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] 0.01 256 2 2 256 1 0.001 64 0.01 2
#> [11] 128 16 64 0.0625 16 128 0.0625 256 2 0.001
#> [21] 128 0.01 8 64 64
random_disk(25)
#> Class 'disk'
#> [1] 22 38 41 24 23 27 40 16 21 48 10 47 30 44 20 25 29 30 33 19 12 45 19 24 33
random_rsi(25)
#> Class 'rsi'
#> [1] S S I I S R S S S S S S R I R I I I R I R I 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] 8 2 0.125 32 4 <=0.001 0.0625 0.25 8
#> [10] 0.002 32 8 <=0.001 <=0.001 4 0.025 0.005 16
#> [19] 0.0625 0.002 0.005 0.025 64 0.025 0.002
random_mic(25, "Klebsiella pneumoniae", "meropenem") # range 0.0625-16
#> Class 'mic'
#> [1] 16 1 4 16 32 8 16 <=0.5 32 4 64 8
#> [13] 64 <=0.5 1 8 1 1 <=0.5 1 16 <=0.5 8 2
#> [25] 64
random_mic(25, "Streptococcus pneumoniae", "meropenem") # range 0.0625-4
#> Class 'mic'
#> [1] 0.5 0.5 1 1 8 16 4 0.125 2
#> [10] 2 1 1 8 <=0.025 16 4 16 1
#> [19] 1 4 2 0.0625 0.125 <=0.025 1
random_disk(25, "Klebsiella pneumoniae") # range 8-50
#> Class 'disk'
#> [1] 17 22 48 47 18 37 40 13 34 50 33 31 14 30 24 34 13 21 43 31 36 33 45 46 39
random_disk(25, "Klebsiella pneumoniae", "ampicillin") # range 11-17
#> Class 'disk'
#> [1] 12 17 11 11 15 14 14 13 14 11 13 11 16 15 12 14 17 11 17 14 13 17 16 13 16
random_disk(25, "Streptococcus pneumoniae", "ampicillin") # range 12-27
#> Class 'disk'
#> [1] 17 16 18 18 22 16 21 25 15 22 25 26 26 26 19 22 25 19 24 27 23 20 17 23 27
# }