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] 0.0625 128 2 4 16 2 4 16 1 0.25
#> [11] 8 0.01 0.002 16 8 32 128 0.5 4 128
#> [21] >=256 >=256 2 0.005 0.001
random_disk(25)
#> Class 'disk'
#> [1] 22 40 45 27 37 43 39 32 34 49 43 14 41 11 29 13 27 8 16 45 7 11 23 39 50
random_rsi(25)
#> Class 'rsi'
#> [1] I S R S S I R R I R R R R R S S R S I I S I R S 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] 16 0.01 0.025 16 0.0625 >=64 8 16 0.001 0.001
#> [11] 1 4 0.025 0.125 0.005 >=64 0.005 0.25 >=64 4
#> [21] 16 0.01 0.001 0.001 0.125
random_mic(25, "Klebsiella pneumoniae", "meropenem") # range 0.0625-16
#> Class 'mic'
#> [1] 4 4 2 0.5 4 16 2 4 0.5 >=32 0.5 8 >=32 4 >=32
#> [16] 16 1 0.5 0.5 2 16 8 16 4 4
random_mic(25, "Streptococcus pneumoniae", "meropenem") # range 0.0625-4
#> Class 'mic'
#> [1] 4 <=0.0625 <=0.0625 <=0.0625 >=16 4 2 0.5
#> [9] 0.125 2 2 4 0.125 <=0.0625 0.125 0.5
#> [17] 0.5 8 1 1 0.25 0.125 0.5 4
#> [25] <=0.0625
random_disk(25, "Klebsiella pneumoniae") # range 8-50
#> Class 'disk'
#> [1] 20 11 47 15 29 47 48 15 19 13 21 46 38 48 14 39 49 34 41 39 49 42 10 44 44
random_disk(25, "Klebsiella pneumoniae", "ampicillin") # range 11-17
#> Class 'disk'
#> [1] 16 11 12 12 14 14 15 15 13 17 14 17 16 12 12 15 13 13 13 17 17 14 17 14 17
random_disk(25, "Streptococcus pneumoniae", "ampicillin") # range 12-27
#> Class 'disk'
#> [1] 23 26 20 22 25 18 23 18 15 17 22 21 18 25 21 22 21 17 26 15 15 20 19 20 23
# }