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] 0.125 256 2 0.0625 64 0.125 8 16 0.5
#> [10] 8 0.5 16 32 16 256 0.002 0.0625 0.25
#> [19] 256 0.25 128 8 <=0.001 0.002 0.25
random_disk(25)
#> Class 'disk'
#> [1] 6 11 46 8 26 50 29 30 34 45 32 30 23 47 15 48 45 48 46 48 35 44 29 17 16
random_rsi(25)
#> Class 'rsi'
#> [1] R R S S I I R R R I S I R R R I I I R R I R R S 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] 0.125 <=0.001 1 0.025 >=64 0.025 1 0.002 32
#> [10] 1 2 0.025 0.5 0.5 0.002 0.002 0.002 0.25
#> [19] 0.002 >=64 16 8 >=64 <=0.001 4
random_mic(25, "Klebsiella pneumoniae", "meropenem") # range 0.0625-16
#> Class 'mic'
#> [1] 2 8 1 4 1 16 32 1 4 2 2 32 1 8 2 32 4 1 1 8 4 2 2 4 4
random_mic(25, "Streptococcus pneumoniae", "meropenem") # range 0.0625-4
#> Class 'mic'
#> [1] 2 0.25 1 >=4 1 1 <=0.125 0.5 <=0.125
#> [10] 0.5 0.25 >=4 <=0.125 2 1 >=4 <=0.125 0.5
#> [19] 2 0.5 1 >=4 1 0.25 1
random_disk(25, "Klebsiella pneumoniae") # range 8-50
#> Class 'disk'
#> [1] 32 15 47 40 50 46 48 50 49 50 41 41 14 25 47 42 44 41 17 47 8 46 17 42 50
random_disk(25, "Klebsiella pneumoniae", "ampicillin") # range 11-17
#> Class 'disk'
#> [1] 15 12 13 13 12 12 14 15 11 13 11 17 13 17 11 14 15 14 17 16 14 16 15 15 12
random_disk(25, "Streptococcus pneumoniae", "ampicillin") # range 12-27
#> Class 'disk'
#> [1] 18 25 19 26 18 21 15 23 21 15 17 16 16 17 27 26 18 27 15 23 19 26 15 21 15
# }