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] 0.01 1 0.125 >=256 32 0.005 0.25 0.25 1
#> [10] 32 64 0.125 32 4 0.0625 16 <=0.001 >=256
#> [19] 1 1 32 0.125 2 16 0.5
random_disk(25)
#> Class 'disk'
#> [1] 18 26 28 25 20 42 41 9 45 22 49 25 50 32 23 20 23 41 46 28 46 40 48 37 24
random_sir(25)
#> Class 'sir'
#> [1] S S R R S S R R R I I S S I I I R I I R I R R I 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] 0.001 32 128 128 8 4 0.25 0.005 0.01 128
#> [11] 0.002 0.01 0.25 0.002 0.025 1 4 0.25 16 128
#> [21] 128 8 0.5 0.0625 16
random_mic(25, "Klebsiella pneumoniae", "meropenem") # range 0.0625-16
#> Class 'mic'
#> [1] 0.5 16 0.5 0.5 >=32 8 8 1 8 >=32 >=32 2 0.5 0.5 1
#> [16] 2 0.5 4 2 1 0.5 >=32 2 0.5 0.25
random_mic(25, "Streptococcus pneumoniae", "meropenem") # range 0.0625-4
#> Class 'mic'
#> [1] 1 1 0.25 2 <=0.125 2 0.25 1 0.5
#> [10] 0.5 4 <=0.125 0.25 4 0.25 0.5 2 <=0.125
#> [19] 2 1 1 0.25 <=0.125 0.5 <=0.125
random_disk(25, "Klebsiella pneumoniae") # range 8-50
#> Class 'disk'
#> [1] 41 46 50 12 9 33 34 12 50 35 19 12 41 34 13 48 10 42 16 20 10 49 29 17 42
random_disk(25, "Klebsiella pneumoniae", "ampicillin") # range 11-17
#> Class 'disk'
#> [1] 12 13 11 16 16 14 14 12 13 17 17 16 13 13 13 15 15 17 13 17 15 11 12 16 12
random_disk(25, "Streptococcus pneumoniae", "ampicillin") # range 12-27
#> Class 'disk'
#> [1] 17 23 25 25 19 23 18 25 16 17 15 22 24 15 22 17 15 26 25 25 21 25 22 16 27
# }