getNcomp {timeOmics} | R Documentation

## Get optimal number of components

### 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.

### Usage

    getNcomp(object, max.ncomp = NULL, X, Y = NULL, indY = NULL, ...)

### Arguments

`object` | A mixOmics object of the class 'pca', 'spca', 'mixo_pls', 'mixo_spls', 'block.pls', 'block.spls'
`max.ncomp` | integer, maximum number of component to include. If no argument is given, 'max.ncomp=object$ncomp'
`X` | a numeric matrix/data.frame or a list of data.frame for `block.pls`
`Y` | (only for `pls`, optional for `block.spls`) a numeric matrix, with the same nrow as `X`
`indY` | (optional and only for `block.pls`, if Y is not provided), an integer which indicates the position of the matrix response in the list X
`...` | Other arguments to be passed to methods (pca, pls, block.pls)

### Value

`getNcomp` returns a list with class "ncomp.tune.silhouette" containing the following components:

`ncomp` | a vector containing the tested ncomp
`silhouette` | a vector containing the average silhouette coefficient by ncomp
`dmatrix` | the distance matrix used to compute silhouette coefficient

### See Also

`getCluster`, `silhouette`, `pca`, `pls`, `block.pls`

### 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)

[Package timeOmics version 1.0.1 Index]