mvabund (version 4.2.1)

ridgeParamEst: 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.

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

.

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).

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

# NOT RUN {
data(spider)
spiddat <- mvabund(spider$abund)
X <- as.matrix(spider$x)

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