Package: refund 0.1-35

Julia Wrobel

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.

Authors:Jeff Goldsmith [aut], Fabian Scheipl [aut], Lei Huang [aut], Julia Wrobel [aut, cre], Chongzhi Di [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], Erjia Cui [aut], Ruonan Li [ctb], Zheyuan Li [ctb]

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refund/json (API)

# Install 'refund' in R:
install.packages('refund', repos = c('https://refunders.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/refunders/refund/issues

Datasets:
  • COVID19 - The US weekly all-cause mortality and COVID19-associated deaths in 2020
  • DTI - Diffusion Tensor Imaging: tract profiles and outcomes
  • DTI2 - Diffusion Tensor Imaging: more fractional anisotropy profiles and outcomes
  • PEER.Sim - Simulated longitudinal data with functional predictor and scalar response, and structural information associated with predictor function
  • Q - Simulated longitudinal data with functional predictor and scalar response, and structural information associated with predictor function
  • cd4 - Observed CD4 cell counts
  • content - The CONTENT child growth study
  • gasoline - Octane numbers and NIR spectra of gasoline
  • sofa - SOFA (Sequential Organ Failure Assessment) Data

On CRAN:

58 exports 39 stars 4.31 score 59 dependencies 15 dependents 3 mentions 424 scripts 1.9k downloads

Last updated 6 months agofrom:3b13697891. Checks:OK: 1 WARNING: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKSep 11 2024
R-4.5-winWARNINGSep 11 2024
R-4.5-linuxWARNINGSep 11 2024
R-4.4-winWARNINGSep 11 2024
R-4.4-macWARNINGSep 11 2024
R-4.3-winWARNINGSep 11 2024
R-4.3-macWARNINGSep 11 2024

Exports:afaf_oldbayes_fosrccb.fpccmdscale_lanczoscoefboot.pffrfbpsffffpcffpcplotfgamfosrfosr.permfosr.perm.fitfosr.perm.testfosr.vsfosr2sfpcfpca.facefpca.lfdafpca.scfpca.ssvdfpca2sfpcrgibbs_cs_fpcagibbs_cs_wishgibbs_mult_fpcagibbs_mult_wishgls_cslflf_oldlf.vdlpeerlpfrmfpca.facemfpca.scols_cspco_predict_preprocesspcrepeerpeer_oldpffrpffr.checkpffrGLSpffrSimpfrpfr_oldpwcvqq.pffrrerlrt.pfrsffvb_cs_fpcavb_cs_wishvb_mult_fpcavb_mult_wishvis.fgamvis.pfr

Dependencies:abindashbitopsbootcliclustercolorspacedeSolvefansifarverfdafdsFNNgamm4ggplot2gluegrpreggtablehdrcdeisobandkernlabKernSmoothkslabelinglatticelifecyclelme4locfitmagicmagrittrMASSMatrixmclustmgcvminqamulticoolmunsellmvtnormnlmenloptrpbspcaPPpillarpkgconfigpracmaR6rainbowRColorBrewerRcppRcppEigenRCurlrlangRLRsimscalestibbleutf8vctrsviridisLitewithr

