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] 0.01 0.002 4 0.125 0.25 0.25 4 1 1 0.125
#> [11] 1 64 2 0.005 0.005 0.25 0.002 0.005 0.25 0.0625
#> [21] 1 256 64 0.005 0.5
random_disk(25)
#> Class 'disk'
#> [1] 20 44 20 18 7 41 37 11 47 40 41 49 38 12 34 33 20 22 32 27 35 48 48 24 40
random_sir(25)
#> Class 'sir'
#> [1] R I I R S I R R R S I S I I I S R S R S I S R R S
# \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] >=32 0.002 0.25 0.001 4 1 0.25 0.005 0.025 0.025
#> [11] 0.5 16 0.25 0.001 4 0.025 0.0625 0.5 8 4
#> [21] 1 0.002 8 0.5 0.001
random_mic(25, "Klebsiella pneumoniae", "meropenem") # range 0.0625-16
#> Class 'mic'
#> [1] 2 >=32 8 >=32 16 >=32 16 4 1 2 16 1 1 >=32 >=32
#> [16] 16 >=32 1 >=32 >=32 8 1 16 4 16
random_mic(25, "Streptococcus pneumoniae", "meropenem") # range 0.0625-4
#> Class 'mic'
#> [1] <=0.125 8 <=0.125 2 1 1 0.25 1 8
#> [10] <=0.125 2 2 1 0.25 1 4 1 0.25
#> [19] <=0.125 0.5 <=0.125 2 0.25 2 8
random_disk(25, "Klebsiella pneumoniae") # range 8-50
#> Class 'disk'
#> [1] 49 18 23 28 48 32 8 40 13 41 15 47 24 10 42 41 33 33 23 49 49 30 22 49 48
random_disk(25, "Klebsiella pneumoniae", "ampicillin") # range 11-17
#> Class 'disk'
#> [1] 14 14 13 17 14 11 13 17 16 16 12 13 13 17 14 16 15 14 17 15 12 15 12 13 11
random_disk(25, "Streptococcus pneumoniae", "ampicillin") # range 12-27
#> Class 'disk'
#> [1] 21 25 26 18 15 19 26 18 26 20 21 23 23 27 26 26 18 27 27 22 26 16 25 15 19
# }