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] 2 0.5 1 0.005 0.005 1 0.25 0.025 0.125 1
#> [11] 0.0625 0.002 0.005 >=32 0.01 >=32 1 0.001 16 4
#> [21] 8 8 16 0.25 0.25
random_disk(25)
#> Class 'disk'
#> [1] 8 20 13 26 9 46 49 48 45 50 43 26 45 39 25 10 48 11 43 47 44 27 46 45 24
random_rsi(25)
#> Class 'rsi'
#> [1] R R R S I I R R R S S S R R I I S S S I R R R S 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] 0.001 128 0.005 0.025 0.025 16 32 64 0.25 0.025
#> [11] 0.001 >=256 0.002 128 0.001 128 32 8 0.0625 0.005
#> [21] 0.25 4 8 0.25 64
random_mic(25, "Klebsiella pneumoniae", "meropenem") # range 0.0625-16
#> Class 'mic'
#> [1] 4 >=64 <=1 <=1 2 2 32 16 <=1 32 4 >=64 >=64 32 8
#> [16] 32 8 16 8 8 32 >=64 4 16 16
random_mic(25, "Streptococcus pneumoniae", "meropenem") # range 0.0625-4
#> Class 'mic'
#> [1] 0.125 2 0.5 0.5 1 4 0.125 1
#> [9] >=8 <=0.0625 0.25 4 0.25 <=0.0625 0.5 >=8
#> [17] <=0.0625 >=8 <=0.0625 4 0.25 0.25 1 >=8
#> [25] <=0.0625
random_disk(25, "Klebsiella pneumoniae") # range 8-50
#> Class 'disk'
#> [1] 45 25 24 50 48 29 26 38 37 44 38 41 40 40 43 20 14 47 40 47 20 12 34 48 49
random_disk(25, "Klebsiella pneumoniae", "ampicillin") # range 11-17
#> Class 'disk'
#> [1] 17 17 17 12 12 14 14 13 15 16 14 14 17 11 17 14 15 14 12 14 13 12 12 14 16
random_disk(25, "Streptococcus pneumoniae", "ampicillin") # range 12-27
#> Class 'disk'
#> [1] 25 26 25 16 17 21 15 18 20 26 15 19 15 24 23 16 15 16 17 15 27 27 16 19 26
# }