refund (version 0.1-23)

fosr: Function-on-scalar regression

Description

Fit linear regression with functional responses and scalar predictors, with efficient selection of optimal smoothing parameters.

Usage

fosr(
  formula = NULL,
  Y = NULL,
  fdobj = NULL,
  data = NULL,
  X,
  con = NULL,
  argvals = NULL,
  method = c("OLS", "GLS", "mix"),
  gam.method = c("REML", "ML", "GCV.Cp", "GACV.Cp", "P-REML", "P-ML"),
  cov.method = c("naive", "mod.chol"),
  lambda = NULL,
  nbasis = 15,
  norder = 4,
  pen.order = 2,
  multi.sp = ifelse(method == "OLS", FALSE, TRUE),
  pve = 0.99,
  max.iter = 1,
  maxlam = NULL,
  cv1 = FALSE,
  scale = FALSE
)

Arguments

formula

Formula for fitting fosr. If used, data argument must not be null.

Y, fdobj

the functional responses, given as either an \(n\times d\) matrix Y or a functional data object (class "fd") as in the fda package.

data

data frame containing the predictors and responses.

X

the model matrix, whose columns represent scalar predictors. Should ordinarily include a column of 1s.

con

a row vector or matrix of linear contrasts of the coefficient functions, to be constrained to equal zero.

argvals

the \(d\) argument values at which the coefficient functions will be evaluated.

method

estimation method: "OLS" for penalized ordinary least squares, "GLS" for penalized generalized least squares, "mix" for mixed effect models.

gam.method

smoothing parameter selection method, to be passed to gam: "REML" for restricted maximum likelihood, "GCV.Cp" for generalized cross-validation.

cov.method

covariance estimation method: the current options are naive or modified Cholesky. See Details.

lambda

smoothing parameter value. If NULL, the smoothing parameter(s) will be estimated. See Details.

nbasis, norder

number of basis functions, and order of splines (the default, 4, gives cubic splines), for the B-spline basis used to represent the coefficient functions. When the functional responses are supplied using fdobj, these arguments are ignored in favor of the values pertaining to the supplied object.

pen.order

order of derivative penalty.

multi.sp

a logical value indicating whether separate smoothing parameters should be estimated for each coefficient function. Currently must be FALSE if method = "OLS".

pve

if method = 'mix', the percentage of variance explained by the principal components; defaults to 0.99.

max.iter

maximum number of iterations if method = "GLS".

maxlam

maximum smoothing parameter value to consider (when lamvec=NULL; see lofocv).

cv1

logical value indicating whether a cross-validation score should be computed even if a single fixed lambda is specified (when method = "OLS").

scale

logical value or vector determining scaling of the matrix X (see scale, to which the value of this argument is passed).

Value

An object of class fosr, which is a list with the following elements:

fd

object of class "fd" representing the estimated coefficient functions. Its main components are a basis and a matrix of coefficients with respect to that basis.

pca.resid

if method = "mix", an object representing a functional PCA of the residuals, performed by fpca.sc if the responses are in raw form or by pca.fd if in functional-data-object form.

U

if method = "mix", an \(n\times m\) matrix of random effects, where \(m\) is the number of functional PC's needed to explain proportion pve of the residual variance. These random effects can be interpreted as shrunken FPC scores.

yhat, resid

objects of the same form as the functional responses (see arguments Y and fdobj), giving the fitted values and residuals.

est.func

matrix of values of the coefficient function estimates at the points given by argvals.

se.func

matrix of values of the standard error estimates for the coefficient functions, at the points given by argvals.

argvals

points at which the coefficient functions are evaluated.

fit

fit object outputted by amc.

edf

effective degrees of freedom of the fit.

lambda

smoothing parameter, or vector of smoothing parameters.

cv

cross-validated integrated squared error if method="OLS", otherwise NULL.

roughness

value of the roughness penalty.

resp.type

"raw" or "fd", indicating whether the responses were supplied in raw or functional-data-object form.

Details

The GLS method requires estimating the residual covariance matrix, which has dimension \(d\times d\) when the responses are given by Y, or \(nbasis\times nbasis\) when they are given by fdobj. When cov.method = "naive", the ordinary sample covariance is used. But this will be singular, or nonsingular but unstable, in high-dimensional settings, which are typical. cov.method = "mod.chol" implements the modified Cholesky method of Pourahmadi (1999) for estimation of covariance matrices whose inverse is banded. The number of bands is chosen to maximize the p-value for a sphericity test (Ledoit and Wolf, 2002) applied to the "prewhitened" residuals. Note, however, that the banded inverse covariance assumption is sometimes inappropriate, e.g., for periodic functional responses.

There are three types of values for argument lambda:

  1. if a scalar, this value is used as the smoothing parameter (but only for the initial model, if method = "GLS");

  2. if a vector, this is used as a grid of values for optimizing the cross-validation score (provided method = "OLS"; otherwise an error message is issued).

Please note that currently, if multi.sp = TRUE, then lambda must be NULL and method must be "GLS".

References

Ledoit, O., and Wolf, M. (2002). Some hypothesis tests for the covariance matrix when the dimension is large compared to the sample size. Annals of Statistics, 30(4), 1081--1102.

Pourahmadi, M. (1999). Joint mean-covariance models with applications to longitudinal data: unconstrained parameterisation. Biometrika, 86(3), 677--690.

Ramsay, J. O., and Silverman, B. W. (2005). Functional Data Analysis, 2nd ed., Chapter 13. New York: Springer.

Reiss, P. T., Huang, L., and Mennes, M. (2010). Fast function-on-scalar regression with penalized basis expansions. International Journal of Biostatistics, 6(1), article 28. Available at https://works.bepress.com/phil_reiss/16/

See Also

plot.fosr

Examples

# NOT RUN {
require(fda)
# The first two lines, adapted from help(fRegress) in package fda,
# set up a functional data object representing daily average
# temperatures at 35 sites in Canada
daybasis25 <- create.fourier.basis(rangeval=c(0, 365), nbasis=25,
                  axes=list('axesIntervals'))
Temp.fd <- with(CanadianWeather, smooth.basisPar(day.5,
                dailyAv[,,'Temperature.C'], daybasis25)$fd)

modmat = cbind(1, model.matrix(~ factor(CanadianWeather$region) - 1))
constraints = matrix(c(0,1,1,1,1), 1)

# Penalized OLS with smoothing parameter chosen by grid search
olsmod = fosr(fdobj = Temp.fd, X = modmat, con = constraints, method="OLS", lambda=100*10:30)
plot(olsmod, 1)

# Test use formula to fit fosr
set.seed(2121)
data1 <- pffrSim(scenario="ff", n=40)
formod = fosr(Y~xlin+xsmoo, data=data1)
plot(formod, 1)

# Penalized GLS
glsmod = fosr(fdobj = Temp.fd, X = modmat, con = constraints, method="GLS")
plot(glsmod, 1)
# }