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] 0.125 0.025 0.0625 8 4 >=64 2 0.025 0.0625
#> [10] 0.0625 4 <=0.002 32 0.025 0.01 0.125 8 >=64
#> [19] 0.0625 0.01 <=0.002 0.005 1 0.125 <=0.002
random_disk(25)
#> Class 'disk'
#> [1] 18 6 18 6 12 41 34 46 48 22 6 8 35 45 35 39 23 11 12 42 26 35 39 40 16
random_rsi(25)
#> Class 'rsi'
#> [1] S S R S S S S I R R R S R S I R S R I S R R 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] 2 4 32 0.125 128 0.25 0.025 <=0.001 0.25
#> [10] 1 0.005 <=0.001 2 4 0.005 1 0.005 32
#> [19] 8 64 128 4 1 128 4
random_mic(25, "Klebsiella pneumoniae", "meropenem") # range 0.0625-16
#> Class 'mic'
#> [1] 4 2 4 1 32 4 0.5 2 16 0.25 >=64 1 0.5 2 32
#> [16] 1 >=64 32 >=64 16 1 0.5 8 8 0.5
random_mic(25, "Streptococcus pneumoniae", "meropenem") # range 0.0625-4
#> Class 'mic'
#> [1] 1 0.025 0.125 0.5 1 8 0.25 0.025 4 0.25 0.125 4
#> [13] 1 0.5 0.125 2 8 4 0.125 0.5 8 0.25 0.025 2
#> [25] 2
random_disk(25, "Klebsiella pneumoniae") # range 8-50
#> Class 'disk'
#> [1] 40 44 38 42 13 50 38 49 45 46 32 45 17 50 31 27 43 40 19 47 45 22 19 26 41
random_disk(25, "Klebsiella pneumoniae", "ampicillin") # range 11-17
#> Class 'disk'
#> [1] 17 16 13 13 14 12 12 13 12 12 11 14 11 13 11 14 15 17 11 14 12 13 13 14 12
random_disk(25, "Streptococcus pneumoniae", "ampicillin") # range 12-27
#> Class 'disk'
#> [1] 15 23 17 20 23 15 16 15 15 21 22 17 22 23 22 23 17 15 16 24 18 24 26 23 18
# }