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 0.125 0.002 0.0625 16 32 0.25 0.005 32
#> [10] 32 0.025 0.025 0.01 16 0.25 32 0.005 8
#> [19] >=128 0.002 0.01 0.002 8 <=0.001 0.01
random_disk(25)
#> Class 'disk'
#> [1] 39 44 20 34 35 49 41 9 45 26 38 38 43 44 43 27 44 29 42 27 11 46 7 43 46
random_sir(25)
#> Class 'sir'
#> [1] S I R S S R R I S R S S S R R I I I R S I R S I 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] 2 1 0.0625 0.01 1 0.25 0.125 0.005 0.125 >=64
#> [11] 0.25 0.025 0.125 1 0.005 0.25 0.025 32 0.25 32
#> [21] 32 0.0625 0.125 0.01 0.125
random_mic(25, "Klebsiella pneumoniae", "meropenem") # range 0.0625-16
#> Class 'mic'
#> [1] 2 1 2 8 2 4 <=0.5 <=0.5 >=16 >=16 1 4
#> [13] 4 4 >=16 1 4 <=0.5 4 2 1 2 1 2
#> [25] 2
random_mic(25, "Streptococcus pneumoniae", "meropenem") # range 0.0625-4
#> Class 'mic'
#> [1] 1 0.25 1 <=0.025 2 2 0.125 0.5 1
#> [10] 0.0625 <=0.025 1 0.5 0.125 >=4 >=4 0.25 0.125
#> [19] 0.125 0.5 <=0.025 <=0.025 0.25 0.5 0.5
random_disk(25, "Klebsiella pneumoniae") # range 8-50
#> Class 'disk'
#> [1] 14 34 36 16 21 47 29 46 32 45 27 45 25 37 42 36 34 30 49 28 22 45 46 41 34
random_disk(25, "Klebsiella pneumoniae", "ampicillin") # range 11-17
#> Class 'disk'
#> [1] 15 14 14 11 13 11 16 17 12 11 11 15 15 16 14 11 12 13 14 14 16 17 14 16 12
random_disk(25, "Streptococcus pneumoniae", "ampicillin") # range 12-27
#> Class 'disk'
#> [1] 27 19 26 21 24 27 23 22 19 25 23 27 25 25 21 20 20 27 21 19 26 22 26 27 24
# }