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#' Orthogonal Polynomial Basis Functions
#'
#' `step_poly` creates a *specification* of a recipe
#' step that will create new columns that are basis expansions of
#' variables using orthogonal polynomials.
#'
#' @inheritParams step_pca
#' @inheritParams step_center
#' @param objects A list of [stats::poly()] objects
#' created once the step has been trained.
#' @param degree The polynomial degree (an integer).
#' @param options A list of options for [stats::poly()]
#' which should not include `x`, `degree`, or `simple`. Note that
#' the option `raw = TRUE` will produce the regular polynomial
#' values (not orthogonalized).
#' @template step-return
#' @family individual transformation steps
#' @export
#' @details `step_poly` can create new features from a single
#' variable that enable fitting routines to model this variable in
#' a nonlinear manner. The extent of the possible nonlinearity is
#' determined by the `degree` argument of
#' [stats::poly()]. The original variables are removed
#' from the data and new columns are added. The naming convention
#' for the new variables is `varname_poly_1` and so on.
#'
#' # Tidying
#'
#' When you [`tidy()`][tidy.recipe()] this step, a tibble with columns
#' `terms` (the columns that will be affected) and `degree` is returned.
#'
#' @template case-weights-not-supported
#'
#' @examplesIf rlang::is_installed("modeldata")
#' data(biomass, package = "modeldata")
#'
#' biomass_tr <- biomass[biomass$dataset == "Training", ]
#' biomass_te <- biomass[biomass$dataset == "Testing", ]
#'
#' rec <- recipe(
#' HHV ~ carbon + hydrogen + oxygen + nitrogen + sulfur,
#' data = biomass_tr
#' )
#'
#' quadratic <- rec %>%
#' step_poly(carbon, hydrogen)
#' quadratic <- prep(quadratic, training = biomass_tr)
#'
#' expanded <- bake(quadratic, biomass_te)
#' expanded
#'
#' tidy(quadratic, number = 1)
step_poly <-
function(recipe,
...,
role = "predictor",
trained = FALSE,
objects = NULL,
degree = 2,
options = list(),
skip = FALSE,
id = rand_id("poly")) {
if (!is_tune(degree) & !is_varying(degree)) {
degree <- as.integer(degree)
}
if (any(names(options) == "degree")) {
degree <- options$degree
message(
paste(
"The `degree` argument is now a main argument instead of being",
"within `options`."
)
)
}
add_step(
recipe,
step_poly_new(
terms = enquos(...),
trained = trained,
role = role,
objects = objects,
degree = degree,
options = options,
skip = skip,
id = id
)
)
}
step_poly_new <-
function(terms, role, trained, objects, degree, options, skip, id) {
step(
subclass = "poly",
terms = terms,
role = role,
trained = trained,
objects = objects,
degree = degree,
options = options,
skip = skip,
id = id
)
}
poly_wrapper <- function(x, args) {
args$x <- x
args$simple <- FALSE
poly_obj <- do.call("poly", args)
## don't need to save the original data so keep 1 row
out <- matrix(NA, ncol = ncol(poly_obj), nrow = 1)
class(out) <- c("poly", "basis", "matrix")
attr(out, "degree") <- attr(poly_obj, "degree")
attr(out, "coefs") <- attr(poly_obj, "coefs")
out
}
#' @export
prep.step_poly <- function(x, training, info = NULL, ...) {
col_names <- recipes_eval_select(x$terms, training, info)
check_type(training[, col_names], types = c("double", "integer"))
opts <- x$options
opts$degree <- x$degree
obj <- lapply(training[, col_names], poly_wrapper, opts)
for (i in seq(along.with = col_names)) {
attr(obj[[i]], "var") <- col_names[i]
}
step_poly_new(
terms = x$terms,
role = x$role,
trained = TRUE,
objects = obj,
degree = x$degree,
options = x$options,
skip = x$skip,
id = x$id
)
}
#' @export
bake.step_poly <- function(object, new_data, ...) {
col_names <- names(object$objects)
check_new_data(col_names, object, new_data)
new_names <- purrr::map(object$objects, ~ paste(attr(.x, "var"), "poly", 1:ncol(.x), sep = "_"))
# Start with n-row, 0-col tibble for the empty selection case
new_tbl <- tibble::new_tibble(x = list(), nrow = nrow(new_data))
for (i in seq_along(col_names)) {
i_col_name <- col_names[[i]]
i_col <- new_data[[i_col_name]]
i_object <- object$objects[[i]]
i_new_names <- new_names[[i]]
new_cols <- predict(i_object, i_col)
colnames(new_cols) <- i_new_names
new_cols <- tibble::as_tibble(new_cols)
new_tbl[i_new_names] <- new_cols
}
new_data <- dplyr::bind_cols(new_data, new_tbl)
new_data <- dplyr::select(new_data, -dplyr::all_of(col_names))
new_data
}
print.step_poly <-
function(x, width = max(20, options()$width - 35), ...) {
title <- "Orthogonal polynomials on "
print_step(names(x$objects), x$terms, x$trained, title, width)
invisible(x)
}
#' @rdname tidy.recipe
#' @export
tidy.step_poly <- function(x, ...) {
if (is_trained(x)) {
res <- tibble(terms = names(x$objects), degree = x$degree)
} else {
term_names <- sel2char(x$terms)
res <- tibble(terms = term_names, degree = x$degree)
}
res$id <- x$id
res
}
#' @export
tunable.step_poly <- function(x, ...) {
tibble::tibble(
name = c("degree"),
call_info = list(
list(pkg = "dials", fun = "degree_int")
),
source = "recipe",
component = "step_poly",
component_id = x$id
)
}
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