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] >=256 32 <=0.001 32 1 0.005 0.5 4 0.0625
#> [10] 128 >=256 >=256 8 0.125 8 0.002 1 0.005
#> [19] 128 0.25 0.025 8 <=0.001 <=0.001 16
random_disk(25)
#> Class 'disk'
#> [1] 18 7 50 40 43 33 21 21 43 17 40 46 46 9 14 13 27 14 17 18 42 19 19 30 36
random_sir(25)
#> Class 'sir'
#> [1] R R S R S R S S I I I S R I S S R I I R I I S 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] 1 0.25 32 32 0.25 0.002 0.25 16 0.125
#> [10] 0.5 16 <=0.001 4 2 0.005 0.5 0.025 8
#> [19] 2 64 32 0.5 0.005 <=0.001 0.0625
random_mic(25, "Klebsiella pneumoniae", "meropenem") # range 0.0625-16
#> Class 'mic'
#> [1] 1 2 0.25 0.5 1 1 0.5 0.5 0.5 16 1 1 0.5 0.5 1
#> [16] 16 1 16 0.5 2 4 8 4 1 1
random_mic(25, "Streptococcus pneumoniae", "meropenem") # range 0.0625-4
#> Class 'mic'
#> [1] <=0.025 1 0.25 <=0.025 0.0625 <=0.025 0.125 >=4 >=4
#> [10] 1 1 1 1 <=0.025 0.25 1 0.0625 0.25
#> [19] 0.125 <=0.025 0.125 0.125 >=4 0.25 >=4
random_disk(25, "Klebsiella pneumoniae") # range 8-50
#> Class 'disk'
#> [1] 47 39 14 30 49 29 13 31 35 41 11 42 18 34 35 22 36 14 48 40 41 46 12 32 34
random_disk(25, "Klebsiella pneumoniae", "ampicillin") # range 11-17
#> Class 'disk'
#> [1] 13 11 17 11 14 12 13 16 12 13 11 11 15 15 15 17 11 11 16 12 12 16 14 11 17
random_disk(25, "Streptococcus pneumoniae", "ampicillin") # range 12-27
#> Class 'disk'
#> [1] 15 19 16 23 16 27 15 20 27 21 26 20 20 27 22 26 19 26 19 26 23 23 16 17 24
# }