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] <=0.001 0.01 0.5 0.005 16 0.01 0.125 2 0.005
#> [10] 1 8 0.5 0.01 64 128 256 128 0.5
#> [19] 2 256 0.005 0.125 1 <=0.001 2
random_disk(25)
#> Class 'disk'
#> [1] 49 14 6 19 16 27 29 24 37 47 22 42 45 48 38 50 50 44 29 42 9 34 48 42 47
random_sir(25)
#> Class 'sir'
#> [1] R S S R I S I R R R S I R S R I S S R R 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] 0.001 8 0.001 0.025 0.5 16 0.5 0.005 1 16
#> [11] 0.0625 16 0.025 0.5 0.5 64 0.125 0.25 0.001 0.002
#> [21] 0.025 32 2 2 0.25
random_mic(25, "Klebsiella pneumoniae", "meropenem") # range 0.0625-16
#> Class 'mic'
#> [1] 2 >=32 >=32 8 16 4 1 <=0.5 >=32 1 1 8
#> [13] 8 2 <=0.5 8 8 16 4 16 2 >=32 16 <=0.5
#> [25] <=0.5
random_mic(25, "Streptococcus pneumoniae", "meropenem") # range 0.0625-4
#> Class 'mic'
#> [1] 0.5 4 0.125 2 1 0.0625 0.0625 8 0.5 0.5
#> [11] 0.0625 0.125 0.025 4 8 1 4 0.0625 0.0625 4
#> [21] 0.025 0.025 2 8 4
random_disk(25, "Klebsiella pneumoniae") # range 8-50
#> Class 'disk'
#> [1] 48 32 50 49 47 30 38 18 49 32 25 47 11 48 17 38 12 42 50 43 45 46 43 48 49
random_disk(25, "Klebsiella pneumoniae", "ampicillin") # range 11-17
#> Class 'disk'
#> [1] 17 15 13 16 12 17 17 14 15 12 12 14 17 13 17 11 12 15 14 11 17 17 15 15 13
random_disk(25, "Streptococcus pneumoniae", "ampicillin") # range 12-27
#> Class 'disk'
#> [1] 26 20 22 24 25 19 19 20 21 21 16 19 24 22 23 17 18 25 26 22 17 15 19 19 15
# }