refund: Regression with Functional Data
Version 0.1-16

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.

Browse man pages Browse package API and functions Browse package files

AuthorJeff 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 publication2016-08-03 10:09:56
MaintainerLei Huang <huangracer@gmail.com>
LicenseGPL (>= 2)
Version0.1-16
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("refund")

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

Functions

DTI Man page
DTI2 Man page
Omegas Man page Source code
PEER.Sim Man page
Predict.matrix.dt.smooth Man page Source code
Predict.matrix.fpc.smooth Man page Source code
Predict.matrix.pco.smooth Man page Source code
Predict.matrix.pcre.random.effect Man page Source code
Predict.matrix.peer.smooth Man page Source code
Predict.matrix.pi.smooth Man page Source code
Predict.matrix.pss.smooth Man page Source code
Q Man page
QTFunc Source code
Xt_siginv_X Man page Source code
af Man page Source code
af_old Man page Source code
amc Man page Source code
bayes_fosr Man page Source code
ccb.fpc Man page Source code
cd4 Man page
checkError Man page
cmdscale_lanczos Man page Source code
coef.pffr Man page Source code
coef.pfr Man page
coefboot.pffr Man page Source code
coefficients.pfr Man page Source code
create.prep.func Man page Source code
decorrelate Man page
expand.call Man page Source code
f_sum Man page Source code
f_sum2 Man page Source code
f_sum4 Man page Source code
f_trace Man page Source code
fbps Man page Source code
ff Man page Source code
ffpc Man page Source code
ffpcplot Man page Source code
fgam Man page Source code
first.last_test Man page
fitted.pffr Man page Source code
fosr Man page Source code
fosr.perm Man page Source code
fosr.perm.fit Man page Source code
fosr.perm.test Man page Source code
fosr.vs Man page Source code
fosr2s Man page Source code
fpc Man page Source code
fpca.face Man page Source code
fpca.lfda Man page Source code
fpca.sc Man page Source code
fpca.ssvd Man page Source code
fpca2s Man page Source code
fpcr Man page Source code
fpcr.setup Man page Source code
gasoline Man page
getL Source code
getNPC.DonohoGavish Man page Source code
getRsq Man page
getShrtlbls Man page Source code
getSpandDist Man page
getTF Man page Source code
gibbs_cs_fpca Man page Source code
gibbs_cs_wish Man page Source code
gibbs_mult_fpca Man page Source code
gibbs_mult_wish Man page Source code
gls_cs Man page Source code
imwd_test Man page
irreg2mat Man page Source code
lf Man page Source code
lf.vd Man page Source code
lf_old Man page Source code
list2df Man page Source code
lofocv Man page Source code
lpeer Man page Source code
lpfr Man page Source code
lw.test Man page Source code
mfpca.sc Man page Source code
model.matrix.pffr Man page Source code
modify_nm Source code Source code
ndefault Source code
ols_cs Man page Source code
osplinepen2d Man page Source code
parse.predict.pfr Man page Source code
pco Man page
pco_predict_preprocess Man page Source code
pcre Man page Source code
peer Man page Source code
peer_old Man page Source code
pffr Man page Source code
pffr.check Man page Source code
pffrGLS Man page Source code
pffrSim Man page Source code
pfr Man page Source code
pfr_old Man page Source code
pfr_plot.gam Man page Source code
plot.fosr Man page Source code
plot.fosr.perm Man page Source code
plot.fosr.vs Man page Source code
plot.fpcr Man page Source code
plot.lpeer Man page Source code
plot.mgcv.smooth Man page Source code
plot.peer Man page Source code
plot.pffr Man page Source code
plot.pfr Man page Source code
plot.random.effect Man page
poridge Man page
postprocess.pfr Man page Source code
predict.fbps Man page Source code
predict.fgam Man page Source code
predict.fosr.vs Man page Source code
predict.pffr Man page Source code
predict.pfr Man page Source code
predict.pfr_old Source code
preprocess.pfr Man page Source code
print.summary.pffr Man page Source code
pspline.setting Man page Source code
pwcv Man page Source code
qq.pffr Man page Source code
quadWeights Man page Source code
re Man page Source code
refund Man page
refund-package Man page
residuals.pffr Man page Source code
rlrt.pfr Man page Source code
safeDeparse Man page Source code
select_knots Source code
sff Man page Source code
smooth.construct.dt.smooth.spec Man page Source code
smooth.construct.fame.smooth.spec Source code
smooth.construct.fpc.smooth.spec Man page Source code
smooth.construct.pco.smooth.spec Man page Source code
smooth.construct.pcre.smooth.spec Man page Source code
smooth.construct.peer.smooth.spec Man page Source code
smooth.construct.pi.smooth.spec Man page Source code
smooth.construct.ps_c.smooth.spec Source code
smooth.construct.pss.smooth.spec Man page Source code
sofa Man page
summary.pffr Man page Source code
summary.pfr Man page Source code
trace_lv Source code
vb_cs_fpca Man page Source code
vb_cs_wish Man page Source code
vb_mult_fpca Man page Source code
vb_mult_wish Man page Source code
vis.fgam Man page Source code
vis.pfr Man page Source code

