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 64 0.25 2 1 2 0.125 4 0.25
#> [10] 1 0.025 <=0.002 0.25 64 0.0625 0.005 0.01 8
#> [19] 8 1 2 0.025 <=0.002 >=256 0.25
random_disk(25)
#> Class 'disk'
#> [1] 30 26 41 36 23 42 33 16 10 41 21 24 39 49 34 47 32 44 20 33 41 48 15 9 6
random_rsi(25)
#> Class 'rsi'
#> [1] S S S I S I R I S I R I I R R I S S I S I I I 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] 0.125 0.25 0.025 16 0.005 0.125 0.5 0.0625 4 16
#> [11] 16 1 2 1 0.01 0.005 0.125 0.002 0.01 0.25
#> [21] 0.5 0.002 0.0625 >=32 16
random_mic(25, "Klebsiella pneumoniae", "meropenem") # range 0.0625-16
#> Class 'mic'
#> [1] 2 2 1 >=16 2 >=16 2 4 8 2 2 8 2 2 1
#> [16] >=16 >=16 4 2 2 1 2 4 >=16 2
random_mic(25, "Streptococcus pneumoniae", "meropenem") # range 0.0625-4
#> Class 'mic'
#> [1] 0.25 0.5 8 0.0625 1 0.5 <=0.025 0.125 <=0.025
#> [10] 4 0.0625 0.25 0.0625 <=0.025 0.25 0.0625 1 0.125
#> [19] 2 <=0.025 2 0.25 8 1 0.125
random_disk(25, "Klebsiella pneumoniae") # range 8-50
#> Class 'disk'
#> [1] 16 50 45 44 44 18 37 24 21 47 26 16 15 43 43 15 40 35 30 15 21 41 8 29 15
random_disk(25, "Klebsiella pneumoniae", "ampicillin") # range 11-17
#> Class 'disk'
#> [1] 15 11 14 15 11 16 16 14 17 13 14 11 16 12 14 12 17 12 15 11 14 11 14 13 16
random_disk(25, "Streptococcus pneumoniae", "ampicillin") # range 12-27
#> Class 'disk'
#> [1] 21 16 18 21 25 26 19 21 26 17 18 15 24 15 18 20 17 24 17 19 26 18 17 16 15
# }