Add manydist dissimilarities to a recipe

`step_mdist()` is a [recipes::recipe()] step that replaces selected predictors by a distance-based representation computed with [mdist()]. It is designed for distance-based learning workflows, especially nearest-neighbour prediction and clustering models that operate on dissimilarity matrices.

Usage

step_mdist(
  recipe,
  ...,
  role = "predictor",
  trained = FALSE,
  output = "distance_to_training",
  preset = "custom",
  method_cat = "tot_var_dist",
  method_num = "none",
  commensurable = FALSE,
  ncomp = NULL,
  threshold = NULL,
  columns = NULL,
  train_predictors = NULL,
  preprocessor = NULL,
  skip = FALSE,
  id = recipes::rand_id("mdist")
)

Arguments

recipe: A recipe object.
...: Selector(s) for the predictor columns to be used in [mdist()]. These are passed to [recipes::recipes_eval_select()] during preparation.
role: Role for the new distance columns. The default is `"predictor"`.
trained: Logical for recipes internals. Do not set manually.
output: Character string specifying the type of distance output. `"distance_to_training"` returns distances from the baked data to the training observations and is the usual choice for prediction workflows. `"pairwise"` returns the within-training pairwise dissimilarity matrix and is intended for training-only distance-based clustering workflows.
preset: Character string specifying the distance preset passed to [mdist()]. Available values include `"custom"`, `"gower"`, `"unbiased_dependent"`, `"u_dep"`, `"u_indep"`, `"u_mix"`, `"hl"`, `"gudmm"`, `"dkss"`, `"mod_gower"`, and `"euclidean"`.
method_cat: Character string specifying the categorical-variable dissimilarity passed to [mdist()] when `preset = "custom"`. Common values include `"matching"` and `"tvd"`. Use [all_dist_method_specs()] to inspect available methods.
method_num: Character string specifying the numerical-variable preprocessing passed to [mdist()] when `preset = "custom"`. Available options include `"none"` for no preprocessing, `"std"` for standard-deviation scaling, `"range"` for range scaling, `"robust"` for inter-quartile-range-based scaling, and `"pc_scores"` for principal-component score scaling.
commensurable: Logical. If `TRUE`, dissimilarities are scaled so that the average contribution of each variable to the overall distance is equal to 1, when supported by the selected distance specification.
ncomp: Integer or `NULL`. Number of principal components to retain when `method_num = "pc_scores"`. If `NULL`, all available components are used unless `threshold` is supplied and supported by the underlying method.
threshold: Numeric or `NULL`. Optional cumulative variance threshold used when `method_num = "pc_scores"`.
columns: Names of columns selected at prep time. Used internally by recipes.
train_predictors: Training predictors stored at prep time. Used internally by recipes to compute distances from new observations to the training observations.
preprocessor: Internal fitted manydist preprocessor.
skip: Logical. Standard recipes argument indicating whether the step should be skipped when baking new data.
id: Character string. Unique step identifier.

Value

An updated recipe with a manydist step.

Details

The step can produce either distances from new observations to the training observations, or the within-training pairwise dissimilarity matrix. The former is the usual choice for supervised prediction workflows; the latter is useful for distance-based clustering workflows fitted on the training data.

During [recipes::prep()], `step_mdist()` stores the selected training predictors and fits the internal manydist preprocessor. During [recipes::bake()], the selected predictors are removed and replaced by distance columns named `dist_1`, `dist_2`, and so on.

With `output = "distance_to_training"`, baking the training data returns the training pairwise distances, while baking new data returns distances from each new observation to each training observation. This rectangular representation is suitable for nearest-neighbour prediction models.

With `output = "pairwise"`, the step returns the within-training pairwise dissimilarity matrix. Baking genuinely new data is not supported in this mode, because the output is intended for training-only clustering workflows such as [pam_dist()] or [spectral_dist()].

