refund: Regression with Functional Data

Methods for regression for functional data, including function-on-scalar, scalar-on-function, and function-on-function regression. Some of the functions are applicable to image data.

Author
Jeff Goldsmith [aut], Fabian Scheipl [aut], Lei Huang [aut, cre], Julia Wrobel [aut], Jonathan Gellar [aut], Jaroslaw Harezlak [aut], Mathew W. McLean [aut], Bruce Swihart [aut], Luo Xiao [aut], Ciprian Crainiceanu [aut], Philip T. Reiss [aut], Yakuan Chen [ctb], Sonja Greven [ctb], Lan Huo [ctb], Madan Gopal Kundu [ctb], So Young Park [ctb], David L. Miller [ctb], Ana-Maria Staicu [ctb]
Date of publication
2016-08-03 10:09:56
Maintainer
Lei Huang <huangracer@gmail.com>
License
GPL (>= 2)
Version
0.1-16

View on CRAN

Man pages

af
Construct an FGAM regression term
af_old
Construct an FGAM regression term
amc
Additive model with constraints
bayes_fosr
Bayesian Function-on-scalar regression
ccb.fpc
Corrected confidence bands using functional principal...
cd4
Observed CD4 cell counts
cmdscale_lanczos
Faster multi-dimensional scaling
coefboot.pffr
Simple bootstrap CIs for pffr
coefficients.pfr
Extract coefficient functions from a fitted pfr-object
coef.pffr
Get estimated coefficients from a pffr fit
create.prep.func
Construct a function for preprocessing functional predictors
DTI
Diffusion Tensor Imaging: tract profiles and outcomes
DTI2
Diffusion Tensor Imaging: more fractional anisotropy profiles...
expand.call
Return call with all possible arguments
fbps
Sandwich smoother for matrix data
ff
Construct a function-on-function regression term
ffpc
Construct a PC-based function-on-function regression term
ffpcplot
Plot PC-based function-on-function regression terms
fgam
Functional Generalized Additive Models
fosr
Function-on-scalar regression
fosr2s
Two-step function-on-scalar regression
fosr.perm
Permutation testing for function-on-scalar regression
fosr.vs
Function-on Scalar Regression with variable selection
fpc
Construct a FPC regression term
fpca2s
Functional principal component analysis by a two-stage method
fpca.face
Functional principal component analysis with fast covariance...
fpca.lfda
Longitudinal Functional Data Analysis using FPCA
fpca.sc
Functional principal components analysis by smoothed...
fpca.ssvd
Smoothed FPCA via iterative penalized rank one SVDs.
fpcr
Functional principal component regression
f_sum
Sum computation 1
f_sum2
Sum computation 2
f_sum4
Sum computation 2
f_trace
Trace computation
gasoline
Octane numbers and NIR spectra of gasoline
getTF
Get recognized transformation function
gibbs_cs_fpca
Cross-sectional FoSR using a Gibbs sampler and FPCA
gibbs_cs_wish
Cross-sectional FoSR using a Gibbs sampler and Wishart prior
gibbs_mult_fpca
Multilevel FoSR using a Gibbs sampler and FPCA
gibbs_mult_wish
Multilevel FoSR using a Gibbs sampler and Wishart prior
gls_cs
Cross-sectional FoSR using GLS
lf
Construct an FLM regression term
lf_old
Construct an FLM regression term
lf.vd
Construct a VDFR regression term
lofocv
Leave-one-function-out cross-validation
lpeer
Longitudinal Functional Models with Structured Penalties
lpfr
Longitudinal penalized functional regression
mfpca.sc
Multilevel functional principal components analysis by...
model.matrix.pffr
Obtain model matrix for a pffr fit
ols_cs
Cross-sectional FoSR using GLS
pco_predict_preprocess
Make predictions using pco basis terms
pcre
pffr-constructor for functional principal component-based...
peer
Construct a PEER regression term in a 'pfr' formula
peer_old
Functional Models with Structured Penalties
PEER.Sim
Simulated longitudinal data with functional predictor and...
pffr
Penalized flexible functional regression
pffr.check
Some diagnostics for a fitted pffr model
pffrGLS
Penalized function-on-function regression with non-i.i.d....
pffrSim
Simulate example data for pffr
pfr
Penalized Functional Regression
pfr_old
Penalized Functional Regression (old version)
pfr_plot.gam
Local version of 'plot.gam'
plot.fosr
Default plotting of function-on-scalar regression objects
plot.fosr.vs
Plot for Function-on Scalar Regression with variable...
plot.fpcr
Default plotting for functional principal component...
plot.lpeer
Plotting of estimated regression functions obtained through...
plot.peer
Plotting of estimated regression functions obtained through...
plot.pffr
Plot a pffr fit
plot.pfr
Plot a pfr object
predict.fbps
Prediction for fast bivarate _P_-spline (fbps)
predict.fgam
Prediction from a fitted FGAM model
predict.fosr.vs
Prediction for Function-on Scalar Regression with variable...
Predict.matrix.dt.smooth
Predict.matrix method for dt basis
Predict.matrix.fpc.smooth
mgcv-style constructor for prediction of FPC terms
Predict.matrix.pcre.random.effect
mgcv-style constructor for prediction of PC-basis functional...
Predict.matrix.peer.smooth
mgcv-style constructor for prediction of PEER terms
Predict.matrix.pi.smooth
Predict.matrix method for pi basis
predict.pffr
Prediction for penalized function-on-function regression
predict.pfr
Prediction from a fitted pfr model
print.summary.pffr
Print method for summary of a pffr fit
pwcv
Pointwise cross-validation for function-on-scalar regression
qq.pffr
QQ plots for pffr model residuals
quadWeights
Compute quadrature weights
re
Random effects constructor for fgam
refund-internal
Internal functions for the refund package
refund-package
Regression with Functional Data
residuals.pffr
Obtain residuals and fitted values for a pffr models
rlrt.pfr
Likelihood Ratio Test and Restricted Likelihood Ratio Test...
sff
Construct a smooth function-on-function regression term
smooth.construct.dt.smooth.spec
Domain Transformation basis constructor
smooth.construct.fpc.smooth.spec
Basis constructor for FPC terms
smooth.construct.pco.smooth.spec
Principal coordinate ridge regression
smooth.construct.pcre.smooth.spec
mgcv-style constructor for PC-basis functional random effects
smooth.construct.peer.smooth.spec
Basis constructor for PEER terms
smooth.construct.pi.smooth.spec
Parametric Interaction basis constructor
smooth.construct.pss.smooth.spec
P-spline constructor with modified 'shrinkage' penalty
sofa
SOFA (Sequential Organ Failure Assessment) Data
summary.pffr
Summary for a pffr fit
summary.pfr
Summary for a pfr fit
vb_cs_fpca
Cross-sectional FoSR using Variational Bayes and FPCA
vb_cs_wish
Cross-sectional FoSR using Variational Bayes and Wishart...
vb_mult_fpca
Multilevel FoSR using Variational Bayes and FPCA
vb_mult_wish
Multilevel FoSR using Variational Bayes and Wishart prior
vis.fgam
Visualization of FGAM objects
vis.pfr
Visualization of PFR objects
Xt_siginv_X
Internal computation function