Files

NAMESPACE
data
data/cd4.RData
data/gasoline.RData
data/PEER.Sim.RData
data/DTI2.RData
data/datalist
data/Q.RData
data/DTI.RData
data/sofa.RData
R
R/fbps.R
R/VB_Mult_Wish.R
R/create.prep.func.R
R/fpcr.R
R/pfr_old.R
R/pffr-utilities.R
R/vis.fgam.R
R/CD4-data.R
R/predict.pfr.R
R/af.R
R/predict.pfr_old.R
R/VB_Mult_FPCA.R
R/rlrt.pfr.R
R/Gibbs_CS_FPCA.R
R/f_trace.R
R/fpcr.setup.R
R/dt_basis.R
R/f_sum.R
R/plot.lpeer.R
R/VB_CS_FPCA.R
R/OLS_CS.R
R/amc.R
R/f_sum4.R
R/pi_basis.R
R/osplinepen2d.R
R/Gibbs_Mult_FPCA.R
R/af_old.R
R/irreg2mat.R
R/DTI2-data.R
R/bayes_fosr.R
R/plot.fosr.vs.R
R/fosr.perm.test.R
R/Omegas.R
R/predict.fosr.vs.R
R/pffr-ffpc.R
R/summary.pfr.R
R/pffr.R
R/lpeer.R
R/peer_old.R
R/pffr-methods.R
R/fpca2s.R
R/plot.fpcr.R
R/fosr.perm.R
R/fpca.ssvd.R
R/fosr.vs.R
R/lf_old.R
R/lofocv.R
R/pffr-pcre.R
R/mfpca.sc.R
R/XtSiginvX.R
R/parse.predict.pfr.R
R/coefficients.pfr.R
R/ccb.fpc.R
R/fosr.R
R/pfr.R
R/pspline.setting.R
R/plot.fosr.perm.R
R/predict.fgam.R
R/GLS_CS.R
R/fpc.R
R/fosr.perm.fit.R
R/lf.R
R/VB_CS_Wish.R
R/postprocess.pfr.R
R/select_knots.R
R/lw.test.R
R/plot.pfr.R
R/PEER.Sim-data.R
R/peer.R
R/pffr-sff.R
R/pffr-ff.R
R/pwcv.R
R/poridge.R
R/Gibbs_Mult_Wish.R
R/pffr-robust.R
R/lf.vd.R
R/quadWeights.R
R/predict.fbps.R
R/Gibbs_CS_Wish.R
R/fosr2s.R
R/plot.fosr.R
R/re.R
R/fpca.lfda.R
R/f_sum2.R
R/fgam.R
R/preprocess.pfr.R
R/gasoline-data.R
R/DTI-data.R
R/lpfr.R
R/vis.pfr.R
R/plot.peer.R
R/fpca.face.R
R/fpca.sc.R
MD5
DESCRIPTION
man
man/smooth.construct.pi.smooth.spec.Rd
man/lpfr.Rd
man/vb_mult_fpca.Rd
man/pwcv.Rd
man/vb_cs_wish.Rd
man/gasoline.Rd
man/plot.pfr.Rd
man/fpca.lfda.Rd
man/amc.Rd
man/ff.Rd
man/lf_old.Rd
man/f_trace.Rd
man/pffrSim.Rd
man/rlrt.pfr.Rd
man/DTI2.Rd
man/f_sum2.Rd
man/Xt_siginv_X.Rd
man/cmdscale_lanczos.Rd
