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] 16 8 8 <=0.001 0.5 16 <=0.001 32 32
#> [10] 0.002 0.25 16 0.5 16 8 0.125 32 4
#> [19] 0.025 0.0625 0.01 4 4 0.125 16
random_disk(25)
#> Class 'disk'
#> [1] 47 47 41 21 6 7 6 11 8 33 32 33 31 32 10 12 19 21 48 13 42 35 42 18 25
random_rsi(25)
#> Class 'rsi'
#> [1] I R S R I I S I S I S S S S I I I I R R S S R S 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] <=0.001 0.125 0.125 0.01 32 0.005 128 8 0.01
#> [10] 0.125 32 0.01 0.5 32 0.002 16 2 0.01
#> [19] 0.5 0.125 32 2 0.5 0.25 0.002
random_mic(25, "Klebsiella pneumoniae", "meropenem") # range 0.0625-16
#> Class 'mic'
#> [1] 1 8 1 0.5 1 1 16 16 4 16 16 16 32 2 1 2 2 16 1
#> [20] 0.5 1 8 4 0.5 16
random_mic(25, "Streptococcus pneumoniae", "meropenem") # range 0.0625-4
#> Class 'mic'
#> [1] 2 2 0.25 1 0.5 0.5 >=4 0.125 2 0.0625
#> [11] 2 0.0625 2 0.0625 0.5 0.25 0.125 0.5 1 >=4
#> [21] 0.25 0.125 2 0.125 0.125
random_disk(25, "Klebsiella pneumoniae") # range 8-50
#> Class 'disk'
#> [1] 26 43 41 44 48 48 40 10 44 13 38 34 15 49 37 12 42 40 39 29 23 23 41 35 44
random_disk(25, "Klebsiella pneumoniae", "ampicillin") # range 11-17
#> Class 'disk'
#> [1] 17 12 16 13 13 13 11 15 15 17 17 13 16 16 12 16 11 15 14 14 14 11 16 16 13
random_disk(25, "Streptococcus pneumoniae", "ampicillin") # range 12-27
#> Class 'disk'
#> [1] 16 24 26 24 27 18 16 16 25 27 25 24 27 18 21 25 27 26 25 22 16 22 15 23 21
# }