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] 2 0.25 64 0.002 1 0.001 0.001 >=256 0.5 0.001
#> [11] 64 >=256 64 0.001 >=256 1 0.025 128 0.125 0.001
#> [21] 0.025 0.5 32 0.002 0.0625
random_disk(25)
#> Class 'disk'
#> [1] 11 47 38 24 40 41 33 14 35 42 37 44 14 48 46 19 48 10 8 46 50 37 34 11 37
random_sir(25)
#> Class 'sir'
#> [1] I R I I R I I R I S R R R I R I I R I S S I I S 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] 0.025 8 1 0.5 0.002 128 0.01 8 0.005 0.0625
#> [11] 1 0.025 0.025 0.125 0.002 4 0.002 0.005 0.025 0.0625
#> [21] 0.5 16 1 4 0.002
random_mic(25, "Klebsiella pneumoniae", "meropenem") # range 0.0625-16
#> Class 'mic'
#> [1] 16 1 4 4 >=32 16 8 2 8 16 >=32 2 4 4 4
#> [16] 8 4 4 1 16 2 16 2 4 1
random_mic(25, "Streptococcus pneumoniae", "meropenem") # range 0.0625-4
#> Class 'mic'
#> [1] 4 0.5 0.5 0.125 1 0.25 0.025 0.125 1 1
#> [11] 0.0625 0.125 0.025 0.025 0.025 0.025 4 0.0625 0.5 0.25
#> [21] 0.025 0.125 2 0.25 0.5
random_disk(25, "Klebsiella pneumoniae") # range 8-50
#> Class 'disk'
#> [1] 39 42 48 39 26 24 10 34 16 48 43 40 14 11 46 17 21 50 43 49 44 41 40 15 46
random_disk(25, "Klebsiella pneumoniae", "ampicillin") # range 11-17
#> Class 'disk'
#> [1] 16 17 11 14 17 15 16 15 11 15 17 12 15 14 16 11 12 17 17 15 12 11 17 15 14
random_disk(25, "Streptococcus pneumoniae", "ampicillin") # range 12-27
#> Class 'disk'
#> [1] 21 19 15 21 17 15 21 22 23 21 22 25 20 18 21 20 26 18 21 19 18 21 16 24 21
# }