wnet: Generalized elastic net in the wavelet domain

In refund.wave: Wavelet-Domain Regression with Functional Data

Description

Performs generalized linear scalar-on-function or scalar-on-image regression in the wavelet domain, by (naive) elastic net.

Usage

wnet(y, xfuncs, covt = NULL, min.scale = 0, nfeatures = NULL, alpha = 1, 
     lambda = NULL, standardize = FALSE, pen.covt = FALSE, 
     filter.number = 10, wavelet.family = "DaubLeAsymm", family = "gaussian", 
     nfold = 5, nsplit = 1, store.cv = FALSE, store.glmnet = FALSE, 
     seed = NULL, ...)

Arguments

y	scalar outcome vector.
xfuncs	functional predictors. For 1D predictors, an n \times d matrix of signals, where n is the length of y and d is the number of sites at which each signal is observed. For 2D predictors, an n \times d \times d array comprising n images of dimension d \times d. For 3D predictors, an n \times d \times d \times d array comprising n images of dimension d \times d \times d. Note that d must be a power of 2.
covt	covariates, if any: an n-row matrix, or a vector of length n.
min.scale	either a scalar, or a vector of candidate values to be compared. Used to control the coarseness level of the wavelet decomposition. Possible values are 0,1,…,log_2(d) - 1.
nfeatures	number(s) of features, i.e. wavelet coefficients, to retain for prediction of y: either a scalar, or a vector of values to be compared.
alpha	elastic net mixing parameter, used by glmnet: either a scalar, or a vector of values to be compared. alpha=1 gives the lasso penalty, while alpha=0 yields the ridge penalty.
lambda	a vector of candidate regularization parameter values. If not supplied, glmnet automatically generates a sequence of candidate values.
standardize	logical, passed to glmnet: should the predictor variables be standardized? Defaults to FALSE, but either way, the coefficients are returned on the original scale.
pen.covt	logical: should the scalar covariates be penalized? If FALSE (the default), penalization is suppressed by setting the appropriate components of penalty.factor to 0 in the call to glmnet.
filter.number	passed to wd, imwd, or wd3D, in the wavethresh package, to select the smoothness of the wavelets.
wavelet.family	family of wavelets: passed to wd, imwd, or wd3D.
family	generalized linear model family. Current version supports "gaussian" (the default) and "binomial".
nfold	the number of validation sets ("folds") into which the data are divided.
nsplit	number of splits into nfold validation sets; CV is computed by averaging over these splits.

store.cv	logical: should the output include a CV result table?
store.glmnet	logical: should the output include the fitted glmnet?
seed	the seed for random data division. If seed = NULL, a random seed is used.
...	other arguments passed to glmnet.

Details

This function supports only the standard discrete wavelet transform (see argument type in wd) with periodic boundary handling (see argument bc in wd).

For 2D predictors, setting min.scale=1 will lead to an error, due to a technical detail regarding imwd. Please contact the authors if a workaround is needed.

Value

An object of class "wnet", which is a list with the following components:

glmnet	if store.glmnet = TRUE, the object returned by glmnet.
fitted.value	the fitted values.
coef.param	parametric coefficient estimates, for the scalar covariates.
fhat	coefficient function estimate.
Rsq	coefficient of determination.
lambda.table	array giving the candidate lambda values, chosen automatically by glmnet, for each combination of the other tuning parameters.
tuning.params	a 2\times 4 table giving the indices and values of min.scale, nfeatures, alpha and lambda that minimize the CV. For example, if alpha=c(0,0.5,1) is specified and the CV-minimizing tuning parameter combination takes alpha to be the 2nd of these values, then the third column of the table is c(2, 0.5).
cv.table	if store.cv = TRUE, a table giving the CV criterion for each combination of min.scale, nfeatures, alpha and lambda. Otherwise, just the minimized CV criterion.
se.cv	if store.cv = TRUE, the standard error of the CV estimate for each combination of min.scale, nfeatures, alpha and lambda.
family	generalized linear model family.

Author(s)

Lan Huo [e-mail] and Yihong Zhao

References

Zhao, Y., Ogden, R. T., and Reiss, P. T. (2012). Wavelet-based LASSO in functional linear regression. Journal of Computational and Graphical Statistics, 21(3), 600–617.

See Also

wcr, wnet.perm

Examples

### 1D functional predictor example ###

data(gasoline)

# input a single value of each tuning parameters
gas.wnet1 <- wnet(gasoline$octane, xfuncs = gasoline$NIR[,1:256], 
             nfeatures= 20, min.scale = 0, alpha = 1)
gas.wpcr1 <- wcr(gasoline$octane, xfuncs = gasoline$NIR[,1:256], min.scale = 0,
                 nfeatures = 20, ncomp = 15)
gas.wpls1 <- wcr(gasoline$octane, xfuncs = gasoline$NIR[,1:256], min.scale = 0, 
                 nfeatures = 20, ncomp = 15, method = "pls")
plot(gas.wnet1)
plot(gas.wpcr1)
plot(gas.wpls1)

# input vectors of candidate tuning parameter values
gas.wnet2 <- wnet(gasoline$octane, xfuncs = gasoline$NIR[,1:256], 
                  nfeatures= 20, min.scale = 0:3, alpha = c(0.9, 1))
gas.wpcr2 <- wcr(gasoline$octane, xfuncs = gasoline$NIR[,1:256], min.scale = 0:3,
                 nfeatures = c(16, 18, 20), ncomp = 10:15)
gas.wpls2 <- wcr(gasoline$octane, xfuncs = gasoline$NIR[,1:256], min.scale = 0:3,
                 nfeatures = c(16, 18, 20), ncomp = 10:15, method = "pls")
plot(gas.wnet2)
plot(gas.wpcr2)
plot(gas.wpls2)

### 2D functional predictor example ###

n = 200; d = 64

# Create true coefficient function
ftrue = matrix(0,d,d)
ftrue[40:46,34:38] = 1

# Generate random functional predictors, and scalar responses
ii = array(rnorm(n*d^2), dim=c(n,d,d))
iimat = ii; dim(iimat) = c(n,d^2)
yy = iimat %*% as.vector(ftrue) + rnorm(n, sd=.3)

mm.wnet <- wnet(yy, xfuncs = ii, min.scale = 4, alpha = 1)

mm.wpls <- wcr(yy, xfuncs = ii, min.scale = 4, nfeatures = 20, ncomp = 6,
                method = "pls")

plot(mm.wnet)
plot(mm.wpls)

### 3D functional predictor example ###

n = 200; d = 16

# Create true coefficient function
ftrue = array(0,dim = rep(d, 3))
ftrue[10:16,12:15, 4:8] = 1

# Generate random functional predictors, and scalar responses
ii = array(rnorm(n*d^3), dim=c(n,rep(d,3)))
iimat = ii; dim(iimat) = c(n,d^3)
yy = iimat %*% as.vector(ftrue) + rnorm(n, sd=.3)

mmm.wnet <- wnet(yy, xfuncs = ii, min.scale = 2, alpha = 1)

mmm.wpls <- wcr(yy, xfuncs = ii, min.scale = 2, nfeatures = 20, ncomp = 6,
                method = "pls")
plot(mmm.wnet)
plot(mmm.wpls)

refund.wave documentation built on May 2, 2019, 5:54 p.m.