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] 0.002 0.001 0.5 0.5 0.01 8 0.0625 0.125 0.025 32
#> [11] 16 0.25 0.0625 0.025 0.01 >=128 4 64 >=128 0.125
#> [21] 4 0.005 >=128 0.0625 0.5
random_disk(25)
#> Class 'disk'
#> [1] 47 50 29 8 33 45 24 41 40 50 48 33 41 8 8 46 26 48 11 13 17 8 26 29 15
random_sir(25)
#> Class 'sir'
#> [1] I S R S I R S R S I S R S S S I I R I S S 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] <=0.001 <=0.001 0.005 0.005 0.5 0.002 0.125 16 1
#> [10] 4 8 16 64 0.0625 4 64 64 0.01
#> [19] 0.002 8 1 0.0625 0.0625 2 1
random_mic(25, "Klebsiella pneumoniae", "meropenem") # range 0.0625-16
#> Class 'mic'
#> [1] 4 16 <=0.5 4 32 4 4 16 16 <=0.5 32 <=0.5
#> [13] 8 16 32 <=0.5 <=0.5 64 16 8 <=0.5 1 4 8
#> [25] 64
random_mic(25, "Streptococcus pneumoniae", "meropenem") # range 0.0625-4
#> Class 'mic'
#> [1] 1 4 4 2 1 2 0.25 <=0.0625
#> [9] 4 1 0.125 1 0.125 4 0.125 <=0.0625
#> [17] 0.125 2 0.125 >=8 4 2 0.5 0.5
#> [25] >=8
random_disk(25, "Klebsiella pneumoniae") # range 8-50
#> Class 'disk'
#> [1] 48 8 8 30 49 17 48 32 32 43 43 28 21 43 27 42 46 22 49 41 30 33 45 36 18
random_disk(25, "Klebsiella pneumoniae", "ampicillin") # range 11-17
#> Class 'disk'
#> [1] 14 16 12 12 11 15 16 16 13 14 13 12 16 17 12 17 11 14 11 17 14 12 11 14 11
random_disk(25, "Streptococcus pneumoniae", "ampicillin") # range 12-27
#> Class 'disk'
#> [1] 24 17 20 17 26 27 26 19 18 21 24 19 19 27 23 17 17 21 24 16 18 21 18 26 19
# }