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] 1 32 0.5 8 0.002 16 32 >=128 <=0.001
#> [10] 0.025 32 16 0.25 0.125 >=128 32 0.25 0.125
#> [19] 2 0.0625 0.5 0.005 0.005 0.5 0.005
random_disk(25)
#> Class 'disk'
#> [1] 20 9 38 12 19 9 15 10 28 47 9 28 40 15 45 50 40 36 31 26 45 35 42 38 18
random_sir(25)
#> Class 'sir'
#> [1] I R I S R S I I R R S S R S R R R I S S R I I I 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] 0.001 1 >=32 0.5 0.5 0.5 16 0.01 0.0625 0.005
#> [11] 4 0.5 4 0.125 0.001 0.125 0.002 0.01 0.5 0.0625
#> [21] >=32 0.001 2 16 0.001
random_mic(25, "Klebsiella pneumoniae", "meropenem") # range 0.0625-16
#> Class 'mic'
#> [1] 8 4 0.5 4 2 4 >=16 >=16 2 1 2 4 2 4 4
#> [16] 8 2 >=16 4 8 4 8 1 4 2
random_mic(25, "Streptococcus pneumoniae", "meropenem") # range 0.0625-4
#> Class 'mic'
#> [1] 0.0625 0.125 4 0.125 0.25 4 8 0.25 1 >=16
#> [11] 8 4 8 0.0625 0.5 0.25 >=16 0.5 2 0.25
#> [21] 4 0.0625 4 2 0.125
random_disk(25, "Klebsiella pneumoniae") # range 8-50
#> Class 'disk'
#> [1] 9 14 25 18 50 13 9 32 46 45 50 46 42 28 29 37 29 14 16 41 29 9 25 44 20
random_disk(25, "Klebsiella pneumoniae", "ampicillin") # range 11-17
#> Class 'disk'
#> [1] 14 12 17 12 11 17 12 16 17 14 11 11 16 12 16 14 17 12 17 17 13 11 13 13 13
random_disk(25, "Streptococcus pneumoniae", "ampicillin") # range 12-27
#> Class 'disk'
#> [1] 18 20 25 26 20 22 24 24 24 18 23 20 16 15 25 17 16 19 24 16 21 15 19 15 22
# }