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 2024 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 1 <=0.001 16 <=0.001 1 0.025 8 0.025
#> [10] 0.125 >=256 16 >=256 16 <=0.001 1 0.005 16
#> [19] 32 64 0.25 16 0.125 8 4
random_disk(25)
#> Class 'disk'
#> [1] 30 7 9 44 30 41 45 40 7 41 49 10 12 19 28 8 33 48 44 46 44 18 37 50 16
random_sir(25)
#> Class 'sir'
#> [1] R S S I S I R I R R S I I S S S S R I I I 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] 0.25 1 >=64 32 <=0.001 >=64 0.025 32 32
#> [10] 0.005 16 1 0.005 4 0.25 8 4 4
#> [19] 0.01 0.25 0.01 0.25 >=64 0.125 0.125
random_mic(25, "Klebsiella pneumoniae", "meropenem") # range 0.0625-16
#> Class 'mic'
#> [1] 8 16 2 2 1 16 8 8 2 2 4 >=32
#> [13] 8 1 16 <=0.5 1 >=32 >=32 >=32 8 4 8 1
#> [25] 16
random_mic(25, "Streptococcus pneumoniae", "meropenem") # range 0.0625-4
#> Class 'mic'
#> [1] <=0.0625 4 2 <=0.0625 4 1 4 0.5
#> [9] 2 4 1 4 0.25 0.25 0.5 0.5
#> [17] <=0.0625 0.5 1 1 0.125 0.125 2 4
#> [25] 2
random_disk(25, "Klebsiella pneumoniae") # range 8-50
#> Class 'disk'
#> [1] 14 39 35 18 41 39 48 44 48 24 26 40 47 10 31 21 31 48 12 24 50 8 25 40 48
random_disk(25, "Klebsiella pneumoniae", "ampicillin") # range 11-17
#> Class 'disk'
#> [1] 11 12 17 14 17 17 13 14 11 13 13 16 16 17 15 13 14 14 15 16 17 11 14 16 14
random_disk(25, "Streptococcus pneumoniae", "ampicillin") # range 12-27
#> Class 'disk'
#> [1] 17 15 16 16 24 15 27 22 24 19 23 25 21 27 23 27 21 21 27 20 26 24 23 25 18
# }