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] 4 0.125 0.25 0.0625 0.125 8 4 0.125 1
#> [10] 128 0.002 0.25 16 64 4 128 32 0.002
#> [19] <=0.001 0.125 0.125 0.005 64 0.0625 <=0.001
random_disk(25)
#> Class 'disk'
#> [1] 7 22 23 44 40 29 7 32 41 7 34 43 37 46 44 49 48 6 13 49 42 12 49 47 46
random_sir(25)
#> Class 'sir'
#> [1] S S S S R I S I R I I R S R I I S S I I I S I 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] 0.0625 0.025 0.01 16 4 0.025 64 128 128 2
#> [11] 0.25 0.125 16 0.125 0.5 0.005 0.25 16 16 1
#> [21] 0.125 64 0.002 1 0.01
random_mic(25, "Klebsiella pneumoniae", "meropenem") # range 0.0625-16
#> Class 'mic'
#> [1] 0.5 8 2 16 >=32 2 0.5 >=32 8 16 0.25 4 4 16 0.5
#> [16] >=32 1 1 0.25 >=32 1 2 1 16 2
random_mic(25, "Streptococcus pneumoniae", "meropenem") # range 0.0625-4
#> Class 'mic'
#> [1] 8 0.5 2 0.125 0.25 >=16 >=16 1
#> [9] 8 0.25 8 1 0.25 0.5 <=0.0625 1
#> [17] 8 0.125 4 8 8 >=16 1 1
#> [25] 1
random_disk(25, "Klebsiella pneumoniae") # range 8-50
#> Class 'disk'
#> [1] 17 25 45 40 20 17 33 24 9 28 19 49 44 12 50 27 12 48 29 49 9 41 45 23 41
random_disk(25, "Klebsiella pneumoniae", "ampicillin") # range 11-17
#> Class 'disk'
#> [1] 17 12 12 16 11 11 15 17 14 17 14 11 12 14 15 14 16 11 14 15 11 12 16 13 11
random_disk(25, "Streptococcus pneumoniae", "ampicillin") # range 12-27
#> Class 'disk'
#> [1] 22 18 25 24 18 19 15 21 25 20 15 17 21 22 26 19 16 26 19 19 19 19 26 27 17
# }