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] 8 0.25 0.01 8 128 0.025 0.5 <=0.002 32
#> [10] 64 16 0.005 0.005 0.025 0.025 0.25 0.025 8
#> [19] 256 256 2 256 0.005 0.025 64
random_disk(25)
#> Class 'disk'
#> [1] 30 16 47 35 37 49 26 34 44 48 27 44 26 41 49 23 7 50 19 34 38 25 21 43 29
random_rsi(25)
#> Class 'rsi'
#> [1] R S S S S I S S R R R I S S S S S S S S R I R I 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] 1 128 0.001 0.01 128 0.01 0.001 0.01 4 128 0.001 0.01
#> [13] 0.002 4 16 32 1 0.25 1 2 64 16 64 16
#> [25] 0.01
random_mic(25, "Klebsiella pneumoniae", "meropenem") # range 0.0625-16
#> Class 'mic'
#> [1] <=1 8 8 8 <=1 2 4 8 >=16 >=16 2 4 8 >=16 8
#> [16] 4 2 >=16 4 <=1 2 >=16 8 8 2
random_mic(25, "Streptococcus pneumoniae", "meropenem") # range 0.0625-4
#> Class 'mic'
#> [1] 1 2 >=16 >=16 4 2 0.5 0.5 0.25
#> [10] 1 0.5 <=0.125 2 4 >=16 4 8 >=16
#> [19] 4 1 <=0.125 0.5 0.5 0.5 2
random_disk(25, "Klebsiella pneumoniae") # range 8-50
#> Class 'disk'
#> [1] 21 36 49 10 16 15 34 46 43 42 33 47 43 50 19 45 45 13 34 9 46 20 42 40 12
random_disk(25, "Klebsiella pneumoniae", "ampicillin") # range 11-17
#> Class 'disk'
#> [1] 16 11 16 13 11 12 11 14 13 11 14 11 12 15 12 12 13 13 17 17 16 13 16 11 15
random_disk(25, "Streptococcus pneumoniae", "ampicillin") # range 12-27
#> Class 'disk'
#> [1] 17 15 25 23 16 23 16 27 26 20 17 16 22 22 27 18 24 17 26 25 27 21 16 27 18
# }