RidgeFusion (version 1.0-3)

RidgeFusedCV: Ridged Fused Validation Likelihood

Description

Calculates the Valdiation Likelihood Score for candidate tuning parameters

Usage

RidgeFusedCV(X,lambda1,lambda2,Fold,tol=10^-6,warm.start=TRUE,scaleCV=FALSE,INF=FALSE)

Arguments

X

A list of length J that contains the data for each class

lambda1

A vector with all possible Ridge tuning parameters

lambda2

A vector with all possible Ridge Fusion tuning parameters

Fold

A list of length K, the number of folds, where each element is a list of length of the number of classes that contains the indices for the kth fold of the jth class. Fold[[1]][[1]] contains the indices of the first fold in class 1, Fold[[1]][[2]] contains the indices of the first fold of class 2

tol

Convergence tolerance for blockwise coordinate descent algorithm at each grid point

warm.start

A True/False variable, that indicates if warm.starts should be used

scaleCV

If TRUE scale invariant method is used

INF

If TRUE sets all inverse covariance matrices equal in the result

Value

An object of class RidgeFusionCV, basically a list including elements

Omega

a list where each element is the precision matrix estimate for the corresponding element of S

BestRidge

The ridge grid point that minimizes the validation likelihood score

BestFusedRidge

The fused ridge grid point that minimizes the validation likelihood score

CV

The matrix of validation likelihood scores and the grid points they match

Examples

## Creating a toy example with 5 variables
library(mvtnorm)
set.seed(526)
p=5
    Sig1=matrix(0,p,p)
	for(j in 1:p){
		for(i in j:p){          
            Sig1[j,i]=.7^abs(i-j)
            Sig1[i,j]=Sig1[j,i]
            
		}
	}
    Sig2=diag(c(rep(2,p-5),rep(1,5)),p,p)
X1=rmvnorm(100,rep(2*log(p)/p,p),Sig1)
Y=rmvnorm(100,,Sig2)

## Creating a list of the data for each class
Z=list(X1,Y)

Samp=list(0,0)
Samp[[1]]=sample(1:100)
Samp[[2]]=sample(1:100)

## Creating Fold list
Fold1=list(0,0)
for(i in 1:5){
	Fold1[[i]]=list(0,0)
	for(j in 1:2){
		Fold1[[i]][[j]]=Samp[[j]][((20*(i-1))+1):(i*20)]
	}
}

## Calculating Validation likelihood scores for
##tuning parameter grid 10^(-1:1) for Ridge, and 10^(2:3) for Ridge Fusion
Tell=RidgeFusedCV(Z,10^(-1:1),10^(2:3),Fold1,scaleCV=TRUE)
Tell
names(Tell)