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 0.0625 0.0625 1 0.002 16 128 0.5 0.5 64
#> [11] 256 4 0.25 0.0625 0.0625 8 0.01 0.25 0.0625 0.005
#> [21] 32 0.125 0.25 128 0.5
random_disk(25)
#> Class 'disk'
#> [1] 50 28 50 33 47 18 38 25 7 49 43 34 26 27 45 40 42 17 22 42 41 25 31 45 29
random_rsi(25)
#> Class 'rsi'
#> [1] S R I R R S S I S I S S S S I I I S S I S R I R 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] 0.025 16 2 16 2 <=0.002 >=64 0.005 4
#> [10] 8 0.25 0.025 0.0625 >=64 >=64 4 0.0625 16
#> [19] 4 4 32 32 >=64 8 4
random_mic(25, "Klebsiella pneumoniae", "meropenem") # range 0.0625-16
#> Class 'mic'
#> [1] 2 4 1 8 4 2 4 >=16 2 >=16 1 8 2 >=16 8
#> [16] 2 >=16 2 2 8 1 2 1 1 4
random_mic(25, "Streptococcus pneumoniae", "meropenem") # range 0.0625-4
#> Class 'mic'
#> [1] 0.0625 0.0625 0.25 0.0625 8 2 <=0.025 2 >=16
#> [10] 2 <=0.025 >=16 1 0.0625 0.125 1 1 1
#> [19] 4 8 0.5 0.5 4 2 0.5
random_disk(25, "Klebsiella pneumoniae") # range 8-50
#> Class 'disk'
#> [1] 41 24 50 49 30 49 31 45 21 40 45 31 17 31 49 31 12 40 50 19 26 8 41 24 47
random_disk(25, "Klebsiella pneumoniae", "ampicillin") # range 11-17
#> Class 'disk'
#> [1] 15 16 16 12 12 16 17 11 11 12 14 12 11 12 15 17 16 17 17 12 17 13 17 15 16
random_disk(25, "Streptococcus pneumoniae", "ampicillin") # range 12-27
#> Class 'disk'
#> [1] 22 15 20 16 22 26 25 25 19 27 17 22 20 19 19 23 16 16 18 19 19 21 19 15 25
# }