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% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/kpca.R
\name{step_kpca}
\alias{step_kpca}
\title{Kernel PCA Signal Extraction}
\usage{
step_kpca(
recipe,
...,
role = "predictor",
trained = FALSE,
num_comp = 5,
res = NULL,
columns = NULL,
options = list(kernel = "rbfdot", kpar = list(sigma = 0.2)),
prefix = "kPC",
keep_original_cols = FALSE,
skip = FALSE,
id = rand_id("kpca")
)
}
\arguments{
\item{recipe}{A recipe object. The step will be added to the
sequence of operations for this recipe.}
\item{...}{One or more selector functions to choose variables
for this step. See \code{\link[=selections]{selections()}} for more details.}
\item{role}{For model terms created by this step, what analysis role should
they be assigned? By default, the new columns created by this step from
the original variables will be used as \emph{predictors} in a model.}
\item{trained}{A logical to indicate if the quantities for
preprocessing have been estimated.}
\item{num_comp}{The number of components to retain as new predictors.
If \code{num_comp} is greater than the number of columns or the number of
possible components, a smaller value will be used. If \code{num_comp = 0}
is set then no transformation is done and selected variables will
stay unchanged.}
\item{res}{An S4 \code{\link[kernlab:kpca]{kernlab::kpca()}} object is stored here once this
preprocessing step has be trained by \code{\link[=prep]{prep()}}.}
\item{columns}{A character string of variable names that will
be populated elsewhere.}
\item{options}{A list of options to \code{\link[kernlab:kpca]{kernlab::kpca()}}. Defaults are set for
the arguments \code{kernel} and \code{kpar} but others can be passed in.
\strong{Note} that the arguments \code{x} and \code{features} should not be passed here
(or at all).}
\item{prefix}{A character string for the prefix of the resulting new
variables. See notes below.}
\item{keep_original_cols}{A logical to keep the original variables in the
output. Defaults to \code{FALSE}.}
\item{skip}{A logical. Should the step be skipped when the
recipe is baked by \code{\link[=bake]{bake()}}? While all operations are baked
when \code{\link[=prep]{prep()}} is run, some operations may not be able to be
conducted on new data (e.g. processing the outcome variable(s)).
Care should be taken when using \code{skip = TRUE} as it may affect
the computations for subsequent operations.}
\item{id}{A character string that is unique to this step to identify it.}
}
\value{
An updated version of \code{recipe} with the new step added to the
sequence of any existing operations.
}
\description{
\code{step_kpca} creates a \emph{specification} of a recipe step that
will convert numeric data into one or more principal components
using a kernel basis expansion.
}
\details{
When performing kPCA with \code{step_kpca()}, you must choose the kernel
function (and any important kernel parameters). This step uses the
\pkg{kernlab} package; the reference below discusses the types of kernels
available and their parameter(s). These specifications can be made in the
\code{kernel} and \code{kpar} slots of the \code{options} argument to \code{step_kpca()}.
Consider using \code{\link[=step_kpca_rbf]{step_kpca_rbf()}} for a radial basis function kernel or
\code{\link[=step_kpca_poly]{step_kpca_poly()}} for a polynomial kernel.
Kernel principal component analysis (kPCA) is an extension of a PCA analysis
that conducts the calculations in a broader dimensionality defined by a
kernel function. For example, if a quadratic kernel function were used,
each variable would be represented by its original values as well as its
square. This nonlinear mapping is used during the PCA analysis and can
potentially help find better representations of the original data.
This step requires the \pkg{kernlab} package.
If not installed, the step will stop with a prompt about installing
the package.
As with ordinary PCA, it is important to center and scale the variables
prior to computing PCA components (\code{\link[=step_normalize]{step_normalize()}} can be used for
this purpose).
The argument \code{num_comp} controls the number of components that will be
retained; the original variables that are used to derive the components are
removed from the data when \code{keep_original_cols = FALSE}. The new components
will have names that begin with \code{prefix} and a sequence of numbers. The
variable names are padded with zeros. For example, if \code{num_comp < 10}, the
new names will be \code{kPC1} - \code{kPC9}. If \code{num_comp = 101}, the names would be
\code{kPC001} - \code{kPC101}.
}
\section{tidy() results}{
When you \code{\link[=tidy.recipe]{tidy()}} this step, a tibble with column
\code{terms} (the selectors or variables selected) is returned.
}
\section{Case weights}{
The underlying operation does not allow for case weights.
}
\examples{
\dontshow{if (rlang::is_installed(c("modeldata", "ggplot2", "kernlab"))) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf}
library(ggplot2)
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
)
kpca_trans <- rec \%>\%
step_YeoJohnson(all_numeric_predictors()) \%>\%
step_normalize(all_numeric_predictors()) \%>\%
step_kpca(all_numeric_predictors())
kpca_estimates <- prep(kpca_trans, training = biomass_tr)
kpca_te <- bake(kpca_estimates, biomass_te)
ggplot(kpca_te, aes(x = kPC1, y = kPC2)) +
geom_point() +
coord_equal()
tidy(kpca_trans, number = 3)
tidy(kpca_estimates, number = 3)
\dontshow{\}) # examplesIf}
}
\references{
Scholkopf, B., Smola, A., and Muller, K. (1997).
Kernel principal component analysis. \emph{Lecture Notes in
Computer Science}, 1327, 583-588.
Karatzoglou, K., Smola, A., Hornik, K., and Zeileis, A. (2004).
kernlab - An S4 package for kernel methods in R. \emph{Journal
of Statistical Software}, 11(1), 1-20.
}
\seealso{
Other multivariate transformation steps:
\code{\link{step_classdist}()},
\code{\link{step_depth}()},
\code{\link{step_geodist}()},
\code{\link{step_ica}()},
\code{\link{step_isomap}()},
\code{\link{step_kpca_poly}()},
\code{\link{step_kpca_rbf}()},
\code{\link{step_mutate_at}()},
\code{\link{step_nnmf_sparse}()},
\code{\link{step_nnmf}()},
\code{\link{step_pca}()},
\code{\link{step_pls}()},
\code{\link{step_ratio}()},
\code{\link{step_spatialsign}()}
}
\concept{multivariate transformation steps}
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