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] 0.001 16 2 >=64 0.125 1 0.002 0.5 0.001 >=64 8 0.125
#> [13] 2 >=64 >=64 0.125 0.005 8 0.125 >=64 0.025 4 0.01 >=64
#> [25] 0.01
random_disk(25)
#> Class 'disk'
#> [1] 31 20 47 41 23 31 34 40 35 9 42 37 46 38 31 41 27 33 49 27 31 21 35 7 48
random_rsi(25)
#> Class 'rsi'
#> [1] I R I S I S S R R S S I S I R I S S I I S S I R 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] 0.0625 0.01 8 0.01 >=64 8 16 0.125 0.25 >=64
#> [11] 32 0.002 0.005 0.002 >=64 0.5 2 8 >=64 0.001
#> [21] 0.01 4 0.005 2 0.005
random_mic(25, "Klebsiella pneumoniae", "meropenem") # range 0.0625-16
#> Class 'mic'
#> [1] 4 8 2 <=0.5 2 <=0.5 2 16 2 4 <=0.5 2
#> [13] 2 1 8 8 16 1 <=0.5 1 16 16 <=0.5 8
#> [25] 2
random_mic(25, "Streptococcus pneumoniae", "meropenem") # range 0.0625-4
#> Class 'mic'
#> [1] 2 0.25 0.125 1 4 >=8 0.25 2 2 4
#> [11] 1 4 0.125 0.0625 0.0625 1 1 1 1 2
#> [21] 0.5 2 0.125 0.125 >=8
random_disk(25, "Klebsiella pneumoniae") # range 8-50
#> Class 'disk'
#> [1] 45 44 33 12 44 48 13 43 34 26 12 10 37 46 48 45 12 44 15 35 31 47 30 33 41
random_disk(25, "Klebsiella pneumoniae", "ampicillin") # range 11-17
#> Class 'disk'
#> [1] 16 11 11 12 11 14 13 11 11 16 14 11 14 16 17 11 17 14 14 14 14 13 11 12 14
random_disk(25, "Streptococcus pneumoniae", "ampicillin") # range 12-27
#> Class 'disk'
#> [1] 21 21 19 19 24 22 16 17 21 24 23 17 21 27 18 19 17 16 27 16 18 27 23 15 25
# }