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 2023 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] 0.005 128 1 0.01 0.002 0.01 4 8 0.01 0.002
#> [11] 8 0.5 2 0.0625 8 2 128 4 0.5 0.125
#> [21] 0.005 0.005 0.125 4 0.001
random_disk(25)
#> Class 'disk'
#> [1] 16 34 40 10 14 49 42 17 17 16 44 22 9 24 40 25 8 47 47 38 17 42 41 41 32
random_sir(25)
#> Class 'sir'
#> [1] S R I I S I S I S R I S I I S I I R S R R S 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] 64 0.025 4 0.005 0.01 1 32 32 0.5
#> [10] 0.5 0.25 32 2 0.5 0.002 0.5 2 0.01
#> [19] 32 64 <=0.001 0.01 2 8 0.025
random_mic(25, "Klebsiella pneumoniae", "meropenem") # range 0.0625-16
#> Class 'mic'
#> [1] 2 >=16 0.25 0.5 0.25 4 2 8 1 8 2 0.5 1 8 0.25
#> [16] 1 >=16 0.5 0.5 1 8 0.5 >=16 4 4
random_mic(25, "Streptococcus pneumoniae", "meropenem") # range 0.0625-4
#> Class 'mic'
#> [1] 2 0.5 <=0.125 <=0.125 <=0.125 0.25 0.25 <=0.125 1
#> [10] 1 1 2 2 4 <=0.125 2 <=0.125 0.25
#> [19] 2 0.5 2 2 <=0.125 0.5 0.5
random_disk(25, "Klebsiella pneumoniae") # range 8-50
#> Class 'disk'
#> [1] 32 41 32 19 38 41 38 37 32 49 38 33 50 44 14 10 47 32 18 29 13 42 22 24 48
random_disk(25, "Klebsiella pneumoniae", "ampicillin") # range 11-17
#> Class 'disk'
#> [1] 13 14 13 16 12 16 16 12 14 15 17 13 14 12 16 12 11 14 17 16 17 13 11 13 14
random_disk(25, "Streptococcus pneumoniae", "ampicillin") # range 12-27
#> Class 'disk'
#> [1] 17 18 24 27 26 24 15 19 17 19 21 15 27 22 26 23 15 25 22 21 17 24 24 15 17
# }