shuffleLabels()

Randomly shuffles the AMR phenotype labels in the ML-ready tibble.

shuffleLabels(ml_input_tibble, seed = 5280)

Arguments

ml_input_tibble

An ML-ready tibble generated by loadMLInputTibble(). This must have a target variable column named either genome_drug.resistant_phenotype ("Resistant" or "Susceptible " classification for one bug/drug combination) or resistant_classes (multi-class classification for determining the drug classes to which each genome is resistant), but not both.

seed

num For reproducible analysis

Value

Pangenome with randomly shuffled AMR phenotype labels

Examples

ml <- tibble::tibble(
  genome_id = paste0("g", 1:6),
  genome_drug.resistant_phenotype = rep(c("Resistant", "Susceptible"), each = 3),
  feat_a = c(1L, 0L, 1L, 0L, 1L, 0L)
)
shuffleLabels(ml, seed = 42)
#> Shuffling phenotype labels (for baseline models).
#> # A tibble: 6 × 3
#>   genome_id genome_drug.resistant_phenotype feat_a
#>   <chr>     <chr>                            <int>
#> 1 g1        Resistant                            1
#> 2 g2        Susceptible                          0
#> 3 g3        Susceptible                          1
#> 4 g4        Susceptible                          0
#> 5 g5        Resistant                            1
#> 6 g6        Resistant                            0