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 0.01 32 1 8 4 0.001 0.01 0.001 >=256 0.125 0.002
#> [13] 128 0.002 0.125 16 >=256 0.5 0.01 0.025 0.5 16 >=256 8
#> [25] 4
random_disk(25)
#> Class 'disk'
#> [1] 11 37 41 7 16 27 11 6 46 21 9 47 6 17 37 39 40 39 41 12 25 50 42 29 14
random_rsi(25)
#> Class 'rsi'
#> [1] S I S I I R S R S S I I R I R I R S S S S S I I 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] >=128 4 0.01 0.25 0.005 0.01 0.25 0.01 >=128
#> [10] 1 <=0.001 2 32 2 8 4 >=128 0.025
#> [19] 0.5 32 8 >=128 4 64 4
random_mic(25, "Klebsiella pneumoniae", "meropenem") # range 0.0625-16
#> Class 'mic'
#> [1] 32 8 >=64 32 4 >=64 16 >=64 2 32 >=64 >=64 4 32 16
#> [16] >=64 8 4 4 8 32 >=64 2 16 16
random_mic(25, "Streptococcus pneumoniae", "meropenem") # range 0.0625-4
#> Class 'mic'
#> [1] 0.125 8 8 16 8 8 4 0.25
#> [9] <=0.0625 16 16 8 16 0.5 8 16
#> [17] 4 <=0.0625 1 1 1 0.5 <=0.0625 0.5
#> [25] 0.5
random_disk(25, "Klebsiella pneumoniae") # range 8-50
#> Class 'disk'
#> [1] 29 24 16 48 36 18 44 16 9 28 50 15 50 35 23 12 11 19 35 50 35 35 33 35 46
random_disk(25, "Klebsiella pneumoniae", "ampicillin") # range 11-17
#> Class 'disk'
#> [1] 14 14 12 14 14 17 16 17 12 15 14 12 14 11 15 12 15 12 11 14 16 15 16 13 13
random_disk(25, "Streptococcus pneumoniae", "ampicillin") # range 12-27
#> Class 'disk'
#> [1] 16 20 18 23 20 22 24 23 18 27 23 27 26 26 17 21 21 19 23 17 26 25 18 25 18
# }