man/pco_predict_preprocess.Rd
man/af.Rd
man/fpcr.Rd
man/mfpca.sc.Rd
man/gibbs_mult_wish.Rd
man/peer_old.Rd
man/gibbs_cs_fpca.Rd
man/lf.vd.Rd
man/fpc.Rd
man/pffr.check.Rd
man/smooth.construct.dt.smooth.spec.Rd
man/sff.Rd
man/quadWeights.Rd
man/Predict.matrix.fpc.smooth.Rd
man/cd4.Rd
man/gibbs_cs_wish.Rd
man/vb_cs_fpca.Rd
man/smooth.construct.pss.smooth.spec.Rd
man/pfr_old.Rd
man/f_sum.Rd
man/smooth.construct.pco.smooth.spec.Rd
man/bayes_fosr.Rd
man/pcre.Rd
man/create.prep.func.Rd
man/expand.call.Rd
man/gls_cs.Rd
man/predict.pffr.Rd
man/Predict.matrix.pcre.random.effect.Rd
man/Predict.matrix.pi.smooth.Rd
man/plot.fosr.vs.Rd
man/plot.fosr.Rd
man/plot.fpcr.Rd
man/pffr.Rd
man/ffpcplot.Rd
man/residuals.pffr.Rd
man/coefboot.pffr.Rd
man/lpeer.Rd
man/PEER.Sim.Rd
man/smooth.construct.pcre.smooth.spec.Rd
man/refund-internal.Rd
man/lofocv.Rd
man/peer.Rd
man/fosr.perm.Rd
man/pffrGLS.Rd
man/fpca.sc.Rd
man/smooth.construct.peer.smooth.spec.Rd
man/predict.fbps.Rd
man/vb_mult_wish.Rd
man/pfr.Rd
man/plot.lpeer.Rd
man/fosr2s.Rd
man/Predict.matrix.dt.smooth.Rd
man/predict.pfr.Rd
man/ffpc.Rd
man/af_old.Rd
man/summary.pfr.Rd
man/fpca2s.Rd
man/vis.pfr.Rd
man/qq.pffr.Rd
man/sofa.Rd
man/re.Rd
man/gibbs_mult_fpca.Rd
man/fosr.vs.Rd
man/coefficients.pfr.Rd
man/fgam.Rd
man/refund-package.Rd
man/fosr.Rd
man/predict.fosr.vs.Rd
man/summary.pffr.Rd
man/plot.peer.Rd
man/vis.fgam.Rd
man/print.summary.pffr.Rd
man/f_sum4.Rd
man/plot.pffr.Rd
man/ols_cs.Rd
man/getTF.Rd
man/model.matrix.pffr.Rd
man/lf.Rd
man/coef.pffr.Rd
man/fpca.face.Rd
man/DTI.Rd
man/ccb.fpc.Rd
man/fbps.Rd
man/predict.fgam.Rd
man/Predict.matrix.peer.smooth.Rd
man/fpca.ssvd.Rd
man/smooth.construct.fpc.smooth.spec.Rd
man/pfr_plot.gam.Rd
refund documentation built on May 19, 2017, 11:05 p.m.