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] 2 8 2 0.125 2 0.025 0.025 0.005 0.002
#> [10] <=0.001 4 0.025 0.005 0.01 2 0.025 2 16
#> [19] 0.25 >=256 0.125 0.002 0.002 64 >=256
random_disk(25)
#> Class 'disk'
#> [1] 46 42 10 43 25 9 15 8 50 21 42 19 29 7 35 49 39 32 44 20 34 29 43 12 49
random_rsi(25)
#> Class 'rsi'
#> [1] R R R I S R R S R S R R R S R S I I S S S I I I R
# \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] 0.005 0.002 128 0.25 0.025 32 4 0.125 >=256
#> [10] 8 <=0.001 <=0.001 0.002 32 0.5 16 0.005 0.005
#> [19] 4 0.01 16 128 8 >=256 <=0.001
random_mic(25, "Klebsiella pneumoniae", "meropenem") # range 0.0625-16
#> Class 'mic'
#> [1] 0.5 4 16 1 2 4 0.25 1 16 2 16 2 0.5 1 2
#> [16] 16 0.25 0.5 16 0.5 1 8 8 0.5 8
random_mic(25, "Streptococcus pneumoniae", "meropenem") # range 0.0625-4
#> Class 'mic'
#> [1] 4 <=0.025 0.0625 0.125 0.0625 2 <=0.025 1 0.125
#> [10] 0.125 <=0.025 0.25 <=0.025 0.25 <=0.025 4 2 0.125
#> [19] 0.25 0.125 0.25 2 0.0625 8 0.0625
random_disk(25, "Klebsiella pneumoniae") # range 8-50
#> Class 'disk'
#> [1] 27 18 14 44 20 49 14 31 33 50 49 36 46 41 48 10 38 45 48 46 22 18 39 46 47
random_disk(25, "Klebsiella pneumoniae", "ampicillin") # range 11-17
#> Class 'disk'
#> [1] 12 17 14 13 17 12 17 11 16 15 12 14 15 11 15 12 14 13 13 14 11 11 17 17 11
random_disk(25, "Streptococcus pneumoniae", "ampicillin") # range 12-27
#> Class 'disk'
#> [1] 15 27 15 16 19 26 27 16 26 19 22 24 24 20 24 25 23 22 23 17 24 24 26 23 25
# }