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_rsi(size = NULL, prob_RSI = 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_RSI
a vector of length 3: the probabilities for "R" (1st value), "S" (2nd value) and "I" (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 rsi_translation 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] 2 64 0.025 0.5 0.001 0.001 >=128 >=128 4 0.5 0.002 0.01
#> [13] 4 32 32 0.125 0.125 0.005 2 16 0.001 0.125 0.002 0.01
#> [25] 0.01
random_disk(25)
#> Class 'disk'
#> [1] 7 27 48 15 19 48 10 49 9 18 37 43 23 37 26 29 6 40 36 19 36 10 33 18 32
random_rsi(25)
#> Class 'rsi'
#> [1] I R R I S R I I I S S S R S S I S I I R S R I 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] 64 0.005 4 4 0.002 0.001 8 64 32 0.005
#> [11] 1 0.025 0.01 2 0.01 0.5 64 4 8 0.002
#> [21] 64 0.01 0.005 0.5 0.0625
random_mic(25, "Klebsiella pneumoniae", "meropenem") # range 0.0625-16
#> Class 'mic'
#> [1] 16 16 1 2 2 16 16 8 2 2 >=32 4 1 4 16
#> [16] 16 16 2 1 2 16 8 16 2 8
random_mic(25, "Streptococcus pneumoniae", "meropenem") # range 0.0625-4
#> Class 'mic'
#> [1] 1 0.125 8 0.0625 0.025 0.025 0.5 8 0.125 0.5
#> [11] 8 1 0.5 0.125 1 0.25 8 0.0625 2 2
#> [21] 0.125 0.0625 1 4 0.125
random_disk(25, "Klebsiella pneumoniae") # range 8-50
#> Class 'disk'
#> [1] 42 27 16 43 29 46 49 22 27 8 36 28 40 44 41 8 12 45 44 42 38 49 24 40 10
random_disk(25, "Klebsiella pneumoniae", "ampicillin") # range 11-17
#> Class 'disk'
#> [1] 13 16 16 11 17 17 14 14 11 13 15 15 12 12 11 12 16 14 17 15 15 14 14 12 14
random_disk(25, "Streptococcus pneumoniae", "ampicillin") # range 12-27
#> Class 'disk'
#> [1] 27 17 19 26 24 23 23 25 17 27 15 15 26 20 19 26 22 19 18 26 21 20 17 24 23
# }