 0.025 0.001 0.002 8 0.005 128 128 64
#> [11] 2 0.005 0.5 4 16 32 0.005 16 8 0.25
#> [21] 32 4 2 0.025 0.002
random_mic(25, "Klebsiella pneumoniae", "meropenem") # range 0.0625-16
#> Class 'mic'
#> [1] 0.5 4 16 8 8 4 4 1 32 0.5 0.25 2 0.5 8 1
#> [16] 16 1 8 1 0.5 4 8 8 0.25 2
random_mic(25, "Streptococcus pneumoniae", "meropenem") # range 0.0625-4
#> Class 'mic'
#> [1] >=4 0.5 0.5 0.125 0.5 1 0.25 0.25 0.0625 0.25
#> [11] 0.125 0.5 2 0.0625 0.5 0.25 0.25 0.125 0.5 0.125
#> [21] 1 0.0625 0.5 >=4 1
random_disk(25, "Klebsiella pneumoniae") # range 8-50
#> Class 'disk'
#> [1] 19 45 28 16 45 33 40 22 20 31 16 38 26 50 39 49 31 27 13 27 29 47 14 41 43
random_disk(25, "Klebsiella pneumoniae", "ampicillin") # range 11-17
#> Class 'disk'
#> [1] 12 11 14 13 15 13 13 16 14 15 17 17 11 11 14 17 12 17 13 14 14 13 16 11 17
random_disk(25, "Streptococcus pneumoniae", "ampicillin") # range 12-27
#> Class 'disk'
#> [1] 22 24 26 21 17 26 21 20 20 23 27 17 25 17 19 24 23 21 24 18 21 25 24 21 15
# }