Readme and manuals

Help Manual

Help pageTopics
Construct an FGAM regression termaf
Construct an FGAM regression termaf_old
Bayesian Function-on-scalar regressionbayes_fosr
Corrected confidence bands using functional principal componentsccb.fpc
Observed CD4 cell countscd4
Faster multi-dimensional scalingcmdscale_lanczos
Get estimated coefficients from a pffr fitcoef.pffr
Simple bootstrap CIs for pffrcoefboot.pffr
Extract coefficient functions from a fitted pfr-objectcoef.pfr coefficients.pfr
The CONTENT child growth studycontent
The US weekly all-cause mortality and COVID19-associated deaths in 2020COVID19
Construct a function for preprocessing functional predictorscreate.prep.func
Diffusion Tensor Imaging: tract profiles and outcomesDTI
Diffusion Tensor Imaging: more fractional anisotropy profiles and outcomesDTI2
Return call with all possible argumentsexpand.call
Sum computation 1f_sum
Sum computation 2f_sum2
Sum computation 2f_sum4
Trace computationf_trace
Sandwich smoother for matrix datafbps
Construct a function-on-function regression termff
Construct a PC-based function-on-function regression termffpc
Plot PC-based function-on-function regression termsffpcplot
Functional Generalized Additive Modelsfgam
Function-on-scalar regressionfosr
Permutation testing for function-on-scalar regressionfosr.perm fosr.perm.fit fosr.perm.test plot.fosr.perm
Function-on Scalar Regression with variable selectionfosr.vs
Two-step function-on-scalar regressionfosr2s
Construct a FPC regression termfpc
Functional principal component analysis with fast covariance estimationfpca.face
Longitudinal Functional Data Analysis using FPCAfpca.lfda
Functional principal components analysis by smoothed covariancefpca.sc
Smoothed FPCA via iterative penalized rank one SVDs.fpca.ssvd
Functional principal component analysis by a two-stage methodfpca2s
Functional principal component regressionfpcr
Octane numbers and NIR spectra of gasolinegasoline
Cross-sectional FoSR using a Gibbs sampler and FPCAgibbs_cs_fpca
Cross-sectional FoSR using a Gibbs sampler and Wishart priorgibbs_cs_wish
Multilevel FoSR using a Gibbs sampler and FPCAgibbs_mult_fpca
Multilevel FoSR using a Gibbs sampler and Wishart priorgibbs_mult_wish
Cross-sectional FoSR using GLSgls_cs
Construct an FLM regression termlf
Construct an FLM regression termlf_old
Construct a VDFR regression termlf.vd
Longitudinal Functional Models with Structured Penaltieslpeer
Longitudinal penalized functional regressionlpfr
Multilevel functional principal components analysis with fast covariance estimationmfpca.face
Multilevel functional principal components analysis by smoothed covariancemfpca.sc
Obtain model matrix for a pffr fitmodel.matrix.pffr
Cross-sectional FoSR using GLSols_cs
Make predictions using pco basis termspco_predict_preprocess
pffr-constructor for functional principal component-based functional random intercepts.pcre
Construct a PEER regression term in a 'pfr' formulapeer
Functional Models with Structured Penaltiespeer_old
Simulated longitudinal data with functional predictor and scalar response, and structural information associated with predictor functionPEER.Sim Q
Penalized flexible functional regressionpffr
Some diagnostics for a fitted pffr modelpffr.check
Penalized function-on-function regression with non-i.i.d. residualspffrGLS
Simulate example data for pffrpffrSim
Penalized Functional Regressionpfr
Penalized Functional Regression (old version)pfr_old
Default plotting of function-on-scalar regression objectsplot.fosr
Plot for Function-on Scalar Regression with variable selectionplot.fosr.vs
Default plotting for functional principal component regression outputplot.fpcr
Plotting of estimated regression functions obtained through 'lpeer()'plot.lpeer
Plotting of estimated regression functions obtained through 'peer()'plot.peer
Plot a pffr fitplot.pffr
Plot a pfr objectplot.pfr
Prediction for fast bivariate _P_-spline (fbps)predict.fbps
Prediction from a fitted FGAM modelpredict.fgam
Prediction from a fitted bayes_fosr modelpredict.fosr
Prediction for Function-on Scalar Regression with variable selectionpredict.fosr.vs
Predict.matrix method for dt basisPredict.matrix.dt.smooth
mgcv-style constructor for prediction of FPC termsPredict.matrix.fpc.smooth
mgcv-style constructor for prediction of PC-basis functional random effectsPredict.matrix.pcre.random.effect
mgcv-style constructor for prediction of PEER termsPredict.matrix.peer.smooth
Predict.matrix method for pi basisPredict.matrix.pi.smooth
Prediction for penalized function-on-function regressionpredict.pffr
Prediction from a fitted pfr modelpredict.pfr
Print method for summary of a pffr fitprint.summary.pffr
Pointwise cross-validation for function-on-scalar regressionpwcv
QQ plots for pffr model residualsqq.pffr
Compute quadrature weightsquadWeights
Random effects constructor for fgamre
Obtain residuals and fitted values for a pffr modelsfitted.pffr residuals.pffr
Likelihood Ratio Test and Restricted Likelihood Ratio Test for inference of functional predictorsrlrt.pfr
Construct a smooth function-on-function regression termsff
Domain Transformation basis constructorsmooth.construct.dt.smooth.spec
Basis constructor for FPC termssmooth.construct.fpc.smooth.spec
Principal coordinate ridge regressionpco poridge Predict.matrix.pco.smooth smooth.construct.pco.smooth.spec
mgcv-style constructor for PC-basis functional random effectssmooth.construct.pcre.smooth.spec
Basis constructor for PEER termssmooth.construct.peer.smooth.spec
Parametric Interaction basis constructorsmooth.construct.pi.smooth.spec
P-spline constructor with modified 'shrinkage' penaltysmooth.construct.pss.smooth.spec
SOFA (Sequential Organ Failure Assessment) Datasofa
Summary for a pffr fitsummary.pffr
Summary for a pfr fitsummary.pfr
Cross-sectional FoSR using Variational Bayes and FPCAvb_cs_fpca
Cross-sectional FoSR using Variational Bayes and Wishart priorvb_cs_wish
Multilevel FoSR using Variational Bayes and FPCAvb_mult_fpca
Multilevel FoSR using Variational Bayes and Wishart priorvb_mult_wish
Visualization of FGAM objectsvis.fgam
Visualization of PFR objectsvis.pfr
Internal computation functionXt_siginv_X