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_sir(size = NULL, prob_SIR = 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_SIR
a vector of length 3: the probabilities for "S" (1st value), "I" (2nd value) and "R" (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 clinical_breakpoints 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] 0.025 0.005 32 32 0.002 0.25 64 32 0.25
#> [10] 0.5 128 <=0.001 <=0.001 <=0.001 0.25 0.005 >=256 8
#> [19] 64 8 >=256 0.025 4 0.125 128
random_disk(25)
#> Class 'disk'
#> [1] 50 37 42 49 34 38 41 43 38 18 20 50 28 38 29 41 41 11 17 11 43 30 36 11 14
random_sir(25)
#> Class 'sir'
#> [1] I R R R S R R I I R I I R S S S S S S S I R R I 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] 0.25 0.0625 >=128 <=0.001 64 0.025 >=128 0.002 64
#> [10] 0.25 0.25 0.0625 64 16 4 0.025 0.25 0.125
#> [19] >=128 16 0.5 >=128 2 16 64
random_mic(25, "Klebsiella pneumoniae", "meropenem") # range 0.0625-16
#> Class 'mic'
#> [1] <=1 2 2 >=32 <=1 8 2 16 16 <=1 8 <=1 <=1 16 8
#> [16] 8 8 >=32 4 <=1 <=1 8 <=1 <=1 2
random_mic(25, "Streptococcus pneumoniae", "meropenem") # range 0.0625-4
#> Class 'mic'
#> [1] 8 0.025 1 0.0625 0.25 0.5 2 16 16 2
#> [11] 8 0.25 1 1 8 4 0.0625 0.025 16 0.025
#> [21] 0.025 0.25 0.5 0.5 1
random_disk(25, "Klebsiella pneumoniae") # range 8-50
#> Class 'disk'
#> [1] 26 47 32 16 38 25 17 14 11 15 35 50 49 36 35 31 46 24 45 13 15 10 36 17 50
random_disk(25, "Klebsiella pneumoniae", "ampicillin") # range 11-17
#> Class 'disk'
#> [1] 15 14 17 11 11 13 12 11 12 14 13 15 15 14 15 17 11 14 12 13 12 14 12 14 14
random_disk(25, "Streptococcus pneumoniae", "ampicillin") # range 12-27
#> Class 'disk'
#> [1] 17 25 25 25 17 27 23 17 19 15 23 21 25 23 20 18 19 18 26 18 16 21 17 22 26
# }