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 0.125 64 0.025 4 32 0.5 0.5 1 0.001
#> [11] 0.005 0.001 16 2 0.0625 1 0.005 0.001 0.002 64
#> [21] 0.125 0.001 0.25 256 0.25
random_disk(25)
#> Class 'disk'
#> [1] 22 17 48 24 33 35 46 9 46 34 48 48 30 42 8 44 15 41 34 27 42 47 19 32 29
random_rsi(25)
#> Class 'rsi'
#> [1] S S R S R S R S I R I I R S R S S I R I S I S 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] 0.125 8 0.25 0.01 4 0.5 0.005 0.01 256
#> [10] 16 2 0.0625 0.5 0.002 0.125 32 32 0.002
#> [19] <=0.001 4 0.005 0.002 <=0.001 256 0.125
random_mic(25, "Klebsiella pneumoniae", "meropenem") # range 0.0625-16
#> Class 'mic'
#> [1] 4 4 8 16 2 16 <=1 8 2 16 8 <=1 64 2 4 2 2 2 2
#> [20] 64 8 8 4 32 4
random_mic(25, "Streptococcus pneumoniae", "meropenem") # range 0.0625-4
#> Class 'mic'
#> [1] 1 0.025 0.0625 >=4 0.5 0.5 0.5 0.5 >=4 >=4
#> [11] 0.25 0.025 0.025 0.125 >=4 1 >=4 1 1 0.5
#> [21] 2 0.25 1 1 1
random_disk(25, "Klebsiella pneumoniae") # range 8-50
#> Class 'disk'
#> [1] 46 27 10 49 45 44 27 26 10 43 35 37 42 42 46 37 19 18 41 17 29 50 10 23 50
random_disk(25, "Klebsiella pneumoniae", "ampicillin") # range 11-17
#> Class 'disk'
#> [1] 11 17 11 14 14 12 14 11 14 15 14 11 12 15 16 11 13 13 16 12 15 14 14 17 15
random_disk(25, "Streptococcus pneumoniae", "ampicillin") # range 12-27
#> Class 'disk'
#> [1] 27 27 20 21 24 17 21 21 22 18 16 27 27 22 19 25 25 21 15 19 27 21 18 21 17
# }