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] 0.5 2 64 0.125 0.002 0.002 0.025 0.01 0.125
#> [10] 0.0625 2 8 0.0625 <=0.001 0.005 0.01 64 0.01
#> [19] 8 4 128 0.025 0.002 0.0625 1
random_disk(25)
#> Class 'disk'
#> [1] 14 47 8 11 16 15 29 41 30 34 42 48 31 11 30 49 13 47 13 35 9 50 41 16 48
random_rsi(25)
#> Class 'rsi'
#> [1] R I R R I I I R R R I R S I S R S R S I S R I R 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] 1 0.01 0.125 4 0.0625 2 64 >=256 8 0.125
#> [11] 0.002 16 64 0.0625 128 0.025 8 128 >=256 128
#> [21] 0.025 0.001 0.5 4 0.002
random_mic(25, "Klebsiella pneumoniae", "meropenem") # range 0.0625-16
#> Class 'mic'
#> [1] 32 32 1 16 2 16 16 8 2 4 16 1 4 16 2 1 1 8 16 8 2 16 16 1 8
random_mic(25, "Streptococcus pneumoniae", "meropenem") # range 0.0625-4
#> Class 'mic'
#> [1] <=0.025 8 1 0.125 2 <=0.025 0.5 0.5 0.125
#> [10] <=0.025 2 8 0.0625 >=16 0.0625 8 0.25 2
#> [19] >=16 0.25 >=16 0.125 <=0.025 >=16 >=16
random_disk(25, "Klebsiella pneumoniae") # range 8-50
#> Class 'disk'
#> [1] 33 15 41 31 31 36 49 42 34 9 42 31 16 37 50 42 17 44 40 46 8 40 44 42 46
random_disk(25, "Klebsiella pneumoniae", "ampicillin") # range 11-17
#> Class 'disk'
#> [1] 16 15 12 17 11 12 15 17 11 12 14 17 15 14 13 12 11 16 13 17 13 13 15 16 12
random_disk(25, "Streptococcus pneumoniae", "ampicillin") # range 12-27
#> Class 'disk'
#> [1] 20 17 25 16 19 17 21 23 27 24 15 27 25 22 21 15 23 25 20 18 21 15 21 17 24
# }