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 2024 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] <=0.005 0.25 1 0.0625 128 0.01 1 4 128
#> [10] <=0.005 0.25 0.5 0.125 0.01 0.25 2 8 16
#> [19] 0.125 0.5 >=256 >=256 >=256 0.25 16
random_disk(25)
#> Class 'disk'
#> [1] 24 14 46 41 9 8 22 41 50 38 48 48 28 43 47 30 13 13 38 14 48 47 21 6 22
random_sir(25)
#> Class 'sir'
#> [1] I I I I I I S R R S I S S R I R R R I S S R R I 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] 0.025 4 1 0.0625 0.005 0.002 2 0.002 >=128 0.0625
#> [11] 0.125 0.5 0.002 0.01 0.001 0.002 0.01 32 64 0.005
#> [21] 0.01 1 4 1 32
random_mic(25, "Klebsiella pneumoniae", "meropenem") # range 0.0625-16
#> Class 'mic'
#> [1] <=1 4 4 2 32 4 32 16 <=1 32 8 8 32 8 4 32 <=1 <=1 16
#> [20] 8 32 8 16 4 8
random_mic(25, "Streptococcus pneumoniae", "meropenem") # range 0.0625-4
#> Class 'mic'
#> [1] 0.125 >=16 0.125 >=16 2 0.5 1 0.5
#> [9] 0.125 0.5 <=0.0625 0.25 0.25 0.5 >=16 >=16
#> [17] 1 >=16 8 0.25 8 0.25 >=16 >=16
#> [25] 0.125
random_disk(25, "Klebsiella pneumoniae") # range 8-50
#> Class 'disk'
#> [1] 42 36 49 13 45 50 37 33 30 14 23 15 30 9 21 47 32 17 48 47 24 23 14 27 48
random_disk(25, "Klebsiella pneumoniae", "ampicillin") # range 11-17
#> Class 'disk'
#> [1] 13 16 13 16 13 11 17 12 16 14 14 15 11 16 12 13 14 12 13 12 15 12 12 13 17
random_disk(25, "Streptococcus pneumoniae", "ampicillin") # range 12-27
#> Class 'disk'
#> [1] 16 20 25 24 21 22 21 16 15 18 18 25 19 26 27 26 21 21 19 25 15 22 19 24 26
# }