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 <=0.001 1 16 2 0.025 0.005 0.25 <=0.001
#> [10] 0.002 8 0.002 <=0.001 0.025 256 <=0.001 8 0.25
#> [19] 16 4 1 1 0.25 0.005 0.0625
random_disk(25)
#> Class 'disk'
#> [1] 31 45 50 48 45 18 18 19 9 37 23 45 35 18 34 47 36 31 12 21 7 42 30 9 40
random_rsi(25)
#> Class 'rsi'
#> [1] I I I I I R R S S I R R I I R R R I S S R I I S S
# \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] 0.01 0.25 <=0.002 8 0.0625 0.125 128 4 4
#> [10] 2 4 0.005 16 <=0.002 1 0.005 0.25 0.5
#> [19] 0.01 0.025 2 0.125 64 <=0.002 <=0.002
random_mic(25, "Klebsiella pneumoniae", "meropenem") # range 0.0625-16
#> Class 'mic'
#> [1] 2 8 1 16 2 8 16 <=0.5 2 1 2 1
#> [13] <=0.5 1 8 <=0.5 1 16 4 16 <=0.5 4 16 1
#> [25] 8
random_mic(25, "Streptococcus pneumoniae", "meropenem") # range 0.0625-4
#> Class 'mic'
#> [1] 0.0625 2 4 0.5 0.125 0.0625 <=0.025 2 0.25
#> [10] <=0.025 2 0.5 1 4 0.25 <=0.025 0.25 <=0.025
#> [19] 2 0.125 0.0625 <=0.025 2 1 0.25
random_disk(25, "Klebsiella pneumoniae") # range 8-50
#> Class 'disk'
#> [1] 22 12 42 49 11 15 16 24 16 42 48 15 48 13 45 47 45 39 48 36 11 40 50 42 36
random_disk(25, "Klebsiella pneumoniae", "ampicillin") # range 11-17
#> Class 'disk'
#> [1] 17 13 11 16 14 15 11 13 14 12 13 11 12 14 13 11 16 15 12 15 15 13 12 14 16
random_disk(25, "Streptococcus pneumoniae", "ampicillin") # range 12-27
#> Class 'disk'
#> [1] 19 16 27 26 25 23 23 20 19 15 22 23 21 22 15 17 24 21 19 21 27 25 16 15 20
# }