koplsPlotCVDiagnostics {kopls}R Documentation

Overview plot of cross-validation results

Description

Produces overview plots of cross-validation results retured from the koplsCV function.

Usage

koplsPlotCVDiagnostics(model.full, plot.values = FALSE)

Arguments

model.full The cross-validation model result (see koplsCV ).
plot.values If TRUE, the exact values will be displayed on the bars as text labels.

Details

Produces 2x2 panels of bar plots, containing the total explained variation (R2X), the Y-orthogonal explained variation (R2XO), the Y-correlated explained variation (R2XC) and the predicted variation from cross-validation (Q2Y).

Author(s)

Max Bylesjo and Mattias Rantalainen

References

Rantalainen M, Bylesjo M, Cloarec O, Nicholson JK, Holmes E and Trygg J. Kernel-based orthogonal projections to latent structures (K-OPLS), J Chemometrics 2007; 21:376-385. doi:10.1002/cem.1071.

Examples


## Load data set
data(koplsExample)

## Define kernel function parameter
sigma<-25 

## Construct kernel
Ktr<-koplsKernel(Xtr,NULL,'g',sigma)

## Find optimal number of Y-orthogonal components by cross-validation
## The cross-validation tests models with Y-orthogonal components 0 through numYo
modelCV<-koplsCV(Ktr,Ytr,1,3,nrcv=7,cvType='nfold',preProcK='mc',preProcY='mc',modelType='da')

## Visualize results
koplsPlotCVDiagnostics(modelCV)
title("Statistics from K-OPLS cross-validation of original data")


[Package kopls version 1.0.3 Index]