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#' Non-Negative Splines
#'
#' `step_spline_nonnegative` creates a *specification* of a recipe
#' step that creates non-negative spline features.
#'
#' @inheritParams step_spline_b
#' @param degree A nonnegative integer specifying the degree of the piecewise
#' polynomial. The default value is 3 for cubic splines. Zero degree is allowed
#' for piecewise constant basis functions.
#' @param options A list of options for [splines2::mSpline()]
#' which should not include `x`, `df`, `degree`, `periodic`, or `intercept`.
#' @return An object with classes `"step_spline_nonnegative"` and `"step"`.
#' @export
#' @details
#'
#' Spline transformations take a numeric column and create multiple features
#' that, when used in a model, can estimate nonlinear trends between the column
#' and some outcome. The degrees of freedom determines how many new features
#' are added to the data.
#'
#' This function generates M-splines (Curry, and Schoenberg 1988) which are
#' non-negative and have interesting statistical properties (such as integrating
#' to one). A zero-degree M-spline generates box/step functions while a first
#' degree basis function is triangular.
#'
#' Setting `periodic = TRUE` in the list passed to `options`, a periodic version
#' of the spline is used.
#'
#' If the spline expansion fails for a selected column, the step will
#' remove that column's results (but will retain the original data). Use the
#' `tidy()` method to determine which columns were used.
#'
#' # Tidying
#'
#' When you [`tidy()`][tidy.recipe()] this step, a tibble with column
#' `terms` (the columns that will be affected) is returned.
#'
#' @references
#' Curry, H.B., Schoenberg, I.J. (1988). On Polya Frequency Functions IV: The
#' Fundamental Spline Functions and their Limits. In: de Boor, C. (eds) I. J.
#' Schoenberg Selected Papers. Contemporary Mathematicians. Birkhäuser, Boston,
#' MA
#'
#' Ramsay, J. O. "Monotone Regression Splines in Action." Statistical Science,
#' vol. 3, no. 4, 1988, pp. 425–41
#' @examplesIf rlang::is_installed(c("modeldata", "ggplot2"))
#' library(tidyr)
#' library(dplyr)
#'
#' library(ggplot2)
#' data(ames, package = "modeldata")
#'
#' spline_rec <- recipe(Sale_Price ~ Longitude, data = ames) %>%
#' step_spline_nonnegative(Longitude, deg_free = 6, keep_original_cols = TRUE) %>%
#' prep()
#'
#' tidy(spline_rec, number = 1)
#'
#' # Show where each feature is active
#' spline_rec %>%
#' bake(new_data = NULL,-Sale_Price) %>%
#' pivot_longer(c(starts_with("Longitude_")), names_to = "feature", values_to = "value") %>%
#' mutate(feature = gsub("Longitude_", "feature ", feature)) %>%
#' filter(value > 0) %>%
#' ggplot(aes(x = Longitude, y = value)) +
#' geom_line() +
#' facet_wrap(~ feature)
#' @template case-weights-not-supported
#' @seealso [splines2::mSpline()]
step_spline_nonnegative <-
function(recipe,
...,
role = "predictor",
trained = FALSE,
deg_free = 10,
degree = 3,
complete_set = FALSE,
options = NULL,
keep_original_cols = FALSE,
results = NULL,
skip = FALSE,
id = rand_id("spline_nonnegative")) {
recipes_pkg_check(required_pkgs.step_spline_nonnegative())
add_step(
recipe,
step_spline_nonnegative_new(
terms = enquos(...),
trained = trained,
role = role,
deg_free = deg_free,
degree = degree,
complete_set = complete_set,
options = options,
keep_original_cols = keep_original_cols,
results = results,
skip = skip,
id = id
)
)
}
step_spline_nonnegative_new <-
function(terms, trained, role, deg_free, degree, complete_set, options,
keep_original_cols, results, na_rm, skip, id) {
step(
subclass = "spline_nonnegative",
terms = terms,
role = role,
trained = trained,
deg_free = deg_free,
degree = degree,
complete_set = complete_set,
options = options,
keep_original_cols = keep_original_cols,
results = results,
skip = skip,
id = id
)
}
# ------------------------------------------------------------------------------
prep.step_spline_nonnegative <- function(x, training, info = NULL, ...) {
col_names <- recipes_eval_select(x$terms, training, info)
check_type(training[, col_names], types = c("double", "integer"))
res <-
purrr::map2(
training[, col_names],
col_names,
~ spline2_create(
.x,
nm = .y,
.fn = "mSpline",
df = x$deg_free,
complete_set = x$complete_set,
degree = x$degree,
fn_opts = x$options
)
)
# check for errors
bas_res <- purrr::map_lgl(res, is.null)
res <- res[!bas_res]
col_names <- col_names[!bas_res]
names(res) <- col_names
step_spline_nonnegative_new(
terms = x$terms,
role = x$role,
trained = TRUE,
deg_free = x$deg_free,
degree = x$degree,
complete_set = x$complete_set,
options = x$options,
keep_original_cols = x$keep_original_cols,
results = res,
skip = x$skip,
id = x$id
)
}
bake.step_spline_nonnegative <- function(object, new_data, ...) {
orig_names <- names(object$results)
if (length(orig_names) > 0) {
new_cols <- purrr::map2_dfc(object$results, new_data[, orig_names], spline2_apply)
new_data <- bind_cols(new_data, new_cols)
keep_original_cols <- get_keep_original_cols(object)
if (!keep_original_cols) {
new_data <- new_data[, !(colnames(new_data) %in% orig_names), drop = FALSE]
}
}
new_data
}
# ------------------------------------------------------------------------------
print.step_spline_nonnegative <-
function(x, width = max(20, options()$width - 30), ...) {
title <- "Non-negative spline expansion "
cols_used <- names(x$results)
if (length(cols_used) == 0) {
cols_used <- "<none>"
}
print_step(cols_used, x$terms, x$trained, title, width)
invisible(x)
}
#' @rdname tidy.recipe
#' @export
tidy.step_spline_nonnegative <- function(x, ...) {
if (is_trained(x)) {
terms <- names(x$results)
if (length(terms) == 0) {
terms <- "<none>"
}
} else {
terms <- sel2char(x$terms)
}
tibble(terms = terms, id = x$id)
}
# ------------------------------------------------------------------------------
#' @rdname required_pkgs.recipe
#' @export
required_pkgs.step_spline_nonnegative <- function(x, ...) {
c("splines2")
}
# ------------------------------------------------------------------------------
#' @export
tunable.step_spline_nonnegative <- function(x, ...) {
tibble::tibble(
name = c("deg_free", "degree"),
call_info = list(
list(pkg = "dials", fun = "spline_degree", range = c(2L, 15L)),
list(pkg = "dials", fun = "degree", range = c(0L, 3L))
),
source = "recipe",
component = "step_spline_nonnegative",
component_id = x$id
)
}
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