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 32 0.001 2 0.005 >=256 64 16 0.125
#> [11] 8 0.0625 0.005 0.5 >=256 128 32 0.005 0.001 0.025
#> [21] 16 0.025 8 8 0.25
random_disk(25)
#> Class 'disk'
#> [1] 50 6 29 7 10 23 32 46 48 21 42 49 17 8 11 35 19 19 27 33 49 49 28 24 28
random_rsi(25)
#> Class 'rsi'
#> [1] S S I I S S R I S R R R I R I R S I R R S R S 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] 32 0.01 0.0625 >=64 32 0.5 8 <=0.001 1
#> [10] 0.01 0.125 1 0.005 16 0.01 4 2 1
#> [19] 0.01 0.002 0.025 0.125 <=0.001 >=64 32
random_mic(25, "Klebsiella pneumoniae", "meropenem") # range 0.0625-16
#> Class 'mic'
#> [1] 8 8 <=0.5 <=0.5 8 <=0.5 >=32 4 4 2 1 <=0.5
#> [13] <=0.5 <=0.5 1 16 16 8 16 <=0.5 4 1 1 <=0.5
#> [25] 4
random_mic(25, "Streptococcus pneumoniae", "meropenem") # range 0.0625-4
#> Class 'mic'
#> [1] 1 0.25 <=0.0625 0.5 >=16 0.25 <=0.0625 2
#> [9] 8 1 <=0.0625 >=16 4 2 <=0.0625 0.125
#> [17] 0.25 1 2 8 1 0.25 2 0.25
#> [25] 0.25
random_disk(25, "Klebsiella pneumoniae") # range 8-50
#> Class 'disk'
#> [1] 48 11 16 42 45 29 50 43 35 25 13 17 20 35 47 24 29 40 40 50 48 44 50 14 43
random_disk(25, "Klebsiella pneumoniae", "ampicillin") # range 11-17
#> Class 'disk'
#> [1] 14 16 13 15 11 17 14 17 16 17 12 12 16 14 17 17 12 13 13 14 16 16 17 14 11
random_disk(25, "Streptococcus pneumoniae", "ampicillin") # range 12-27
#> Class 'disk'
#> [1] 25 27 27 25 19 18 15 16 16 18 18 24 15 20 25 27 26 19 24 20 24 27 18 19 25
# }