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] 0.0625 0.01 4 64 0.005 32 2 0.01 <=0.001
#> [10] 8 128 64 2 8 0.002 0.01 0.0625 0.25
#> [19] 64 0.01 16 0.25 0.0625 >=256 <=0.001
random_disk(25)
#> Class 'disk'
#> [1] 29 36 20 49 33 28 28 23 39 22 10 47 23 49 47 42 30 47 22 37 47 9 19 45 37
random_rsi(25)
#> Class 'rsi'
#> [1] I S I I I S R R S I R I I R I R S R S R S I R 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] 0.005 32 0.025 0.005 0.005 4 2 0.005 0.01
#> [10] 0.5 2 0.25 0.025 2 <=0.001 0.5 8 4
#> [19] 8 0.025 8 0.025 8 2 0.0625
random_mic(25, "Klebsiella pneumoniae", "meropenem") # range 0.0625-16
#> Class 'mic'
#> [1] 16 16 4 32 0.5 >=64 8 1 1 >=64 0.5 32 >=64 0.5 >=64
#> [16] 0.5 32 16 4 1 32 >=64 0.5 0.5 1
random_mic(25, "Streptococcus pneumoniae", "meropenem") # range 0.0625-4
#> Class 'mic'
#> [1] >=8 2 1 >=8 2 2 >=8 1 0.5
#> [10] 1 1 2 0.5 2 0.5 0.5 0.5 >=8
#> [19] 0.25 <=0.125 1 <=0.125 0.25 0.5 2
random_disk(25, "Klebsiella pneumoniae") # range 8-50
#> Class 'disk'
#> [1] 42 24 15 28 24 44 34 35 49 40 50 26 49 10 50 42 24 43 18 14 47 41 50 33 29
random_disk(25, "Klebsiella pneumoniae", "ampicillin") # range 11-17
#> Class 'disk'
#> [1] 14 15 15 12 17 12 11 16 13 12 14 12 14 16 15 17 11 13 13 13 13 12 15 11 13
random_disk(25, "Streptococcus pneumoniae", "ampicillin") # range 12-27
#> Class 'disk'
#> [1] 23 16 24 19 17 23 16 21 15 19 21 22 16 23 26 15 25 22 20 26 26 16 22 26 23
# }