lrpca: Logratio principal component analysis with condition indices

In ToolsForCoDa: Multivariate Tools for Compositional Data Analysis

Description

Function lrpca performs logratio principal component analysis. It returns the variance decomposition, principal components, biplot coordinates and a table with condition indices.

Usage

lrpca(Xcom)

Arguments

Xcom	A matrix with compositions in its rows

Details

Calculations are based on the singular value decompositon of the clr transformed compositions.

Value

Fp	matrix with principal components
Fs	matrix with standardized principal components
Gp	biplot markers for parts (principal coordinates)
Gs	biplot markers for parts (standard coordinates)
La	eigenvalues
D	singular values
decom	table with variance decomposition
kappalist	table with condition indices and eigenvectors

Author(s)

Jan Graffelman ([e-mail])

See Also

princomp,

Examples

data(bentonites)
Ben <- bentonites[,1:8]
Ben.com <- Ben/rowSums(Ben)
out.lrpca <- lrpca(Ben.com)

Example output

Loading required package: MASS
Loading required package: calibrate
Loading required package: robCompositions
Loading required package: ggplot2
Loading required package: pls

Attaching package: ‘pls’

The following object is masked from ‘package:stats’:

    loadings

Loading required package: data.table
Registered S3 method overwritten by 'GGally':
  method from   
  +.gg   ggplot2
sROC 0.1-2 loaded

ToolsForCoDa documentation built on Sept. 20, 2021, 5:19 p.m.