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] 128 0.025 2 1 32 0.125 16 >=256 0.025
#> [10] 0.025 <=0.002 0.01 1 <=0.002 >=256 2 16 1
#> [19] 4 64 8 8 0.005 0.0625 0.5
random_disk(25)
#> Class 'disk'
#> [1] 37 44 23 13 39 50 44 18 36 31 40 46 36 29 34 45 32 48 46 45 28 10 50 17 47
random_rsi(25)
#> Class 'rsi'
#> [1] I I S I I S I I R R I S S I S I S S R I R R R I 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] 4 <=0.001 8 <=0.001 >=256 0.025 <=0.001 0.5 4
#> [10] 0.25 2 0.002 0.002 1 128 0.125 <=0.001 0.005
#> [19] 0.5 4 0.125 2 128 16 32
random_mic(25, "Klebsiella pneumoniae", "meropenem") # range 0.0625-16
#> Class 'mic'
#> [1] 4 8 <=1 2 32 8 8 4 4 8 2 8 16 2 64 4 <=1 <=1 <=1
#> [20] 32 4 2 8 16 16
random_mic(25, "Streptococcus pneumoniae", "meropenem") # range 0.0625-4
#> Class 'mic'
#> [1] <=0.125 0.5 1 <=0.125 0.25 4 0.25 0.5 4
#> [10] 0.5 4 2 <=0.125 >=8 0.5 >=8 0.5 2
#> [19] 0.5 >=8 0.25 1 <=0.125 <=0.125 0.25
random_disk(25, "Klebsiella pneumoniae") # range 8-50
#> Class 'disk'
#> [1] 37 15 44 15 46 50 48 20 41 40 41 25 41 50 47 40 20 27 18 16 47 42 45 40 46
random_disk(25, "Klebsiella pneumoniae", "ampicillin") # range 11-17
#> Class 'disk'
#> [1] 17 16 15 13 13 17 16 13 16 14 14 13 11 17 12 17 12 16 16 17 17 11 14 16 13
random_disk(25, "Streptococcus pneumoniae", "ampicillin") # range 12-27
#> Class 'disk'
#> [1] 19 22 23 22 24 18 25 23 26 25 19 21 18 18 23 15 24 17 17 24 22 20 26 26 16
# }