ridgeParamEst: Estimation of the ridge parameter

In mvabund: Statistical Methods for Analysing Multivariate Abundance Data

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

If only.ridge=FALSE the returned list additionally contains the element:

minLL

the minimum of the negative log-likelihood

.

Author(s)

David Warton <[e-mail]> 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$abund)
X <- as.matrix(spider$x)

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

mvabund documentation built on March 18, 2022, 7:25 p.m.