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] 0.025 16 2 64 0.5 0.01 8 2 16 0.025
#> [11] 0.125 0.002 0.001 16 0.0625 1 0.001 0.001 0.0625 2
#> [21] 0.025 0.001 64 32 64
random_disk(25)
#> Class 'disk'
#> [1] 26 50 43 50 14 13 12 7 15 49 10 6 48 40 38 45 43 50 36 45 36 29 27 37 34
random_sir(25)
#> Class 'sir'
#> [1] R I S I R R R S I S S R R I S I R S I R I I R R I
# \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 >=64 4 0.01 4 16 0.0625 <=0.001 >=64
#> [10] <=0.001 0.005 0.002 0.01 <=0.001 0.0625 2 0.0625 <=0.001
#> [19] 2 1 0.025 8 0.0625 >=64 0.005
random_mic(25, "Klebsiella pneumoniae", "meropenem") # range 0.0625-16
#> Class 'mic'
#> [1] 1 0.5 0.5 4 >=32 4 1 2 4 4 2 0.5 1 2 8
#> [16] 1 >=32 >=32 0.5 8 0.5 2 0.5 4 >=32
random_mic(25, "Streptococcus pneumoniae", "meropenem") # range 0.0625-4
#> Class 'mic'
#> [1] 1 0.0625 0.0625 0.125 0.25 2 0.0625 0.0625 0.125 1
#> [11] 0.0625 0.125 0.125 4 0.0625 4 0.125 0.25 0.5 1
#> [21] 0.0625 0.0625 0.5 0.125 0.5
random_disk(25, "Klebsiella pneumoniae") # range 8-50
#> Class 'disk'
#> [1] 40 12 48 48 41 39 44 22 46 45 19 9 37 49 50 18 9 42 14 16 50 39 14 45 44
random_disk(25, "Klebsiella pneumoniae", "ampicillin") # range 11-17
#> Class 'disk'
#> [1] 13 13 17 14 17 12 11 11 14 17 15 15 14 15 13 13 15 11 11 17 12 12 14 13 14
random_disk(25, "Streptococcus pneumoniae", "ampicillin") # range 12-27
#> Class 'disk'
#> [1] 25 23 24 18 15 27 25 17 24 18 17 15 16 21 27 16 24 20 17 23 25 22 19 23 24
# }