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 agent, 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 agent 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] 128 32 128 0.01 0.005 0.125 32 256 64 256 0.001 0.001
#> [13] 4 0.025 32 1 0.5 32 1 0.001 0.5 0.5 0.005 0.001
#> [25] 8
random_disk(25)
#> Class 'disk'
#> [1] 18 41 42 38 50 47 45 30 44 7 22 24 47 42 41 7 40 39 6 35 9 23 9 48 45
random_rsi(25)
#> Class 'rsi'
#> [1] I R I S S I R I I R S R S I S I R S S I R S R R I
# \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] 16 0.025 16 0.0625 2 4 4 4 0.001 0.002
#> [11] 0.001 64 0.005 0.005 0.025 32 8 0.001 0.25 0.005
#> [21] 2 32 16 0.005 0.5
random_mic(25, "Klebsiella pneumoniae", "meropenem") # range 0.0625-16
#> Class 'mic'
#> [1] 0.5 0.5 2 4 4 0.5 2 16 8 >=64 32 0.5 4 2 >=64
#> [16] 0.5 4 8 32 >=64 32 4 0.5 16 32
random_mic(25, "Streptococcus pneumoniae", "meropenem") # range 0.0625-4
#> Class 'mic'
#> [1] 0.25 8 8 4 8 8 4 4 1 1 0.5 2 4 2 0.25
#> [16] 0.25 0.5 8 4 2 0.5 4 1 4 8
random_disk(25, "Klebsiella pneumoniae") # range 8-50
#> Class 'disk'
#> [1] 17 43 50 49 46 32 47 35 39 31 14 46 50 37 15 39 40 33 24 26 40 44 31 31 46
random_disk(25, "Klebsiella pneumoniae", "ampicillin") # range 11-17
#> Class 'disk'
#> [1] 16 12 11 15 13 16 16 12 17 12 12 16 16 15 16 11 14 15 11 15 12 17 12 12 16
random_disk(25, "Streptococcus pneumoniae", "ampicillin") # range 12-27
#> Class 'disk'
#> [1] 24 19 21 27 21 25 22 18 25 17 25 20 27 25 16 17 16 24 18 17 20 17 18 20 25
# }