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 2 4 0.01 <=0.001 0.01 8 0.01 8
#> [10] 4 16 64 0.01 0.005 0.25 0.125 0.25 8
#> [19] 0.025 1 8 0.005 0.01 <=0.001 0.01
random_disk(25)
#> Class 'disk'
#> [1] 11 40 41 23 18 8 43 47 14 7 13 50 15 45 42 46 44 47 47 44 42 11 22 49 42
random_sir(25)
#> Class 'sir'
#> [1] R S R I S R I I S I S I S I I R I S S R S S I R 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] 0.005 32 0.025 0.002 0.025 1 0.25 0.5 0.25 0.125
#> [11] 32 16 0.0625 0.01 0.002 4 0.002 0.005 2 32
#> [21] 2 0.01 0.025 0.5 64
random_mic(25, "Klebsiella pneumoniae", "meropenem") # range 0.0625-16
#> Class 'mic'
#> [1] 8 1 8 1 4 16 2 1 4 2 16 1 4 1 1 1 16 4 8 1 2 1 8 4 16
random_mic(25, "Streptococcus pneumoniae", "meropenem") # range 0.0625-4
#> Class 'mic'
#> [1] 0.0625 1 0.125 0.125 <=0.025 <=0.025 0.0625 >=8 0.0625
#> [10] 4 2 0.0625 1 >=8 0.125 2 0.25 4
#> [19] 0.125 0.125 1 >=8 0.5 4 0.25
random_disk(25, "Klebsiella pneumoniae") # range 8-50
#> Class 'disk'
#> [1] 43 36 15 45 10 35 19 20 36 49 43 22 38 49 45 47 23 28 27 27 41 50 41 48 13
random_disk(25, "Klebsiella pneumoniae", "ampicillin") # range 11-17
#> Class 'disk'
#> [1] 11 14 15 15 17 12 11 17 15 13 16 12 11 12 13 14 15 11 16 13 12 12 13 16 15
random_disk(25, "Streptococcus pneumoniae", "ampicillin") # range 12-27
#> Class 'disk'
#> [1] 26 24 20 19 16 23 16 17 25 26 15 23 18 18 19 26 18 15 16 25 24 27 23 16 23
# }