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] 4 >=128 0.0625 0.005 1 <=0.002 0.005 64 <=0.002
#> [10] 0.5 64 1 0.125 0.01 4 0.01 0.005 64
#> [19] 64 64 64 16 64 0.125 2
random_disk(25)
#> Class 'disk'
#> [1] 47 13 36 12 41 13 11 37 13 47 39 16 10 46 22 36 16 46 16 44 47 12 40 18 24
random_sir(25)
#> Class 'sir'
#> [1] I S I S S S S S R I R I I S R R S I S R R S 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] 2 0.025 1 2 64 0.25 16 4 128
#> [10] 32 0.0625 4 0.0625 2 1 <=0.005 0.01 0.125
#> [19] 16 4 0.025 4 4 32 16
random_mic(25, "Klebsiella pneumoniae", "meropenem") # range 0.0625-16
#> Class 'mic'
#> [1] 2 2 8 16 8 8 16 4 4 2 4 8 16 4 8 8 1 16 16 2 1 2 4 1 16
random_mic(25, "Streptococcus pneumoniae", "meropenem") # range 0.0625-4
#> Class 'mic'
#> [1] >=4 1 2 <=0.125 0.5 2 1 0.5 0.25
#> [10] <=0.125 2 0.25 <=0.125 <=0.125 2 2 <=0.125 >=4
#> [19] 2 0.5 <=0.125 0.5 0.5 1 2
random_disk(25, "Klebsiella pneumoniae") # range 8-50
#> Class 'disk'
#> [1] 27 43 17 42 21 27 42 19 21 17 26 40 14 9 34 16 49 30 41 31 40 43 46 45 8
random_disk(25, "Klebsiella pneumoniae", "ampicillin") # range 11-17
#> Class 'disk'
#> [1] 15 11 13 11 11 12 17 11 12 12 17 17 16 14 14 16 14 15 12 17 15 15 16 12 15
random_disk(25, "Streptococcus pneumoniae", "ampicillin") # range 12-27
#> Class 'disk'
#> [1] 26 20 19 18 19 25 22 23 19 18 15 25 19 18 22 24 16 22 26 22 21 21 23 23 23
# }