Separate persistent pairs by homological degree

The function step_pd_degree() creates a specification of a recipe step that will separate data sets of persistent pairs by homological degree. The input and output must be list-columns.

step_pd_degree(
  recipe,
  ...,
  role = "persistence diagram",
  trained = FALSE,
  hom_degrees = NULL,
  columns = NULL,
  keep_original_cols = FALSE,
  skip = FALSE,
  id = rand_id("pd_degree")
)

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 variables for this step. See selections() for more details.
role: For model terms created by this step, what analysis role should they be assigned? By default, the new columns created by this step from the original variables will be used as predictors in a model.
trained: A logical to indicate if the quantities for preprocessing have been estimated.
hom_degrees: Integer vector of homological degrees.
columns: A character string of the selected variable names. This field is a placeholder and will be populated once prep() is used.
keep_original_cols: A logical to keep the original variables in the output. Defaults to FALSE.
skip: A logical. Should the step be skipped when the recipe is baked by bake()? While all operations are baked when prep() 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.

Value

An updated version of recipe with the new step added to the sequence of any existing operations.

Details

The hom_degrees argument sets the homological degrees for which to return new list-columns. If not NULL (the default), it is intersected with the degrees found in any specified columns of the training data; otherwise all found degrees are used. This parameter cannot be tuned.

Examples

dat <- data.frame(
  roads = I(list(eurodist, UScitiesD * 1.6)),
  topos = I(list(volcano, 255 - volcano))
)

ph_rec <- recipe(~ ., data = dat) %>% 
  step_pd_point_cloud(roads, keep_original_cols = FALSE) %>% 
  step_pd_raster(topos, keep_original_cols = FALSE) %>% 
  step_pd_degree(roads_pd, topos_pd)
ph_prep <- prep(ph_rec, training = dat)
(ph_res <- bake(ph_prep, dat))
#> # A tibble: 2 × 4
#>   roads_pd_0      roads_pd_1     topos_pd_0      topos_pd_1    
#>   <list>          <list>         <list>          <list>        
#> 1 <PHom [20 × 3]> <PHom [3 × 3]> <PHom [13 × 3]> <PHom [5 × 3]>
#> 2 <PHom [9 × 3]>  <PHom [1 × 3]> <PHom [7 × 3]>  <PHom [1 × 3]>

tidy(ph_rec, number = 3)
#> # A tibble: 2 × 3
#>   terms    value id             
#>   <chr>    <dbl> <chr>          
#> 1 roads_pd    NA pd_degree_xb20B
#> 2 topos_pd    NA pd_degree_xb20B
tidy(ph_prep, number = 3)
#> # A tibble: 2 × 3
#>   terms    value id             
#>   <chr>    <dbl> <chr>          
#> 1 roads_pd    NA pd_degree_xb20B
#> 2 topos_pd    NA pd_degree_xb20B

with_degs <- recipe(~ ., data = dat) %>% 
  step_pd_point_cloud(roads, keep_original_cols = FALSE) %>% 
  step_pd_raster(topos, keep_original_cols = FALSE) %>% 
  step_pd_degree(roads_pd, topos_pd, hom_degrees = c(1, 2))
with_degs <- prep(with_degs, training = dat)
bake(with_degs, dat)
#> # A tibble: 2 × 2
#>   roads_pd_1     topos_pd_1    
#>   <list>         <list>        
#> 1 <PHom [3 × 3]> <PHom [5 × 3]>
#> 2 <PHom [1 × 3]> <PHom [1 × 3]>

Separate persistent pairs by homological degree

Arguments

Value

Details

See also

Examples