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#' Natural spline basis functions
#'
#' `step_ns()` creates a *specification* of a recipe step that will create new
#' columns that are basis expansions of variables using natural splines.
#'
#' @inheritParams step_pca
#' @inheritParams step_center
#' @param deg_free The degrees of freedom for the natural spline. As the
#' degrees of freedom for a natural 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 objects A list of [splines::ns()] objects
#' created once the step has been trained.
#' @param options A list of options for [splines::ns()]
#' which should not include `x` or `df`.
#' @template step-return
#' @family individual transformation steps
#' @export
#' @details `step_ns` 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` or `knots` arguments of
#' [splines::ns()]. The original variables are removed
#' from the data and new columns are added. The naming convention
#' for the new variables is `varname_ns_1` and so on.
#'
#' # Tidying
#'
#' When you [`tidy()`][tidy.recipe()] this step, a tibble is returned with
#' columns `terms` and `id`:
#'
#' \describe{
#' \item{terms}{character, the selectors or variables selected}
#' \item{id}{character, id of this step}
#' }
#'
#' ```{r, echo = FALSE, results="asis"}
#' step <- "step_ns"
#' result <- knitr::knit_child("man/rmd/tunable-args.Rmd")
#' cat(result)
#' ```
#'
#' @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_ns(carbon, hydrogen)
#' with_splines <- prep(with_splines, training = biomass_tr)
#'
#' expanded <- bake(with_splines, biomass_te)
#' expanded
step_ns <-
function(recipe,
...,
role = "predictor",
trained = FALSE,
objects = NULL,
deg_free = 2,
options = list(),
keep_original_cols = FALSE,
skip = FALSE,
id = rand_id("ns")) {
add_step(
recipe,
step_ns_new(
terms = enquos(...),
trained = trained,
deg_free = deg_free,
role = role,
objects = objects,
options = options,
keep_original_cols = keep_original_cols,
skip = skip,
id = id
)
)
}
step_ns_new <-
function(terms, role, trained, deg_free, objects, options, keep_original_cols,
skip, id) {
step(
subclass = "ns",
terms = terms,
role = role,
trained = trained,
deg_free = deg_free,
objects = objects,
options = options,
keep_original_cols = keep_original_cols,
skip = skip,
id = id
)
}
ns_statistics <- function(x, args) {
# Only do the parameter computations from splines::bs() / splines::ns(), don't evaluate at x.
degree <- 1L
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 {
if (is.null(args$knots)) {
knots <- numeric()
} else {
knots <- args$knots
}
}
# Only construct the data necessary for splines_predict
out <- matrix(NA, ncol = degree + length(knots) + intercept, nrow = 1L)
class(out) <- c("ns", "basis", "matrix")
attr(out, "degree") <- 3L
attr(out, "knots") <- knots
attr(out, "Boundary.knots") <- boundary
attr(out, "intercept") <- intercept
out
}
ns_predict <- function(object, x) {
xu <- unique(x)
ru <- predict(object, xu)
res <- ru[match(x, xu), ]
copy_attrs <- c("class", "knots", "Boundary.knots", "intercept")
attributes(res)[copy_attrs] <- attributes(ru)[copy_attrs]
res
}
#' @export
prep.step_ns <- 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
obj <- lapply(training[, col_names], ns_statistics, opt)
for (i in seq(along.with = col_names)) {
attr(obj[[i]], "var") <- col_names[i]
}
step_ns_new(
terms = x$terms,
role = x$role,
trained = TRUE,
deg_free = x$deg_free,
objects = obj,
options = x$options,
keep_original_cols = get_keep_original_cols(x),
skip = x$skip,
id = x$id
)
}
#' @export
bake.step_ns <- function(object, new_data, ...) {
col_names <- names(object$objects)
check_new_data(col_names, object, new_data)
for (col_name in col_names) {
new_values <- bs_predict(object$objects[[col_name]], new_data[[col_name]])
new_names <- paste(col_name, "ns", names0(ncol(new_values), ""), sep = "_")
colnames(new_values) <- new_names
new_values <- check_name(new_values, new_data, object, new_names)
new_data <- vctrs::vec_cbind(new_data, new_values)
}
new_data <- remove_original_cols(new_data, object, col_names)
new_data
}
#' @export
print.step_ns <-
function(x, width = max(20, options()$width - 28), ...) {
title <- "Natural splines on "
print_step(names(x$objects), x$terms, x$trained, title, width)
invisible(x)
}
#' @rdname tidy.recipe
#' @export
tidy.step_ns <- function(x, ...) {
if (is_trained(x)) {
terms <- names(x$objects)
} else {
terms <- sel2char(x$terms)
}
tibble(terms = terms, id = x$id)
}
#' @export
tunable.step_ns <- function(x, ...) {
tibble::tibble(
name = c("deg_free"),
call_info = list(
list(pkg = "dials", fun = "spline_degree", range = c(1L, 15L))
),
source = "recipe",
component = "step_ns",
component_id = x$id
)
}
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