--- a
+++ b/man/getNcomp.Rd
@@ -0,0 +1,58 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/getNcomp.R
+\name{getNcomp}
+\alias{getNcomp}
+\title{Get optimal number of components}
+\usage{
+getNcomp(object, max.ncomp = NULL, X, Y = NULL, indY = NULL, ...)
+}
+\arguments{
+\item{object}{A mixOmics object of the class `pca`, `spca`, `mixo_pls`, `mixo_spls`, `block.pls`, `block.spls`}
+
+\item{max.ncomp}{integer, maximum number of component to include.
+If no argument is given, `max.ncomp=object$ncomp`}
+
+\item{X}{a numeric matrix/data.frame or a list of data.frame for \code{block.pls}}
+
+\item{Y}{(only for \code{pls}, optional for \code{block.spls}) a numeric matrix, with the same nrow as \code{X}}
+
+\item{indY}{(optional and only for \code{block.pls}, if Y is not provided), an integer which indicates the position of the matrix response in the list X}
+
+\item{...}{Other arguments to be passed to methods (pca, pls, block.pls)}
+}
+\value{
+\code{getNcomp} returns a list with class "ncomp.tune.silhouette" containing the following components:
+
+\item{ncomp}{a vector containing the tested ncomp}
+\item{silhouette}{a vector containing the average silhouette coefficient by ncomp}
+\item{dmatrix}{the distance matrix used to compute silhouette coefficient}
+}
+\description{
+Compute the average silhouette coefficient for a given set of components on a mixOmics result.
+Foreach given ncomp, the mixOmics method is performed with the sames arguments and the given `ncomp`.
+Longitudinal clustering is performed and average silhouette coefficient is computed.
+}
+\examples{
+# random input data
+demo <- suppressWarnings(get_demo_cluster())
+
+# pca
+pca.res <- mixOmics::pca(X=demo$X, ncomp = 5)
+res.ncomp <- getNcomp(pca.res, max.ncomp = 4, X = demo$X)
+plot(res.ncomp)
+
+# pls
+pls.res <- mixOmics::pls(X=demo$X, Y=demo$Y)
+res.ncomp <- getNcomp(pls.res, max.ncomp = 4, X = demo$X, Y=demo$Y)
+plot(res.ncomp)
+
+# block.pls
+block.pls.res <- suppressWarnings(mixOmics::block.pls(X=list(X=demo$X, Z=demo$Z), Y=demo$Y))
+res.ncomp <- suppressWarnings(getNcomp(block.pls.res, max.ncomp = 4,
+                                       X=list(X=demo$X, Z=demo$Z), Y=demo$Y))
+plot(res.ncomp)
+
+}
+\seealso{
+\code{\link{getCluster}}, \code{\link{silhouette}}, \code{\link[mixOmics]{pca}}, \code{\link[mixOmics]{pls}}, \code{\link[mixOmics]{block.pls}}
+}