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#' B-Spline Basis Functions
#'
#' `step_bs` creates a *specification* of a recipe step
#' that will create new columns that are basis expansions of
#' variables using B-splines.
#'
#' @inheritParams step_pca
#' @inheritParams step_center
#' @param objects A list of [splines::bs()] objects
#' created once the step has been trained.
#' @param deg_free The degrees of freedom for the spline. As the
#' degrees of freedom for a spline increase, more flexible and
#' complex curves can be generated. When a single degree of freedom is used,
#' the result is a rescaled version of the original data.
#' @param degree Degree of polynomial spline (integer).
#' @param options A list of options for [splines::bs()]
#' which should not include `x`, `degree`, or `df`.
#' @template step-return
#' @family individual transformation steps
#' @export
#' @details `step_bs` 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 `df`, `degree`, or `knot` arguments of
#' [splines::bs()]. The original variables are removed
#' from the data and new columns are added. The naming convention
#' for the new variables is `varname_bs_1` and so on.
#'
#' # Tidying
#'
#' When you [`tidy()`][tidy.recipe()] this step, a tibble with column
#' `terms` (the columns that will be affected) 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
#' )
#'
#' with_splines <- rec %>%
#' step_bs(carbon, hydrogen)
#' with_splines <- prep(with_splines, training = biomass_tr)
#'
#' expanded <- bake(with_splines, biomass_te)
#' expanded
step_bs <-
function(recipe,
...,
role = "predictor",
trained = FALSE,
deg_free = NULL,
degree = 3,
objects = NULL,
options = list(),
skip = FALSE,
id = rand_id("bs")) {
add_step(
recipe,
step_bs_new(
terms = enquos(...),
trained = trained,
deg_free = deg_free,
degree = degree,
role = role,
objects = objects,
options = options,
skip = skip,
id = id
)
)
}
step_bs_new <-
function(terms, role, trained, deg_free, degree, objects, options, skip, id) {
step(
subclass = "bs",
terms = terms,
role = role,
trained = trained,
deg_free = deg_free,
degree = degree,
objects = objects,
options = options,
skip = skip,
id = id
)
}
bs_statistics <- function(x, args) {
# Only do the parameter computations from splines::bs() / splines::ns(), don't evaluate at x.
degree <- as.integer(args$degree %||% 3L)
intercept <- as.logical(args$intercept %||% FALSE)
# This behaves differently from splines::ns() if length(x) is 1
boundary <- sort(args$Boundary.knots) %||% range(x)
# This behaves differently from splines::bs() and splines::ns() if num_knots < 0L
# the original implementations issue a warning.
if (!is.null(args$df) && is.null(args$knots) && args$df - degree - intercept >= 1L) {
num_knots <- args$df - degree - intercept
ok <- !is.na(x) & x >= boundary[1L] & x <= boundary[2L]
knots <- unname(quantile(x[ok], seq_len(num_knots) / (num_knots + 1L)))
} else {
knots <- numeric()
}
# Only construct the data necessary for splines_predict
out <- matrix(NA, ncol = degree + length(knots) + intercept, nrow = 1L)
class(out) <- c("bs", "basis", "matrix")
attr(out, "knots") <- knots
attr(out, "Boundary.knots") <- boundary
attr(out, "intercept") <- intercept
attr(out, "degree") <- degree
out
}
bs_predict <- function(object, x) {
xu <- unique(x)
ru <- predict(object, xu)
res <- ru[match(x, xu), ]
copy_attrs <- c("class", "degree", "knots", "Boundary.knots", "intercept")
attributes(res)[copy_attrs] <- attributes(ru)[copy_attrs]
res
}
#' @export
prep.step_bs <- function(x, training, info = NULL, ...) {
col_names <- recipes_eval_select(x$terms, training, info)
check_type(training[, col_names], types = c("double", "integer", "datetime"))
opt <- x$options
opt$df <- x$deg_free
opt$degree <- x$degree
obj <- lapply(training[, col_names], bs_statistics, opt)
for (i in seq(along.with = col_names)) {
attr(obj[[i]], "var") <- col_names[i]
}
step_bs_new(
terms = x$terms,
role = x$role,
trained = TRUE,
deg_free = x$deg_free,
degree = x$degree,
objects = obj,
options = x$options,
skip = x$skip,
id = x$id
)
}
#' @export
bake.step_bs <- function(object, new_data, ...) {
check_new_data(names(object$objects), object, new_data)
## pre-allocate a matrix for the basis functions.
new_cols <- vapply(object$objects, ncol, c(int = 1L))
bs_values <-
matrix(NA, nrow = nrow(new_data), ncol = sum(new_cols))
colnames(bs_values) <- rep("", sum(new_cols))
strt <- 1
for (i in names(object$objects)) {
cols <- (strt):(strt + new_cols[i] - 1)
orig_var <- attr(object$objects[[i]], "var")
bs_values[, cols] <-
bs_predict(object$objects[[i]], getElement(new_data, i))
new_names <-
paste(orig_var, "bs", names0(new_cols[i], ""), sep = "_")
colnames(bs_values)[cols] <- new_names
strt <- max(cols) + 1
new_data[, orig_var] <- NULL
}
new_data <- bind_cols(new_data, as_tibble(bs_values))
new_data
}
print.step_bs <-
function(x, width = max(20, options()$width - 28), ...) {
title <- "B-splines on "
print_step(names(x$objects), x$terms, x$trained, title, width)
invisible(x)
}
#' @rdname tidy.recipe
#' @export
tidy.step_bs <- function(x, ...) {
if (is_trained(x)) {
res <- tibble(terms = names(x$objects))
} else {
cols <- sel2char(x$terms)
res <- tibble(terms = cols)
}
res$id <- x$id
as_tibble(res)
}
# ------------------------------------------------------------------------------
#' @export
tunable.step_bs <- function(x, ...) {
tibble::tibble(
name = c("deg_free", "degree"),
call_info = list(
list(pkg = "dials", fun = "spline_degree", range = c(1L, 15L)),
list(pkg = "dials", fun = "degree_int", range = c(1L, 2L))
),
source = "recipe",
component = "step_bs",
component_id = x$id
)
}
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