step_depth creates a specification of a recipe step that will convert numeric data into measurement of data depth. This is done for each value of a categorical class variable.

step_depth(
  recipe,
  ...,
  class,
  role = "predictor",
  trained = FALSE,
  metric = "halfspace",
  options = list(),
  data = NULL,
  prefix = "depth_",
  skip = FALSE,
  id = rand_id("depth")
)

# S3 method for step_depth
tidy(x, ...)

Arguments

recipe

A recipe object. The step will be added to the sequence of operations for this recipe.

...

One or more selector functions to choose which variables that will be used to create the new features. See selections() for more details. For the tidy method, these are not currently used.

class

A single character string that specifies a single categorical variable to be used as the class.

role

For model terms created by this step, what analysis role should they be assigned?. By default, the function assumes that resulting depth estimates will be used as predictors in a model.

trained

A logical to indicate if the quantities for preprocessing have been estimated.

metric

A character string specifying the depth metric. Possible values are "potential", "halfspace", "Mahalanobis", "simplicialVolume", "spatial", and "zonoid".

options

A list of options to pass to the underlying depth functions. See ddalpha::depth.halfspace(), ddalpha::depth.Mahalanobis(), ddalpha::depth.potential(), ddalpha::depth.projection(), ddalpha::depth.simplicial(), ddalpha::depth.simplicialVolume(), ddalpha::depth.spatial(), ddalpha::depth.zonoid().

data

The training data are stored here once after prep.recipe() is executed.

prefix

A character string that defines the naming convention for new depth columns. Defaults to "depth_". See Details below.

skip

A logical. Should the step be skipped when the recipe is baked by bake.recipe()? While all operations are baked when prep.recipe() is run, some operations may not be able to be conducted on new data (e.g. processing the outcome variable(s)). Care should be taken when using skip = TRUE as it may affect the computations for subsequent operations

id

A character string that is unique to this step to identify it.

x

A step_depth object.

Value

An updated version of recipe with the new step added to the sequence of existing steps (if any). For the tidy method, a tibble with columns terms (the selectors or variables selected) and class.

Details

Data depth metrics attempt to measure how close data a data point is to the center of its distribution. There are a number of methods for calculating death but a simple example is the inverse of the distance of a data point to the centroid of the distribution. Generally, small values indicate that a data point not close to the centroid. step_depth can compute a class-specific depth for a new data point based on the proximity of the new value to the training set distribution.

This step requires the ddalpha package. If not installed, the step will stop with a note about installing the package.

Note that the entire training set is saved to compute future depth values. The saved data have been trained (i.e. prepared) and baked (i.e. processed) up to the point before the location that step_depth occupies in the recipe. Also, the data requirements for the different step methods may vary. For example, using metric = "Mahalanobis" requires that each class should have at least as many rows as variables listed in the terms argument.

The function will create a new column for every unique value of the class variable. The resulting variables will not replace the original values and by default have the prefix depth_. The naming format can be changed using the prefix argument.

Examples

# halfspace depth is the default rec <- recipe(Species ~ ., data = iris) %>% step_depth(all_predictors(), class = "Species") # use zonoid metric instead # also, define naming convention for new columns rec <- recipe(Species ~ ., data = iris) %>% step_depth(all_predictors(), class = "Species", metric = "zonoid", prefix = "zonoid_") rec_dists <- prep(rec, training = iris) dists_to_species <- bake(rec_dists, new_data = iris) dists_to_species
#> # A tibble: 150 x 8 #> Sepal.Length Sepal.Width Petal.Length Petal.Width Species zonoid_setosa #> <dbl> <dbl> <dbl> <dbl> <fct> <dbl> #> 1 5.1 3.5 1.4 0.2 setosa 0.559 #> 2 4.9 3 1.4 0.2 setosa 0.167 #> 3 4.7 3.2 1.3 0.2 setosa 0.299 #> 4 4.6 3.1 1.5 0.2 setosa 0.170 #> 5 5 3.6 1.4 0.2 setosa 0.391 #> 6 5.4 3.9 1.7 0.4 setosa 0.0838 #> 7 4.6 3.4 1.4 0.3 setosa 0.02 #> 8 5 3.4 1.5 0.2 setosa 0.645 #> 9 4.4 2.9 1.4 0.2 setosa 0.02 #> 10 4.9 3.1 1.5 0.1 setosa 0.0200 #> # … with 140 more rows, and 2 more variables: zonoid_versicolor <dbl>, #> # zonoid_virginica <dbl>
tidy(rec, number = 1)
#> # A tibble: 1 x 3 #> terms class id #> <chr> <chr> <chr> #> 1 all_predictors() NA depth_vUNsj
tidy(rec_dists, number = 1)
#> # A tibble: 4 x 3 #> terms class id #> <chr> <chr> <chr> #> 1 Sepal.Length Species depth_vUNsj #> 2 Sepal.Width Species depth_vUNsj #> 3 Petal.Length Species depth_vUNsj #> 4 Petal.Width Species depth_vUNsj