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] 1 16 4 0.125 4 0.005 0.001 0.01 >=128 32
#> [11] 16 0.001 64 64 0.125 0.001 64 0.0625 0.002 0.005
#> [21] 64 2 0.25 0.01 1
random_disk(25)
#> Class 'disk'
#> [1] 28 21 50 8 29 44 46 42 24 6 41 19 39 48 19 18 49 7 15 36 50 50 48 8 35
random_sir(25)
#> Class 'sir'
#> [1] I I I I R S I I R I R S I R I I R R I S S I I S 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] 0.0625 16 0.025 4 32 0.025 0.002 0.0625 2 0.25
#> [11] 0.0625 0.125 0.001 16 0.001 1 0.25 0.5 64 0.005
#> [21] 4 4 0.125 0.002 0.5
random_mic(25, "Klebsiella pneumoniae", "meropenem") # range 0.0625-16
#> Class 'mic'
#> [1] >=16 0.5 8 8 4 >=16 1 1 4 1 8 4 >=16 4 0.5
#> [16] 1 >=16 4 2 2 4 2 8 0.5 1
random_mic(25, "Streptococcus pneumoniae", "meropenem") # range 0.0625-4
#> Class 'mic'
#> [1] >=8 4 2 <=0.0625 0.25 1 1 0.25
#> [9] <=0.0625 0.25 0.5 1 >=8 1 2 <=0.0625
#> [17] >=8 <=0.0625 1 1 1 4 0.125 0.125
#> [25] 2
random_disk(25, "Klebsiella pneumoniae") # range 8-50
#> Class 'disk'
#> [1] 15 46 20 39 24 36 50 42 15 12 11 17 40 16 46 44 48 50 24 50 29 14 39 43 14
random_disk(25, "Klebsiella pneumoniae", "ampicillin") # range 11-17
#> Class 'disk'
#> [1] 16 11 11 13 11 16 17 16 11 11 14 11 11 14 16 14 16 12 12 13 14 13 17 12 11
random_disk(25, "Streptococcus pneumoniae", "ampicillin") # range 12-27
#> Class 'disk'
#> [1] 25 16 23 19 25 20 24 17 27 16 18 17 18 20 19 24 20 23 23 20 19 25 23 17 16
# }