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] 2 0.01 64 0.5 <=0.001 64 4 8 64
#> [10] 0.5 16 0.25 0.005 0.125 0.005 <=0.001 4 0.25
#> [19] 0.002 0.01 0.125 4 64 0.002 >=128
random_disk(25)
#> Class 'disk'
#> [1] 19 48 50 43 37 6 35 42 37 19 33 47 50 45 48 44 47 26 15 23 42 15 38 30 38
random_rsi(25)
#> Class 'rsi'
#> [1] I R S I I S S I S R R S I S I I R R I S S R S I 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] 0.005 0.5 1 0.005 2 0.01 16 0.25 128 0.002 8 0.025
#> [13] 32 16 16 0.001 4 0.005 16 0.125 0.25 8 0.5 64
#> [25] 32
random_mic(25, "Klebsiella pneumoniae", "meropenem") # range 0.0625-16
#> Class 'mic'
#> [1] 16 <=1 2 16 <=1 >=64 <=1 32 4 <=1 2 16 2 2 >=64
#> [16] >=64 2 8 32 >=64 8 8 4 <=1 16
random_mic(25, "Streptococcus pneumoniae", "meropenem") # range 0.0625-4
#> Class 'mic'
#> [1] 1 8 2 <=0.125 0.5 <=0.125 0.5 1 0.5
#> [10] 0.5 8 <=0.125 2 1 2 0.25 1 2
#> [19] 2 2 1 0.25 0.5 8 0.25
random_disk(25, "Klebsiella pneumoniae") # range 8-50
#> Class 'disk'
#> [1] 14 49 37 14 42 20 48 28 49 28 47 21 35 34 35 36 49 31 18 39 25 50 23 32 26
random_disk(25, "Klebsiella pneumoniae", "ampicillin") # range 11-17
#> Class 'disk'
#> [1] 11 11 14 12 16 13 15 11 12 14 14 13 13 12 16 14 11 12 11 11 13 15 17 13 16
random_disk(25, "Streptococcus pneumoniae", "ampicillin") # range 12-27
#> Class 'disk'
#> [1] 22 23 20 17 18 15 20 26 22 26 16 23 23 27 20 18 18 17 25 27 27 15 19 19 19
# }