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] 1 0.5 4 1 <=0.001 0.125 16 256 0.01
#> [10] 0.125 128 4 0.5 16 0.0625 4 0.005 0.01
#> [19] <=0.001 8 64 64 4 0.005 2
random_disk(25)
#> Class 'disk'
#> [1] 47 28 48 25 23 10 14 47 37 13 14 7 23 15 21 7 11 41 41 7 40 30 47 26 11
random_rsi(25)
#> Class 'rsi'
#> [1] S R R I S I R R R R R I I S I S S S R R R R I S 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] 0.125 1 0.0625 2 64 1 0.5 32 64
#> [10] 0.025 16 0.01 0.005 0.5 0.025 0.0625 16 0.25
#> [19] 0.005 <=0.001 0.01 0.002 32 4 2
random_mic(25, "Klebsiella pneumoniae", "meropenem") # range 0.0625-16
#> Class 'mic'
#> [1] >=64 32 32 2 16 2 >=64 32 4 >=64 1 32 32 8 1
#> [16] >=64 4 8 2 4 >=64 16 4 1 4
random_mic(25, "Streptococcus pneumoniae", "meropenem") # range 0.0625-4
#> Class 'mic'
#> [1] 8 8 16 1 2 8 0.25 8 8 0.0625
#> [11] 1 0.0625 8 16 8 0.5 0.025 4 1 0.125
#> [21] 4 0.025 2 0.5 8
random_disk(25, "Klebsiella pneumoniae") # range 8-50
#> Class 'disk'
#> [1] 41 18 36 26 41 46 31 9 9 33 20 47 10 50 29 49 25 17 48 8 37 41 42 31 42
random_disk(25, "Klebsiella pneumoniae", "ampicillin") # range 11-17
#> Class 'disk'
#> [1] 13 15 14 14 11 12 16 12 15 17 13 15 12 11 12 17 16 17 17 15 15 16 11 15 15
random_disk(25, "Streptococcus pneumoniae", "ampicillin") # range 12-27
#> Class 'disk'
#> [1] 19 19 26 15 15 19 15 20 26 20 26 21 23 26 27 21 15 26 24 26 15 17 20 18 23
# }