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 agent, 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 agent 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 2 0.001 0.01 0.125 0.25 0.125 4 0.125 64
#> [11] >=256 0.0625 2 32 16 0.01 0.001 64 1 32
#> [21] 1 >=256 0.5 64 0.5
random_disk(25)
#> Class 'disk'
#> [1] 18 44 40 45 12 48 17 46 17 35 12 9 26 16 42 15 40 44 25 32 49 42 27 40 15
random_rsi(25)
#> Class 'rsi'
#> [1] R R I I S I I R S I R S S I S R R I R I I S 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] 64 >=256 2 0.01 0.025 0.0625 <=0.001 0.125 16
#> [10] 0.005 0.01 <=0.001 <=0.001 0.5 <=0.001 8 0.125 <=0.001
#> [19] 64 0.005 <=0.001 0.005 <=0.001 0.5 0.125
random_mic(25, "Klebsiella pneumoniae", "meropenem") # range 0.0625-16
#> Class 'mic'
#> [1] 2 1 64 8 4 8 8 8 1 64 1 1 8 4 64 2 8 2 2 1 64 1 2 4 1
random_mic(25, "Streptococcus pneumoniae", "meropenem") # range 0.0625-4
#> Class 'mic'
#> [1] 1 <=0.025 0.125 0.25 0.25 2 0.125 >=8 <=0.025
#> [10] 0.25 >=8 2 >=8 1 2 >=8 4 0.5
#> [19] 1 0.25 2 0.0625 >=8 0.25 1
random_disk(25, "Klebsiella pneumoniae") # range 8-50
#> Class 'disk'
#> [1] 32 45 50 29 50 27 46 34 15 47 9 34 47 22 36 34 23 34 33 13 46 11 32 9 24
random_disk(25, "Klebsiella pneumoniae", "ampicillin") # range 11-17
#> Class 'disk'
#> [1] 14 16 15 13 12 14 12 14 14 12 16 12 12 15 16 12 12 12 16 17 13 17 11 16 15
random_disk(25, "Streptococcus pneumoniae", "ampicillin") # range 12-27
#> Class 'disk'
#> [1] 15 19 27 21 22 26 20 24 24 23 22 26 19 18 15 19 22 26 26 26 25 21 20 17 23
# }