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 32 >=128 0.01 0.002 64 0.5 0.125 0.25
#> [10] 0.01 0.01 1 0.125 0.25 64 16 2 0.0625
#> [19] 0.125 0.25 0.005 0.002 0.005 <=0.001 >=128
random_disk(25)
#> Class 'disk'
#> [1] 32 13 27 48 48 41 19 8 40 46 25 43 7 35 15 21 43 24 22 42 48 43 25 16 43
random_sir(25)
#> Class 'sir'
#> [1] R I I S R R R I R I R R S I S R S I I I I S I S 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] 0.5 0.125 4 >=256 1 0.0625 4 0.025 4 >=256
#> [11] 0.025 0.01 16 0.005 16 0.002 0.125 0.005 0.001 4
#> [21] 0.001 8 0.125 >=256 0.125
random_mic(25, "Klebsiella pneumoniae", "meropenem") # range 0.0625-16
#> Class 'mic'
#> [1] <=0.5 16 4 1 <=0.5 2 <=0.5 4 1 4 <=0.5 16
#> [13] 8 8 16 8 1 8 32 <=0.5 1 32 <=0.5 16
#> [25] 16
random_mic(25, "Streptococcus pneumoniae", "meropenem") # range 0.0625-4
#> Class 'mic'
#> [1] 0.25 <=0.0625 0.125 4 >=16 <=0.0625 4 <=0.0625
#> [9] 8 <=0.0625 1 0.125 0.5 4 2 0.125
#> [17] 4 >=16 0.5 0.5 0.5 1 8 1
#> [25] 1
random_disk(25, "Klebsiella pneumoniae") # range 8-50
#> Class 'disk'
#> [1] 38 39 25 42 14 43 18 25 41 14 24 19 45 27 44 40 46 12 50 40 8 45 12 46 29
random_disk(25, "Klebsiella pneumoniae", "ampicillin") # range 11-17
#> Class 'disk'
#> [1] 17 12 17 12 15 16 15 12 13 15 16 14 16 16 17 15 16 14 17 14 15 17 16 17 16
random_disk(25, "Streptococcus pneumoniae", "ampicillin") # range 12-27
#> Class 'disk'
#> [1] 24 25 23 16 25 27 22 16 27 16 24 18 25 20 20 19 22 20 26 24 15 17 20 17 26
# }