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 agent, 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 agent 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 0.001 16 >=256 0.002 16 64 2 16 0.125 0.001 0.005
#> [13] 0.001 0.01 64 0.001 0.002 128 0.5 32 1 0.001 2 0.125
#> [25] 2
random_disk(25)
#> Class 'disk'
#> [1] 31 40 42 6 12 20 44 35 47 47 49 11 41 10 9 7 35 32 48 13 28 15 37 35 28
random_rsi(25)
#> Class 'rsi'
#> [1] I S I S S I I I I R R I I R R R S S I R R I R R 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] 2 1 32 64 <=0.001 2 0.025 8 32
#> [10] 32 0.002 0.005 2 0.025 0.005 0.025 128 32
#> [19] 32 8 128 0.005 1 0.01 0.5
random_mic(25, "Klebsiella pneumoniae", "meropenem") # range 0.0625-16
#> Class 'mic'
#> [1] <=0.5 >=16 1 4 >=16 >=16 2 >=16 8 1 <=0.5 2
#> [13] >=16 4 2 2 8 2 2 4 1 8 >=16 1
#> [25] 1
random_mic(25, "Streptococcus pneumoniae", "meropenem") # range 0.0625-4
#> Class 'mic'
#> [1] <=0.025 <=0.025 0.5 0.125 <=0.025 <=0.025 16 0.5 0.125
#> [10] 8 1 2 16 16 <=0.025 16 0.5 <=0.025
#> [19] 0.25 4 2 0.125 1 1 <=0.025
random_disk(25, "Klebsiella pneumoniae") # range 8-50
#> Class 'disk'
#> [1] 34 18 36 49 44 12 50 42 50 50 28 17 42 40 16 44 24 44 48 10 15 49 49 16 45
random_disk(25, "Klebsiella pneumoniae", "ampicillin") # range 11-17
#> Class 'disk'
#> [1] 17 14 16 16 17 16 16 16 17 13 14 11 15 11 17 12 13 13 14 14 17 16 11 14 11
random_disk(25, "Streptococcus pneumoniae", "ampicillin") # range 12-27
#> Class 'disk'
#> [1] 18 17 15 19 25 23 27 23 15 22 23 17 16 27 22 21 20 19 17 20 25 15 26 24 23
# }