ridgeParamEst {mvabund}R Documentation

Estimation of the ridge parameter

Description

Maximum likelihood estimation of the ridge parameter by cross-validation

Usage

ridgeParamEst(dat, X, weights = rep(1,times=nRows), refs, 
        tol=1.0e-010, only.ridge=FALSE,  doPlot=FALSE,
        col="blue",type="l", ...) 

Arguments

dat the data matrix.
X the design matrix.
weights weights on the cases of the design matrix.
refs a vector specifying validation group membership. Default is to construct refs using a method that is a function of the sample size N: if N<=20, leave-one-out is used refs=1:N, if N<=40, 10-fold Cross Validation is used where group membership is chosen randomly but with equal size groups, otherwise 5-fold CV with random group memberships.
tol the sensitivity in calculations near zero.
only.ridge logical, whether only the ridge Parameters should be passed back or additionally the Cross Validation penalised likelihood.
doPlot logical, whether a plot of -2logL vs a candidate for the ridge parameter should be drawn.
col color of Plot symbols.
type type of Plot symbols.
... further plot arguments.

Details

This function estimates the ridge parameter when applying ridge regularization to a sample correlation matrix of residuals. The ridge parameter is estimated to maximize the normal likelihood as estimated via cross validation (Warton 2008).

Value

A list with the following component:

ridgeParameter the estimated ridge parameter
minLL the minimum of the negative log-likelihood

.

Author(s)

David Warton <David.Warton@unsw.edu.au> and Ulrike Naumann.

References

Warton D.I. (2008). Penalized normal likelihood and ridge regularization of correlation and covariance matrices. Journal of the American Statistical Association 103, 340-349.

See Also

manylm

Examples

data(spider)
spiddat <- mvabund(spider$abund)
X <- spider$x

ridgeParamEst(dat = spiddat, X = model.matrix(spiddat~X))

[Package mvabund version 0.1-7 Index]