Files in this package

refund
refund/NAMESPACE
refund/data
refund/data/cd4.RData
refund/data/gasoline.RData
refund/data/PEER.Sim.RData
refund/data/DTI2.RData
refund/data/datalist
refund/data/Q.RData
refund/data/DTI.RData
refund/data/sofa.RData
refund/R
refund/R/fbps.R
refund/R/VB_Mult_Wish.R
refund/R/create.prep.func.R
refund/R/fpcr.R
refund/R/pfr_old.R
refund/R/pffr-utilities.R
refund/R/vis.fgam.R
refund/R/CD4-data.R
refund/R/predict.pfr.R
refund/R/af.R
refund/R/predict.pfr_old.R
refund/R/VB_Mult_FPCA.R
refund/R/rlrt.pfr.R
refund/R/Gibbs_CS_FPCA.R
refund/R/f_trace.R
refund/R/fpcr.setup.R
refund/R/dt_basis.R
refund/R/f_sum.R
refund/R/plot.lpeer.R
refund/R/VB_CS_FPCA.R
refund/R/OLS_CS.R
refund/R/amc.R
refund/R/f_sum4.R
refund/R/pi_basis.R
refund/R/osplinepen2d.R
refund/R/Gibbs_Mult_FPCA.R
refund/R/af_old.R
refund/R/irreg2mat.R
refund/R/DTI2-data.R
refund/R/bayes_fosr.R
refund/R/plot.fosr.vs.R
refund/R/fosr.perm.test.R
refund/R/Omegas.R
refund/R/predict.fosr.vs.R
refund/R/pffr-ffpc.R
refund/R/summary.pfr.R
refund/R/pffr.R
refund/R/lpeer.R
refund/R/peer_old.R
refund/R/pffr-methods.R
refund/R/fpca2s.R
refund/R/plot.fpcr.R
refund/R/fosr.perm.R
refund/R/fpca.ssvd.R
refund/R/fosr.vs.R
refund/R/lf_old.R
refund/R/lofocv.R
refund/R/pffr-pcre.R
refund/R/mfpca.sc.R
refund/R/XtSiginvX.R
refund/R/parse.predict.pfr.R
refund/R/coefficients.pfr.R
refund/R/ccb.fpc.R
refund/R/fosr.R
refund/R/pfr.R
refund/R/pspline.setting.R
refund/R/plot.fosr.perm.R
refund/R/predict.fgam.R
refund/R/GLS_CS.R
refund/R/fpc.R
refund/R/fosr.perm.fit.R
refund/R/lf.R
refund/R/VB_CS_Wish.R
refund/R/postprocess.pfr.R
refund/R/select_knots.R
refund/R/lw.test.R
refund/R/plot.pfr.R
refund/R/PEER.Sim-data.R
refund/R/peer.R
refund/R/pffr-sff.R
refund/R/pffr-ff.R
refund/R/pwcv.R
refund/R/poridge.R
refund/R/Gibbs_Mult_Wish.R
refund/R/pffr-robust.R
refund/R/lf.vd.R
refund/R/quadWeights.R
refund/R/predict.fbps.R
refund/R/Gibbs_CS_Wish.R
refund/R/fosr2s.R
refund/R/plot.fosr.R
refund/R/re.R
refund/R/fpca.lfda.R
refund/R/f_sum2.R
refund/R/fgam.R
refund/R/preprocess.pfr.R
refund/R/gasoline-data.R
refund/R/DTI-data.R
refund/R/lpfr.R
refund/R/vis.pfr.R
refund/R/plot.peer.R
refund/R/fpca.face.R
refund/R/fpca.sc.R
refund/MD5
refund/DESCRIPTION
refund/man
refund/man/smooth.construct.pi.smooth.spec.Rd
refund/man/lpfr.Rd
refund/man/vb_mult_fpca.Rd
refund/man/pwcv.Rd
refund/man/vb_cs_wish.Rd
refund/man/gasoline.Rd
refund/man/plot.pfr.Rd
refund/man/fpca.lfda.Rd
refund/man/amc.Rd
refund/man/ff.Rd
