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] 4 64 4 32 2 0.002 32 0.125 0.005
#> [10] 256 0.25 16 0.01 8 16 2 0.002 0.25
#> [19] 128 0.0625 1 8 <=0.001 0.002 256
random_disk(25)
#> Class 'disk'
#> [1] 8 13 12 37 22 21 18 18 43 46 34 39 50 7 34 40 40 43 27 50 38 17 20 43 20
random_rsi(25)
#> Class 'rsi'
#> [1] I I R S I I R I S I S S R I I I I R R S I R S R 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] 0.0625 0.125 16 0.0625 4 128 0.005 2 1 2
#> [11] 0.125 128 8 0.125 1 16 1 >=256 0.01 8
#> [21] 2 0.01 64 32 64
random_mic(25, "Klebsiella pneumoniae", "meropenem") # range 0.0625-16
#> Class 'mic'
#> [1] >=32 16 8 1 2 1 1 8 16 2 4 2 4 8 2
#> [16] 8 16 1 >=32 8 2 1 16 8 2
random_mic(25, "Streptococcus pneumoniae", "meropenem") # range 0.0625-4
#> Class 'mic'
#> [1] >=4 1 0.25 0.25 1 1 >=4 0.125 2 1 0.25 0.25
#> [13] 1 0.125 1 0.5 1 2 2 >=4 1 0.5 1 0.5
#> [25] >=4
random_disk(25, "Klebsiella pneumoniae") # range 8-50
#> Class 'disk'
#> [1] 22 13 25 42 48 40 14 25 25 50 31 21 41 40 44 18 49 50 40 25 25 10 49 12 12
random_disk(25, "Klebsiella pneumoniae", "ampicillin") # range 11-17
#> Class 'disk'
#> [1] 11 12 16 12 12 12 12 17 13 17 11 12 13 17 13 14 13 12 16 14 15 16 17 17 17
random_disk(25, "Streptococcus pneumoniae", "ampicillin") # range 12-27
#> Class 'disk'
#> [1] 18 25 20 19 17 27 25 16 22 22 25 23 16 16 27 25 19 18 21 25 22 18 20 18 19
# }