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] 64 0.01 2 32 1 0.25 128 64 0.0625
#> [10] 1 8 32 8 8 0.002 2 256 0.025
#> [19] 0.125 8 0.5 0.01 32 <=0.001 4
random_disk(25)
#> Class 'disk'
#> [1] 36 17 9 45 47 30 42 42 19 11 44 33 18 48 9 44 19 45 31 48 31 9 12 14 34
random_rsi(25)
#> Class 'rsi'
#> [1] S S R S I S S R R R R R R S I I S S I S R R R R 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] 0.025 1 0.01 0.01 0.5 <=0.001 0.25 2 0.5
#> [10] 0.025 32 0.002 8 4 16 >=128 1 1
#> [19] 0.005 0.002 32 0.5 1 0.01 8
random_mic(25, "Klebsiella pneumoniae", "meropenem") # range 0.0625-16
#> Class 'mic'
#> [1] 32 0.5 16 <=0.25 8 4 8 16 >=64 2
#> [11] >=64 4 >=64 32 <=0.25 16 4 1 >=64 32
#> [21] <=0.25 1 32 32 32
random_mic(25, "Streptococcus pneumoniae", "meropenem") # range 0.0625-4
#> Class 'mic'
#> [1] 1 0.5 1 4 8 1 0.5 8 0.125 4
#> [11] 0.25 0.5 1 0.0625 0.0625 4 1 8 1 0.125
#> [21] 0.125 0.5 1 0.125 8
random_disk(25, "Klebsiella pneumoniae") # range 8-50
#> Class 'disk'
#> [1] 41 50 34 42 44 13 43 44 48 46 19 13 36 18 9 43 43 27 29 43 36 45 24 48 41
random_disk(25, "Klebsiella pneumoniae", "ampicillin") # range 11-17
#> Class 'disk'
#> [1] 12 12 16 11 11 12 14 15 15 13 13 16 15 12 14 11 14 12 11 16 12 17 14 13 15
random_disk(25, "Streptococcus pneumoniae", "ampicillin") # range 12-27
#> Class 'disk'
#> [1] 27 16 15 27 22 27 25 20 18 22 18 18 16 24 20 27 19 19 17 22 20 23 23 22 19
# }