refund/man/lf_old.Rd
refund/man/f_trace.Rd
refund/man/pffrSim.Rd
refund/man/rlrt.pfr.Rd
refund/man/DTI2.Rd
refund/man/f_sum2.Rd
refund/man/Xt_siginv_X.Rd
refund/man/cmdscale_lanczos.Rd
refund/man/pco_predict_preprocess.Rd
refund/man/af.Rd
refund/man/fpcr.Rd
refund/man/mfpca.sc.Rd
refund/man/gibbs_mult_wish.Rd
refund/man/peer_old.Rd
refund/man/gibbs_cs_fpca.Rd
refund/man/lf.vd.Rd
refund/man/fpc.Rd
refund/man/pffr.check.Rd
refund/man/smooth.construct.dt.smooth.spec.Rd
refund/man/sff.Rd
refund/man/quadWeights.Rd
refund/man/Predict.matrix.fpc.smooth.Rd
refund/man/cd4.Rd
refund/man/gibbs_cs_wish.Rd
refund/man/vb_cs_fpca.Rd
refund/man/smooth.construct.pss.smooth.spec.Rd
refund/man/pfr_old.Rd
refund/man/f_sum.Rd
refund/man/smooth.construct.pco.smooth.spec.Rd
refund/man/bayes_fosr.Rd
refund/man/pcre.Rd
refund/man/create.prep.func.Rd
refund/man/expand.call.Rd
refund/man/gls_cs.Rd
refund/man/predict.pffr.Rd
refund/man/Predict.matrix.pcre.random.effect.Rd
refund/man/Predict.matrix.pi.smooth.Rd
refund/man/plot.fosr.vs.Rd
refund/man/plot.fosr.Rd
refund/man/plot.fpcr.Rd
refund/man/pffr.Rd
refund/man/ffpcplot.Rd
refund/man/residuals.pffr.Rd
refund/man/coefboot.pffr.Rd
refund/man/lpeer.Rd
refund/man/PEER.Sim.Rd
refund/man/smooth.construct.pcre.smooth.spec.Rd
refund/man/refund-internal.Rd
refund/man/lofocv.Rd
refund/man/peer.Rd
refund/man/fosr.perm.Rd
refund/man/pffrGLS.Rd
refund/man/fpca.sc.Rd
refund/man/smooth.construct.peer.smooth.spec.Rd
refund/man/predict.fbps.Rd
refund/man/vb_mult_wish.Rd
refund/man/pfr.Rd
refund/man/plot.lpeer.Rd
refund/man/fosr2s.Rd
refund/man/Predict.matrix.dt.smooth.Rd
refund/man/predict.pfr.Rd
refund/man/ffpc.Rd
refund/man/af_old.Rd
refund/man/summary.pfr.Rd
refund/man/fpca2s.Rd
refund/man/vis.pfr.Rd
refund/man/qq.pffr.Rd
refund/man/sofa.Rd
refund/man/re.Rd
refund/man/gibbs_mult_fpca.Rd
refund/man/fosr.vs.Rd
refund/man/coefficients.pfr.Rd
refund/man/fgam.Rd
refund/man/refund-package.Rd
refund/man/fosr.Rd
refund/man/predict.fosr.vs.Rd
refund/man/summary.pffr.Rd
refund/man/plot.peer.Rd
refund/man/vis.fgam.Rd
refund/man/print.summary.pffr.Rd
refund/man/f_sum4.Rd
refund/man/plot.pffr.Rd
refund/man/ols_cs.Rd
refund/man/getTF.Rd
refund/man/model.matrix.pffr.Rd
refund/man/lf.Rd
refund/man/coef.pffr.Rd
refund/man/fpca.face.Rd
refund/man/DTI.Rd
refund/man/ccb.fpc.Rd
refund/man/fbps.Rd
refund/man/predict.fgam.Rd
refund/man/Predict.matrix.peer.smooth.Rd
refund/man/fpca.ssvd.Rd
refund/man/smooth.construct.fpc.smooth.spec.Rd
refund/man/pfr_plot.gam.Rd