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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 dplyr verb, 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)

Value

class mic for random_mic() (see as.mic()) and class disk for random_disk() (see as.disk())

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] 0.005  0.025  16     0.002  1      1      8      2      64     1     
#> [11] 0.125  8      256    0.001  0.0625 4      4      16     0.01   0.025 
#> [21] 0.125  16     8      0.005  256   
random_disk(25)
#> Class 'disk'
#>  [1] 43 42 49 41  7 15  8 46 35 41 14 32 43 26 27 21 45 38 49 50 37 45  6 28 20
random_rsi(25)
#> Class 'rsi'
#>  [1] I S S R S R I I I I I R I I S S S R R I S S I 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] 8       0.0625  0.25    64      0.5     16      0.005   0.125   0.025  
#> [10] 4       4       0.5     1       0.025   2       0.025   32      0.0625 
#> [19] <=0.002 0.005   1       0.5     4       32      0.01   
random_mic(25, "Klebsiella pneumoniae", "meropenem") # range 0.0625-16
#> Class 'mic'
#>  [1] 8   4   16  16  2   8   16  16  8   16  16  2   <=1 16  4   <=1 16  <=1 8  
#> [20] 16  2   16  <=1 8   4  
random_mic(25, "Streptococcus pneumoniae", "meropenem") # range 0.0625-4
#> Class 'mic'
#>  [1] <=0.125 0.25    >=4     1       1       0.5     <=0.125 0.25    >=4    
#> [10] 0.25    1       0.25    >=4     0.5     2       >=4     >=4     0.5    
#> [19] 2       <=0.125 1       0.25    2       <=0.125 >=4    

random_disk(25, "Klebsiella pneumoniae") # range 8-50
#> Class 'disk'
#>  [1] 27 23 48 33 20 30 48 15 19 46 27 14 27 39 10 50 23 50 11 37 29 35 33 12 18
random_disk(25, "Klebsiella pneumoniae", "ampicillin") # range 11-17
#> Class 'disk'
#>  [1] 14 14 14 16 13 15 17 12 14 11 11 14 13 11 17 17 17 16 17 17 17 17 13 15 17
random_disk(25, "Streptococcus pneumoniae", "ampicillin") # range 12-27
#> Class 'disk'
#>  [1] 25 16 20 15 23 26 16 22 15 22 15 15 25 20 20 20 15 24 15 25 15 21 20 18 25
# }