├── .gitattributes ├── .gitignore ├── README ├── release2.17 ├── CHANGES.txt ├── Help │ ├── FPCAevalHELP.txt │ ├── FPCApredHELP.txt │ ├── FPCQuadRegHELP.txt │ ├── FPCderPredHELP.txt │ ├── FPCdiagHELP.txt │ ├── FPCfamHELP.txt │ ├── FPCfglmHELP.txt │ ├── FPCpredHELP.txt │ ├── FPCquantileHELP.txt │ ├── FPCregHELP.txt │ ├── FPCscore.pdf │ ├── FQRhelp.txt │ ├── FvolaHELP.txt │ ├── GFLMhelp.txt │ ├── KModeVariationPlot.txt │ ├── ManiHELP.txt │ ├── README │ ├── StickHELP.txt │ ├── StringingHELP.txt │ ├── WFPCAHELP.txt │ ├── createScreePlot.txt │ ├── createSpaghettiPlot.txt │ ├── dynCorrHELP.txt │ ├── fsvdHELP.txt │ ├── fvpHELP.txt │ ├── nonlindynHELP.txt │ ├── pc2.pdf │ ├── pcaHELP.txt │ ├── pcderHELP.txt │ ├── repfHELP.txt │ └── spadisHELP.txt ├── LICENSE.txt ├── PACE │ ├── CheckData.m │ ├── FPCA.m │ ├── FPCA_ku.m │ ├── FPCAeval.m │ ├── FPCApred.m │ ├── KModeVariationPlot.m │ ├── PACE-DER │ │ ├── ._FPCder.m │ │ ├── ._FPCderEval.m │ │ ├── ._FPCderPred.m │ │ ├── ._PCder.m │ │ ├── ._cv_mullwlsnDer.m │ │ ├── ._gcv_mullwlsnDer.m │ │ ├── ._genEigenFun_1.m │ │ ├── ._genMeanFun_1.m │ │ ├── ._getDynamic.m │ │ ├── ._mullwlskDer.m │ │ ├── ._pc_covEder.m │ │ ├── ._pc_covNEder.m │ │ ├── ._setDerOptions.m │ │ ├── ._showDerOptionNames.m │ │ ├── FPCder.m │ │ ├── FPCderEval.m │ │ ├── FPCderPred.m │ │ ├── PCder.m │ │ ├── cv_mullwlsnDer.m │ │ ├── gcv_mullwlsnDer.m │ │ ├── genEigenFun_1.m │ │ ├── genMeanFun_1.m │ │ ├── getDynamic.m │ │ ├── mullwlskDer.m │ │ ├── pc_covEder.m │ │ ├── pc_covNEder.m │ │ ├── setDerOptions.m │ │ └── showDerOptionNames.m │ ├── PACE-DYN │ │ ├── ._transferX.m │ │ ├── transferX.m │ │ └── transferXY.m │ ├── PACE-DiffEq │ │ └── DiffEq.m │ ├── PACE-FAM │ │ ├── ._FPCfam.m │ │ ├── ._cv_common.m │ │ ├── FPCfam.m │ │ └── cv_common.m │ ├── PACE-FARE │ │ ├── fdev.m │ │ ├── fpcinfer.m │ │ ├── fpcinfer1.m │ │ ├── fpcsdaic.m │ │ ├── functmp.m │ │ ├── geteigen.m │ │ ├── getfhat.m │ │ ├── hist1D.m │ │ ├── hist2D.m │ │ ├── hist2fx.m │ │ └── hist2fx2D.m │ ├── PACE-FQR │ │ ├── ._FQR.m │ │ ├── ._iterGLM.m │ │ ├── FQR.m │ │ └── iterGLM.m │ ├── PACE-FVP │ │ ├── ._FVP.m │ │ └── FVP.m │ ├── PACE-Fvola │ │ └── Fvola.m │ ├── PACE-GFLM │ │ ├── ._betaupd.m │ │ ├── ._devGFLM.m │ │ ├── ._gcv1d.m │ │ ├── ._gupd.m │ │ ├── ._iniadj.m │ │ ├── ._iterGFLM.m │ │ ├── ._kernels.m │ │ ├── ._linkfun.m │ │ ├── ._locpoly.m │ │ ├── ._minbwd.m │ │ ├── ._predGFLM.m │ │ ├── ._sigma2upd.m │ │ ├── ._varfun.m │ │ ├── betaupd.m │ │ ├── devGFLM.m │ │ ├── gcv1d.m │ │ ├── gupd.m │ │ ├── iniadj.m │ │ ├── iterGFLM.m │ │ ├── kernels.m │ │ ├── linkfun.m │ │ ├── locpoly.m │ │ ├── minbwd.m │ │ ├── predGFLM.m │ │ ├── sigma2upd.m │ │ └── varfun.m │ ├── PACE-GRM │ │ ├── ._FPCgrm.m │ │ ├── ._QL_param.m │ │ ├── ._glink.m │ │ ├── ._glink_der.m │ │ ├── ._glink_inv.m │ │ ├── ._grm_cov_NP.m │ │ ├── ._grm_mu_NP.m │ │ ├── ._grm_predict.m │ │ ├── ._grm_predict_lopo.m │ │ ├── ._muSimu.m │ │ ├── ._noeig_param.m │ │ ├── ._overdisp.m │ │ ├── ._varf.m │ │ ├── FPCgrm.m │ │ ├── QL_param.m │ │ ├── glink.m │ │ ├── glink_der.m │ │ ├── glink_inv.m │ │ ├── grm_cov_NP.m │ │ ├── grm_mu_NP.m │ │ ├── grm_predict.m │ │ ├── grm_predict_lopo.m │ │ ├── muSimu.m │ │ ├── noeig_param.m │ │ ├── overdisp.m │ │ └── varf.m │ ├── PACE-Mani │ │ ├── ._IsomapII.m │ │ ├── ._L2_distance.m │ │ ├── ._bwCV.m │ │ ├── ._dfun.m │ │ ├── ._dijk.m │ │ ├── ._dijkstra.m │ │ ├── ._h10cv.m │ │ ├── ._hde10cv.m │ │ ├── ._hknn10cv.m │ │ ├── ._kernelval.m │ │ ├── ._lwlsCV.m │ │ ├── ._lwlval.m │ │ ├── ._maniKS.m │ │ ├── ._maniMDS.m │ │ ├── ._maniMethods.m │ │ ├── ._maniModes.m │ │ ├── ._par10cv.m │ │ ├── ._pceig.m │ │ ├── ._predX.m │ │ ├── ._spadis.m │ │ ├── IsomapII.m │ │ ├── L2_distance.m │ │ ├── bwCV.m │ │ ├── dfun.m │ │ ├── dijk.m │ │ ├── dijkstra.m │ │ ├── h10cv.m │ │ ├── hde10cv.m │ │ ├── hknn10cv.m │ │ ├── kernelval.m │ │ ├── lwlsCV.m │ │ ├── lwlval.m │ │ ├── maniKS.m │ │ ├── maniMDS.m │ │ ├── maniMethods.m │ │ ├── maniModes.m │ │ ├── par10cv.m │ │ ├── pceig.m │ │ ├── predX.m │ │ └── spadis.m │ ├── PACE-QuadReg │ │ ├── ._FPCQuadReg.m │ │ ├── ._pre1.m │ │ ├── ._predQ.m │ │ ├── ._qdmscores1.m │ │ ├── FPCQuadReg.m │ │ ├── pre1.m │ │ ├── predQ.m │ │ └── qdmscores1.m │ ├── PACE-Quantile │ │ ├── ._FPCquantile.m │ │ └── FPCquantile.m │ ├── PACE-REG │ │ ├── ._FPCdiag.m │ │ ├── ._FPCpred.m │ │ ├── ._FPCreg.m │ │ ├── ._Rtest.m │ │ ├── ._ask.m │ │ ├── ._checkY.m │ │ ├── ._getB.m │ │ ├── ._getBeta.m │ │ ├── ._getCB.m │ │ ├── ._getDiag.m │ │ ├── ._getNumK.m │ │ ├── ._getQ.m │ │ ├── ._getR2.m │ │ ├── ._getRawCCOV.m │ │ ├── ._getXW.m │ │ ├── ._pre.m │ │ ├── ._predict.m │ │ ├── FPCdiag.m │ │ ├── FPCpred.m │ │ ├── FPCreg.m │ │ ├── Rtest.m │ │ ├── ask.m │ │ ├── checkY.m │ │ ├── getB.m │ │ ├── getBeta.m │ │ ├── getCB.m │ │ ├── getDiag.m │ │ ├── getNumK.m │ │ ├── getQ.m │ │ ├── getR2.m │ │ ├── getRawCCOV.m │ │ ├── getXW.m │ │ ├── pre.m │ │ └── predict.m │ ├── PACE-SVD │ │ ├── ._FSVD.m │ │ ├── ._FSVDdiag.m │ │ ├── ._SVDreg.m │ │ ├── ._cv_srho.m │ │ ├── ._gcv2_mullwlsn.m │ │ ├── ._getB.m │ │ ├── ._getBW.m │ │ ├── ._getSC.m │ │ ├── ._getSC1.m │ │ ├── ._getSOriCurves.backup.m │ │ ├── ._getSOriCurves.m │ │ ├── ._getSScores.m │ │ ├── ._getSScores1.m │ │ ├── ._getSScores2.m │ │ ├── ._mullwlsk_2.m │ │ ├── FSVD.m │ │ ├── FSVDdiag.m │ │ ├── SVDreg.m │ │ ├── cv_srho.m │ │ ├── gcv2_mullwlsn.m │ │ ├── getB.m │ │ ├── getBW.m │ │ ├── getSC.m │ │ ├── getSC1.m │ │ ├── getSOriCurves.backup.m │ │ ├── getSOriCurves.m │ │ ├── getSScores.m │ │ ├── getSScores1.m │ │ ├── getSScores2.m │ │ └── mullwlsk_2.m │ ├── PACE-Stringing │ │ ├── ._Stringing.m │ │ ├── ._SubForString.m │ │ ├── Stringing.m │ │ └── SubForString.m │ ├── PACE-WARP │ │ ├── ._WFPCA.m │ │ ├── ._rtYH.m │ │ ├── ._rthik.m │ │ ├── ._rthik_E.cpp │ │ ├── WFPCA.m │ │ ├── rtYH.m │ │ ├── rthik.m │ │ └── rthik_E.cpp │ ├── PACE-dynCorr │ │ ├── dynCorr.m │ │ └── dynCorr1.m │ ├── PACE-kcfc │ │ ├── allsse.m │ │ ├── cmp2p.m │ │ ├── datap.m │ │ ├── iter_kCFC.m │ │ ├── kCFC.m │ │ └── kcfc │ │ │ ├── CheckData.m │ │ │ ├── FPCA.m │ │ │ ├── FPCAeval.m │ │ │ ├── FPCApred.m │ │ │ ├── FPCAw.m │ │ │ ├── KModeVariationPlot.m │ │ │ ├── PCA.m │ │ │ ├── PCAw.m │ │ │ ├── adjustBW1.m │ │ │ ├── adjustBW2.m │ │ │ ├── binData.m │ │ │ ├── binning.m │ │ │ ├── checkPhiSign.m │ │ │ ├── convertMuPhi.m │ │ │ ├── createCorrPlot.m │ │ │ ├── createDesignPlot.m │ │ │ ├── createSP.m │ │ │ ├── createScreePlot.m │ │ │ ├── createSpaghettiPlot.m │ │ │ ├── cv_mullwlsn.m │ │ │ ├── cv_mullwlsn_120823.m │ │ │ ├── cv_rho.m │ │ │ ├── cvfda_lwls.m │ │ │ ├── designPlotCount.m │ │ │ ├── gaussquad.m │ │ │ ├── gcv_lwls.m │ │ │ ├── gcv_mullwlsn.m │ │ │ ├── gcv_mullwlsn_20120823.m │ │ │ ├── getDist.m │ │ │ ├── getEigens.m │ │ │ ├── getLogLik1.m │ │ │ ├── getLogLik2.m │ │ │ ├── getMinb.m │ │ │ ├── getOriCurves.m │ │ │ ├── getRawCov.m │ │ │ ├── getScores.m │ │ │ ├── getScores1.m │ │ │ ├── getScores2.m │ │ │ ├── getVal.m │ │ │ ├── lgwt.m │ │ │ ├── lwls.m │ │ │ ├── mapX1d.m │ │ │ ├── mapX2d.m │ │ │ ├── minb.m │ │ │ ├── mu_true.m │ │ │ ├── mullwlsk.m │ │ │ ├── mykernel.m │ │ │ ├── mysample.m │ │ │ ├── names.m │ │ │ ├── no_AIC.m │ │ │ ├── no_BIC.m │ │ │ ├── no_FVE.m │ │ │ ├── pc_covE.m │ │ │ ├── pc_covE_120823.m │ │ │ ├── pc_covNE.m │ │ │ ├── pc_est.m │ │ │ ├── permut.m │ │ │ ├── pred_int.m │ │ │ ├── romb.m │ │ │ ├── romb2.m │ │ │ ├── rotate_mlwls.m │ │ │ ├── roundoff.m │ │ │ ├── setOptions.m │ │ │ ├── setVal.m │ │ │ ├── setopts.m │ │ │ ├── showOptionNames.m │ │ │ ├── spadis.m │ │ │ ├── trapz2.m │ │ │ ├── xeig.m │ │ │ ├── xeig3.m │ │ │ └── xeig4.m │ ├── PACE-nonlindyn │ │ ├── ._nonlindyn.m │ │ └── nonlindyn.m │ ├── PACE-repf │ │ ├── FPCAstep1.m │ │ ├── GetEstimate.m │ │ ├── GetMesh.m │ │ ├── GetRepfCov.m │ │ ├── GetXT.m │ │ ├── getRaw2dMean.m │ │ ├── getRawRepfCov.m │ │ ├── mean2d.m │ │ ├── mullwlsk_M.m │ │ └── repfFPCA.m │ ├── PACE-stick │ │ └── stick.m │ ├── PCA.m │ ├── adjustBW1.m │ ├── adjustBW2.m │ ├── binData.m │ ├── binning.m │ ├── checkPhiSign.m │ ├── convertMuPhi.m │ ├── createCorrPlot.m │ ├── createDesignPlot.m │ ├── createSP.m │ ├── createScreePlot.m │ ├── createSpaghettiPlot.m │ ├── cv_mullwlsn.m │ ├── cv_rho.m │ ├── cvfda_lwls.m │ ├── designPlotCount.m │ ├── fit_ev.m │ ├── gaussquad.m │ ├── gcv_lwls.m │ ├── gcv_mullwlsn.m │ ├── getDist.m │ ├── getEigens.m │ ├── getLogLik1.m │ ├── getLogLik2.m │ ├── getMinb.m │ ├── getOriCurves.m │ ├── getRawCov.m │ ├── getScores.m │ ├── getScores1.m │ ├── getScores2.m │ ├── getVal.m │ ├── isregular.m │ ├── lgwt.m │ ├── lwls.m │ ├── mapX1d.m │ ├── mapX2d.m │ ├── minb.m │ ├── mu_true.m │ ├── mullwlsk.m │ ├── mykernel.m │ ├── mysample.m │ ├── names.m │ ├── no_AIC.m │ ├── no_BIC.m │ ├── no_FVE.m │ ├── pc_covE.m │ ├── pc_covNE.m │ ├── pc_est.m │ ├── permut.m │ ├── pred_int.m │ ├── romb.m │ ├── romb2.m │ ├── rotate_mlwls.m │ ├── roundoff.m │ ├── setOptions.m │ ├── setVal.m │ ├── showOptionNames.m │ ├── spadis.m │ ├── trapz2.m │ ├── xeig.m │ ├── xeig3.m │ └── xeig4.m ├── bugs.txt └── examples │ ├── DataforM2.txt │ ├── example.m │ ├── exampleDer.m │ ├── exampleFPCquantile.m │ ├── exampleFVP.m │ ├── exampleFam.m │ ├── exampleIndex.txt │ ├── exampleQuadReg.m │ ├── exampleReg_0.m │ ├── exampleReg_2.m │ ├── exampleReg_scal.m │ ├── exampleStringing.m │ ├── example_DiffEq.m │ ├── example_FQR.m │ ├── example_GFLM.m │ ├── example_Mani.m │ ├── example_SVD.m │ ├── example_WFPCA.m │ ├── example_grm.m │ ├── example_kcfc_growth.m │ ├── example_nonlindyn.m │ ├── example_repf.m │ ├── example_stick.m │ └── growth.dat └── test ├── eigenvalue_fit ├── FPCA.m ├── Hao │ ├── ev_trunc_mild_std.txt │ ├── ev_trunc_mild_true_mean.txt │ ├── ev_trunc_valley_std.txt │ ├── ev_trunc_valley_true_mean.txt │ ├── meanfn with valley.jpg │ ├── mild meanfn.jpg │ ├── read.m │ └── summary.txt ├── PCA.m ├── main.m ├── makeBasis.m ├── matlab.mat ├── myEigenvalues.m ├── n_100_M_1000.mat ├── n_2000_M_100.mat ├── n_500_M_100.mat ├── n_50_M_1000_mu0.mat ├── n_50_M_4000.mat ├── notes.txt ├── outp.m ├── relDiff.m ├── results.xlsx ├── results1.xlsx ├── sim_obs.m ├── thinObs.m └── tmp.xls ├── ev_fit.m ├── makeBasis.m ├── 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