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] 0.125 2 4 2 4 16 0.5 0.001 16 2
#> [11] 0.0625 0.0625 0.125 >=256 0.5 0.005 0.5 >=256 0.025 0.001
#> [21] 0.0625 0.002 2 0.5 0.025
random_disk(25)
#> Class 'disk'
#> [1] 8 46 36 11 43 15 43 50 18 49 26 42 50 39 48 44 34 44 46 6 40 40 45 13 39
random_sir(25)
#> Class 'sir'
#> [1] I S S R I I I R R I I I I R I I S R R I R R S S 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] 8 0.5 1 32 0.25 >=128 1 8 32
#> [10] <=0.001 <=0.001 0.01 0.5 0.002 0.025 1 0.125 2
#> [19] 1 0.01 0.01 0.0625 <=0.001 0.005 16
random_mic(25, "Klebsiella pneumoniae", "meropenem") # range 0.0625-16
#> Class 'mic'
#> [1] 8 1 >=16 >=16 4 0.5 1 8 0.5 8 8 4 8 8 >=16
#> [16] 8 >=16 1 4 >=16 4 >=16 4 1 8
random_mic(25, "Streptococcus pneumoniae", "meropenem") # range 0.0625-4
#> Class 'mic'
#> [1] 16 0.25 1 8 0.125 2 2 2 4 1 1 16
#> [13] 4 2 0.25 0.25 8 4 8 0.125 2 8 8 0.125
#> [25] 2
random_disk(25, "Klebsiella pneumoniae") # range 8-50
#> Class 'disk'
#> [1] 26 40 25 44 10 49 50 46 38 23 11 48 45 11 25 29 47 50 46 8 47 31 40 48 42
random_disk(25, "Klebsiella pneumoniae", "ampicillin") # range 11-17
#> Class 'disk'
#> [1] 14 16 13 14 11 11 15 14 11 16 11 16 17 15 17 13 16 17 17 14 11 15 14 16 13
random_disk(25, "Streptococcus pneumoniae", "ampicillin") # range 12-27
#> Class 'disk'
#> [1] 18 27 27 15 16 18 18 22 17 27 25 20 23 22 22 25 16 20 18 16 16 22 19 18 24
# }