MSGLasso (version 2.1)

MSGLasso.cv: Fit the MSGLasso for a series sets of tuning parameters and use the k-fold cross validation to select the optimal tunning parameter set.

Description

Fit the MSGLasso for a series sets of tuning parameters and use the k-fold cross validation to select the optimal tunning parameter set.

Usage

MSGLasso.cv(X, Y, grpWTs, Pen.L, Pen.G, PQgrps, GRgrps, lam1.v, lamG.v,  fold = 10, seed = 1, Beta.ini = NULL, grp_Norm = NULL)

Arguments

X

numeric predictor matrix (n by p): columns correspond to predictor variables and rows correspond to samples. Missing values are not allowed.

Y

numeric predictor matrix (n by q): columns correspond to response variables and rows correspond to samples. Missing values are not allowed.

grpWTs

user specified adaptive group weighting matrix of g by r, for putting different penalization levels on different groups. Missing values are not allowed.

Pen.L

user specified single-entry level penalization indictor mateix of p by q. 1 for being penalized and 0 for not. Missing values are not allowed.

Pen.G

user specified group level penalization indictor mateix of g by r. 1 for being penalized and 0 for not. Missing values are not allowed.

PQgrps

the group attributing matrix of (p+q) by (gmax+1), where gmax is max number of different groups a single variable belongs to. Each row corresponds to a (predictor or response) varaible, and starts with group indexes the variable belongs to and followed by 999.

GRgrps

the variable attributing matrix of (g+r)*(cmax+1), where cmax is max number of variables a single group contains. Each row corresponds to a (predictor or response) group, and starts with variable indexes the group contains to and followed by 999.

lam1.v

lasso panelty parameter scaler.

lamG.v

group penalty parameter matrix (g by r).

fold

a positive integer for the corss validation fold. Default=5.

seed

a numeric scaler, specifying the seed of the random number generator in R for generating cross validation subset for each fold. Default=1.

Beta.ini

a numeric matrix of p by q, specifying the starting values of the input Beta matrix for each fold. Default using the zero matrix.

grp_Norm

a numeric matrix (g by r) containing starting L2 group norm values. Should be calculated from the Beta starting value matrix Beta.ini.

Value

A list with two components:

Details

Performs a k-fold cross-validation for seaching the optimal tunning parameter associated with the minimal prediction error on a two-dimensional grid.

References

Y. Li, B. Nan and J. Zhu (2015) Multivariate sparse group lasso for the multivariate multiple linear regression with an arbitrary group structure. Biometrics. DOI: 10.1111/biom.12292

Examples

## Not run: 
# #####################################################
# # Simulate data
# #####################################################
# 
# set.seed(sample(1:100,1))
# G.arr <- c(0,20,20,20,20,20,20,20,20,20,20)
# 
# data("Beta.m")
# 
# ######## generate data set for model fitting
# 
# simDataGen<-function(N, Beta, rho, s, G.arr, seed=1){
# 
# P<-nrow(Beta)
# Q<-ncol(Beta)
# gsum<-0
# X.m<-NULL
# 
# set.seed(seed)
# 
# Sig<-matrix(0,P,P)
# jstart <-1
# 
# for(g in 1:length(G.arr)-1){
# X.m<-cbind(X.m, matrix(rnorm(N*G.arr[g+1]),N,G.arr[g+1], byrow=TRUE))
# 
# for(i in 2:P){ for(j in jstart: (i-1)){
# 
#     Sig[i,j]<-rho^(abs(i-j))
# 
#     Sig[j,i]<-Sig[i,j]
# 
# }}
# jstart <- jstart + G.arr[g+1]
# }
# 
# 
# diag(Sig)<-1
# R<-chol(Sig)
# 
# X.m<-X.m%*%R
# 
# SVsum <-0
# 
# for (q in 1:Q){SVsum <-SVsum+var(X.m %*% Beta[,q])}
# sdr =sqrt(s*SVsum/Q)
# 
# E.m <- matrix(rnorm(N*Q,0,sdr),N, Q, byrow=TRUE)
# 
# Y.m<-X.m%*%Beta+E.m
# 
# return(list(X=X.m, Y=Y.m, E=E.m))
# }
# 
# N <-150
# 
# rho=0.5; 
# s=4;
# 
# Data <- simDataGen(N, Beta.m,rho, s, G.arr, seed=sample(1:100,1))
# X.m<-Data$X
# Y.m<-Data$Y
# 
# ################################################
# ## cross validation using the example data
# ################################################
# P <- dim(Beta.m)[1]
# Q <- dim(Beta.m)[2]
# G <- 10
# R <- 10
# 
# gmax <- 1
# cmax <- 20
# GarrStarts <- c(0,20,40,60,80,100,120,140,160,180)
# GarrEnds <- c(19,39,59,79,99,119,139,159,179,199)
# RarrStarts <- c(0,20,40,60,80,100,120,140,160,180)
# RarrEnds <- c(19,39,59,79,99,119,139,159,179,199)
# 
# tmp <- FindingPQGrps(P, Q, G, R, gmax, GarrStarts, GarrEnds, RarrStarts, RarrEnds)
# PQgrps <- tmp$PQgrps
# 
# tmp1 <- Cal_grpWTs(P, Q, G, R, gmax, PQgrps)
# grpWTs <- tmp1$grpWTs
# 
# tmp2 <- FindingGRGrps(P, Q, G, R, cmax, GarrStarts, GarrEnds, RarrStarts, RarrEnds)
# GRgrps <- tmp2$GRgrps
# 
# Pen_L <- matrix(rep(1,P*Q),P,Q, byrow=TRUE)
# Pen_G <- matrix(rep(1,G*R),G,R, byrow=TRUE)
# grp_Norm0 <- matrix(rep(0, G*R), nrow=G, byrow=TRUE)
# 
# lam1.v <- seq(1.0, 1.5, length=6) 
# lamG.v <- seq(0.19, 0.25, length=7) 
# 
# try.cv<- MSGLasso.cv(X.m, Y.m, grpWTs, Pen_L, Pen_G, PQgrps, GRgrps, 
#    lam1.v, lamG.v, fold=5, seed=1)
# MSGLassolam1 <- try.cv$lams.c[which.min(as.vector(try.cv$rss.cv))][[1]]$lam1
# MSGLassolamG  <- try.cv$lams.c[which.min(as.vector(try.cv$rss.cv))][[1]]$lam3
# MSGLassolamG.m <- matrix(rep(MSGLassolamG, G*R),G,R,byrow=TRUE)
#  
# system.time(try <-MSGLasso(X.m, Y.m, grpWTs, Pen_L, Pen_G, PQgrps, GRgrps, 
#     grp_Norm0, MSGLassolam1, MSGLassolamG.m, Beta0=NULL))
# 
# ## End(Not run)