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] 0.005 64 0.001 1 2 0.005 0.025 0.0625 0.005 0.0625
#> [11] >=128 2 8 8 16 0.001 0.125 32 0.01 8
#> [21] 2 0.5 0.0625 64 >=128
random_disk(25)
#> Class 'disk'
#> [1] 7 49 8 41 20 28 40 16 41 42 41 45 36 11 50 25 44 9 24 42 38 49 41 45 9
random_sir(25)
#> Class 'sir'
#> [1] R R S S R I R I I R S S I I I I I I I S I I S I 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] 0.002 64 0.005 0.001 0.5 0.025 2 0.005 0.0625 0.005
#> [11] 0.125 8 2 0.125 16 0.0625 0.001 0.005 0.005 0.01
#> [21] 0.005 64 0.005 0.025 0.0625
random_mic(25, "Klebsiella pneumoniae", "meropenem") # range 0.0625-16
#> Class 'mic'
#> [1] 8 1 >=32 2 8 1 4 16 1 8 1 1 >=32 16 16
#> [16] 16 2 >=32 1 8 8 1 4 1 16
random_mic(25, "Streptococcus pneumoniae", "meropenem") # range 0.0625-4
#> Class 'mic'
#> [1] 1 >=8 0.5 2 1 1 0.25 0.125 4 >=8 >=8 0.125
#> [13] >=8 >=8 4 2 0.25 >=8 >=8 4 >=8 4 0.125 2
#> [25] 2
random_disk(25, "Klebsiella pneumoniae") # range 8-50
#> Class 'disk'
#> [1] 46 14 10 45 47 37 40 15 19 44 16 20 26 46 43 12 10 22 43 49 48 47 13 15 35
random_disk(25, "Klebsiella pneumoniae", "ampicillin") # range 11-17
#> Class 'disk'
#> [1] 11 17 14 15 13 17 17 12 17 14 16 16 11 12 16 12 13 11 15 12 17 15 11 14 11
random_disk(25, "Streptococcus pneumoniae", "ampicillin") # range 12-27
#> Class 'disk'
#> [1] 24 20 20 23 24 25 21 16 27 16 21 21 27 23 23 23 20 15 23 25 21 17 21 16 20
# }