New arguments to step umap

[EmilHvitfeldt]

This PR adds initial and target_weight to step_umap()

[topepo]

I would default it to zero and, if it is not zero, check to make sure that the outcome is not NULL

[EmilHvitfeldt]

That would break backwards compatibility, computation-wise

in main, the following code uses target_weight = 0.5 by default in uwot::umap().

supervised <-
  recipe(Species ~ ., data = iris) %>%
  step_umap(all_predictors(), outcome = vars(Species), num_comp = 2) %>%
  prep()

With this proposed change, setting the outcome variable would no longer have an effect unless they also set the new target_weight.

[topepo]

Ok, go ahead and default it to 1 / 2. They ignore target_weight unless y is passed. This is a modified version of what is in ?umap:

library(uwot)
#> Loading required package: Matrix

ind <- c(1:10, 51:60, 101:110)

iris30 <- iris[ind,]

set.seed(1)
iris_umap_un_1 <-
  umap(
    iris30[, 1:4],
    n_neighbors = 5,
    learning_rate = 0.5,
    init = "random",
    n_epochs = 20,
    target_weight = 0.5
  )

set.seed(1)
iris_umap_un_2 <-
  umap(
    iris30[, 1:4],
    n_neighbors = 5,
    learning_rate = 0.5,
    init = "random",
    n_epochs = 20,
    target_weight = 0.0
  )

# just checking!
all.equal(iris_umap_un_1, iris_umap_un_2)
#> [1] TRUE

set.seed(1)
iris_umap_sup <-
  umap(
    iris30[, 1:4],
    n_neighbors = 5,
    learning_rate = 0.5,
    init = "random",
    n_epochs = 20,
    y = iris30$Species,
    target_weight = 0.5
  )

all.equal(iris_umap_un_1, iris_umap_sup)
#> [1] "Attributes: < Component \"scaled:center\": Mean relative difference: 0.6626731 >"
#> [2] "Mean relative difference: 0.3312773"

^{Created on 2024-01-12 with reprex v2.0.2}

Note that in their man page, they pass the outcome in with the original data as well as with the y argument. That seems like a mistake. My example above avoids that and you get the same results in the first two cases regardless of the target weight.

[EmilHvitfeldt]

I almost forgot. Since we are adding arguments, we need to make sure the step is backwards compatible

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