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] 8 0.002 0.005 64 8 64 4 0.005 0.0625
#> [10] 256 <=0.001 0.025 0.005 8 128 64 0.5 0.01
#> [19] 128 32 256 16 0.025 0.025 2
random_disk(25)
#> Class 'disk'
#> [1] 10 46 26 42 41 24 40 9 42 19 41 9 37 18 21 49 6 43 27 43 43 47 23 43 43
random_sir(25)
#> Class 'sir'
#> [1] S I I I R I I I S S R S I S I S R I S S S I I I R
# \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 1 8 0.25 0.002 8 1 8 4 0.01 0.002 >=128
#> [13] 4 >=128 2 >=128 32 64 0.25 0.001 16 2 0.01 0.002
#> [25] 64
random_mic(25, "Klebsiella pneumoniae", "meropenem") # range 0.0625-16
#> Class 'mic'
#> [1] <=0.5 4 16 <=0.5 4 2 4 1 <=0.5 <=0.5 32 <=0.5
#> [13] 4 4 8 4 16 1 4 4 16 32 32 2
#> [25] 32
random_mic(25, "Streptococcus pneumoniae", "meropenem") # range 0.0625-4
#> Class 'mic'
#> [1] 2 2 1 >=8 0.5 1 4 2 2
#> [10] <=0.125 >=8 4 0.25 <=0.125 0.25 <=0.125 1 4
#> [19] <=0.125 >=8 4 <=0.125 0.25 1 0.25
random_disk(25, "Klebsiella pneumoniae") # range 8-50
#> Class 'disk'
#> [1] 33 42 11 29 50 9 21 21 40 33 49 16 49 27 12 14 40 47 44 8 43 29 48 33 44
random_disk(25, "Klebsiella pneumoniae", "ampicillin") # range 11-17
#> Class 'disk'
#> [1] 16 11 16 11 15 17 15 16 14 17 11 12 11 17 13 13 12 16 16 16 13 12 11 13 13
random_disk(25, "Streptococcus pneumoniae", "ampicillin") # range 12-27
#> Class 'disk'
#> [1] 21 24 21 20 26 24 18 25 19 25 20 19 23 16 21 20 18 18 19 17 16 17 21 18 27
# }