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] 32 2 1 2 32 0.005 8 64 128 128 256 16
#> [13] 0.005 0.01 16 0.5 4 0.001 2 64 0.001 0.002 16 0.01
#> [25] 128
random_disk(25)
#> Class 'disk'
#> [1] 48 19 44 26 24 40 49 9 50 47 12 47 34 17 37 13 47 21 36 20 29 6 30 49 43
random_sir(25)
#> Class 'sir'
#> [1] S I S S S I I S S R I I R R S I I S I S S R I R 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] 32 64 8 0.5 0.25 8 0.0625 32 16
#> [10] 0.0625 <=0.001 0.25 2 0.005 0.125 0.01 0.025 0.025
#> [19] 0.5 32 0.025 16 32 >=128 2
random_mic(25, "Klebsiella pneumoniae", "meropenem") # range 0.0625-16
#> Class 'mic'
#> [1] 8 0.5 2 16 1 8 1 0.25 0.5 2 8 8 1 4 8
#> [16] 1 2 16 16 2 16 2 0.5 4 8
random_mic(25, "Streptococcus pneumoniae", "meropenem") # range 0.0625-4
#> Class 'mic'
#> [1] 0.5 >=8 1 0.25 1 2 >=8 0.125 0.25 0.125 0.25 1
#> [13] 0.125 0.25 0.25 0.25 >=8 0.125 0.5 0.25 0.125 0.25 1 0.5
#> [25] 0.125
random_disk(25, "Klebsiella pneumoniae") # range 8-50
#> Class 'disk'
#> [1] 41 35 31 49 20 49 19 45 43 17 45 47 40 28 19 48 11 40 13 28 48 39 20 17 23
random_disk(25, "Klebsiella pneumoniae", "ampicillin") # range 11-17
#> Class 'disk'
#> [1] 11 11 15 15 14 17 12 16 17 14 12 11 11 16 13 14 14 12 17 14 14 11 12 14 13
random_disk(25, "Streptococcus pneumoniae", "ampicillin") # range 12-27
#> Class 'disk'
#> [1] 21 23 27 25 16 16 20 20 23 23 18 19 15 23 15 24 22 25 21 17 25 15 16 18 22
# }