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] 256 4 128 0.005 32 128 64 256 1
#> [10] 32 0.005 0.025 <=0.001 4 0.005 0.005 64 0.5
#> [19] 0.0625 0.01 1 0.01 4 16 2
random_disk(25)
#> Class 'disk'
#> [1] 44 35 48 44 48 6 18 34 9 13 42 45 41 28 24 21 40 41 41 46 44 42 11 39 38
random_rsi(25)
#> Class 'rsi'
#> [1] I R I S R I S I R I I R R I S I I R R I R S 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] 4 0.025 0.5 0.025 0.01 <=0.001 >=64 0.002 2
#> [10] 0.025 1 2 16 0.01 0.025 >=64 0.0625 >=64
#> [19] 16 0.0625 0.125 32 >=64 0.0625 8
random_mic(25, "Klebsiella pneumoniae", "meropenem") # range 0.0625-16
#> Class 'mic'
#> [1] >=64 2 8 4 8 8 16 2 2 1 2 <=0.5
#> [13] 1 8 4 1 32 2 >=64 1 <=0.5 32 1 2
#> [25] >=64
random_mic(25, "Streptococcus pneumoniae", "meropenem") # range 0.0625-4
#> Class 'mic'
#> [1] 0.5 1 0.25 0.25 <=0.125 8 4 0.5 <=0.125
#> [10] <=0.125 0.25 0.25 2 0.5 0.5 4 0.25 4
#> [19] 4 <=0.125 <=0.125 1 <=0.125 0.5 0.25
random_disk(25, "Klebsiella pneumoniae") # range 8-50
#> Class 'disk'
#> [1] 50 28 14 47 14 30 24 47 44 16 45 32 21 40 9 34 29 32 21 26 49 47 40 23 43
random_disk(25, "Klebsiella pneumoniae", "ampicillin") # range 11-17
#> Class 'disk'
#> [1] 13 11 14 12 16 11 13 16 13 17 14 15 12 13 16 11 17 13 15 14 15 15 16 12 15
random_disk(25, "Streptococcus pneumoniae", "ampicillin") # range 12-27
#> Class 'disk'
#> [1] 24 27 25 18 26 24 24 15 15 16 24 20 24 16 17 27 23 20 24 18 24 23 20 26 24
# }