Examples

if (requireNamespace("palmerpenguins", quietly = TRUE)) {
  data("penguins", package = "palmerpenguins")

  penguins_small <- palmerpenguins::penguins |>
    dplyr::select(
      species, bill_length_mm, bill_depth_mm, flipper_length_mm,
      body_mass_g, island, sex
    ) |>
    tidyr::drop_na()

  # Distance-to-training representation for prediction workflows
  rec <- recipes::recipe(species ~ ., data = penguins_small) |>
    step_mdist(
      recipes::all_predictors(),
      preset = "gower",
      output = "distance_to_training"
    )

  rec_prep <- recipes::prep(rec, training = penguins_small)
  baked <- recipes::bake(rec_prep, new_data = penguins_small)

  baked |> dplyr::slice_head(n=5)

  # Pairwise representation for clustering workflows
  rec_pairwise <- recipes::recipe(~ ., data = penguins_small) |>
    step_mdist(
      recipes::all_predictors(),
      preset = "gower",
      output = "pairwise"
    )

  rec_pairwise_prep <- recipes::prep(rec_pairwise, training = penguins_small)
  pairwise_dist <- recipes::bake(rec_pairwise_prep, new_data = penguins_small)

  pairwise_dist
}
#> Warning: When `preset` is not 'custom', distance-related arguments are ignored: `commensurable`, `method_num`. Set `preset = 'custom'` to specify them manually.
#> Warning: When `preset` is not 'custom', distance-related arguments are ignored: `commensurable`, `method_num`. Set `preset = 'custom'` to specify them manually.
#> # A tibble: 333 × 333
#>    dist_1 dist_2 dist_3 dist_4 dist_5 dist_6 dist_7 dist_8 dist_9 dist_10
#>     <dbl>  <dbl>  <dbl>  <dbl>  <dbl>  <dbl>  <dbl>  <dbl>  <dbl>   <dbl>
#>  1 0      0.181  0.215  0.206  0.0591 0.164  0.0864 0.196  0.0713  0.131 
#>  2 0.181  0      0.0580 0.0777 0.214  0.0290 0.238  0.0452 0.224   0.284 
#>  3 0.215  0.0580 0      0.0536 0.220  0.0595 0.232  0.0444 0.238   0.278 
#>  4 0.206  0.0777 0.0536 0      0.194  0.0729 0.214  0.0883 0.204   0.234 
#>  5 0.0591 0.214  0.220  0.194  0      0.215  0.0703 0.240  0.0222  0.0821
#>  6 0.164  0.0290 0.0595 0.0729 0.215  0      0.251  0.0341 0.233   0.293 
#>  7 0.0864 0.238  0.232  0.214  0.0703 0.251  0      0.277  0.0747  0.0676
#>  8 0.196  0.0452 0.0444 0.0883 0.240  0.0341 0.277  0      0.263   0.323 
#>  9 0.0713 0.224  0.238  0.204  0.0222 0.233  0.0747 0.263  0       0.0632
#> 10 0.131  0.284  0.278  0.234  0.0821 0.293  0.0676 0.323  0.0632  0     
#> # ℹ 323 more rows
#> # ℹ 323 more variables: dist_11 <dbl>, dist_12 <dbl>, dist_13 <dbl>,
#> #   dist_14 <dbl>, dist_15 <dbl>, dist_16 <dbl>, dist_17 <dbl>, dist_18 <dbl>,
#> #   dist_19 <dbl>, dist_20 <dbl>, dist_21 <dbl>, dist_22 <dbl>, dist_23 <dbl>,
#> #   dist_24 <dbl>, dist_25 <dbl>, dist_26 <dbl>, dist_27 <dbl>, dist_28 <dbl>,
#> #   dist_29 <dbl>, dist_30 <dbl>, dist_31 <dbl>, dist_32 <dbl>, dist_33 <dbl>,
#> #   dist_34 <dbl>, dist_35 <dbl>, dist_36 <dbl>, dist_37 <dbl>, …

Usage

Arguments

Value

Details

See also

Examples