fdapace: Functional Data Analysis and Empirical Dynamics

Provides implementation of various methods of Functional Data Analysis (FDA) and Empirical Dynamics. The core of this package is Functional Principal Component Analysis (FPCA), a key technique for functional data analysis, for sparsely or densely sampled random trajectories and time courses, via the Principal Analysis by Conditional Estimation (PACE) algorithm or numerical integration. PACE is useful for the analysis of data that have been generated by a sample of underlying (but usually not fully observed) random trajectories. It does not rely on pre-smoothing of trajectories, which is problematic if functional data are sparsely sampled. PACE provides options for functional regression and correlation, for Longitudinal Data Analysis, the analysis of stochastic processes from samples of realized trajectories, and for the analysis of underlying dynamics. The core computational algorithms are implemented using the 'Eigen' C++ library for numerical linear algebra and 'RcppEigen' "glue".

AuthorXiongtao Dai, Pantelis Z. Hadjipantelis, Hao Ji, Hans-Georg Mueller, Jane-Ling Wang
Date of publication2016-07-15 10:19:26
MaintainerPantelis Z. Hadjipantelis <pantelis@ucdavis.edu>
LicenseBSD_3_clause + file LICENSE
Version0.2.5
https://github.com/functionaldata/tPACE

View on CRAN

Man pages

BwNN: Minimum bandwidth based on kNN criterion.

CheckData: Check data format

CheckOptions: Check option format

ConvertSupport: Convert support of a mu/phi/cov etc. to and from obsGrid and...

CreateBWPlot: Functional Principal Component Analysis Bandwidth Diagnostics...

CreateCovPlot: Create the covariance surface plot based on the results from...

CreateDesignPlot: Create the design plot of the functional data.

CreateDiagnosticsPlot: Functional Principal Component Analysis Diagnostics plot

CreateFuncBoxPlot: Create functional boxplot using 'bagplot', 'KDE' or...

CreateModeOfVarPlot: Functional Principal Component Analysis mode of variation...

CreateOutliersPlot: Functional Principal Component or Functional Singular Value...

CreatePathPlot: Create the fitted sample path plot based on the results from...

CreateScreePlot: Create the scree plot for the fitted eigenvalues

FClust: Functional clustering and identifying substructures of...

FCReg: Functional Concurrent Regression by 2D smoothing method.

fdapace: PACE: Principal Analysis by Conditional Expectation

fitted.FPCA: Fitted functional sample from FPCA object

FPCA: Functional Principal Component Analysis

FPCAder: Take derivative of an FPCA object

FSVD: Functional Singular Value Decomposition

FVPA: Functional Variance Process Analysis for dense functional...

GetCrCorYX: Make cross-correlation matrix from auto- and cross-covariance...

GetCrCorYZ: Make cross-correlation matrix from auto- and cross-covariance...

GetCrCovYX: Functional Cross Covariance between longitudinal variable Y...

GetCrCovYZ: Functional Cross Covariance between longitudinal variable Y...

GetNormalisedSample: Normalise sparse functional sample

kCFC: Functional clustering and identifying substructures of...

Lwls1D: One dimensional local linear kernel smoother

Lwls2D: Two dimensional local linear kernel smoother.

Lwls2Dv1: Two dimensional local linear kernel smoother.

MakeBWtoZscore02y: Z-score body-weight for age 0 to 24 months based on WHO...

MakeFPCAInputs: Format FPCA input

MakeGPFunctionalData: Make Gaussian Process Dense Functional Data sample

MakeHCtoZscore02y: Z-score head-circumference for age 0 to 24 months based on...

MakeLNtoZscore02y: Z-score height for age 0 to 24 months based on WHO standards

medfly25: Number of eggs laid daily from medflies

oldFCReg: Functional Principal Component Analysis Concurrent Regression...

print.FPCA: Print an FPCA object

print.FSVD: Print an FSVD object

SelectK: Selects number of functional principal components for given...

SetOptions: Set the PCA option list

Sparsify: Sparsify densely observed functional data

Wiener: Simulate standard Wiener processes (Brownian motions)

Files in this package

fdapace
fdapace/inst
fdapace/inst/doc
fdapace/inst/doc/fdapaceVignetteKnitr.Rnw
fdapace/inst/doc/fdapaceVignetteKnitr.pdf
fdapace/inst/doc/fdapaceVignetteKnitr.R
fdapace/src
fdapace/src/RCPPvar.cpp
fdapace/src/interp2lin.cpp
fdapace/src/Rmullwlsk.cpp
fdapace/src/CPPlwls1d.cpp
fdapace/src/RCPPmean.cpp
fdapace/src/RmullwlskUniversal.cpp
fdapace/src/trapzRcpp.cpp
fdapace/src/dropZeroElementsXYWin.cpp
fdapace/src/cumtrapzRcpp.cpp
fdapace/src/RmullwlskCC.cpp
fdapace/src/RrotatedMullwlsk.cpp
fdapace/src/GetIndCEScoresCPPnewInd.cpp
fdapace/src/GetIndCEScoresCPP.cpp
fdapace/src/RmullwlskCCsort2.cpp
fdapace/src/RcppExports.cpp
fdapace/NAMESPACE
fdapace/NEWS
fdapace/data
fdapace/data/medfly25.RData
fdapace/R
fdapace/R/GetCrCovYX_old.R fdapace/R/GetRawCov.R fdapace/R/print.FSVD.R fdapace/R/SetDerOption.R fdapace/R/CreateFuncBoxPlot.R fdapace/R/FVPA.R fdapace/R/FPCAder.R fdapace/R/SetOptions.R fdapace/R/MakeGPFunctionalData.R fdapace/R/IsRegular.R fdapace/R/GetINScores.R fdapace/R/FClust.R fdapace/R/GetNormalisedSample.R fdapace/R/GetCount.R fdapace/R/FPCA.R fdapace/R/GetRho.R fdapace/R/Lwls1D.R fdapace/R/GetBinnedCurve.R fdapace/R/ConvertSupport.R fdapace/R/SubsetFPCA.R fdapace/R/medfly25.R fdapace/R/Lwls2D.R fdapace/R/GCVLwls2DV2.R fdapace/R/CheckAndCreateCOPoptions.R fdapace/R/GetSmoothedMeanCurve.R fdapace/R/CheckSVDOptions.R fdapace/R/Lwls2Dv1.R fdapace/R/RotateLwls2DV2.R fdapace/R/FitEigenValues.R fdapace/R/MakeBWtoZscore02y.R fdapace/R/CVLwls1D.R fdapace/R/CreateScreePlot.R fdapace/R/GetMinb.R fdapace/R/CreateDiagnosticsPlot.R fdapace/R/FSVD.R fdapace/R/MapX1D.R fdapace/R/GetMeanDense.R fdapace/R/Sparsify.R fdapace/R/CreatePathPlot.R fdapace/R/print.FPCA.R fdapace/R/PC_CovE.R fdapace/R/GetLogLik.R fdapace/R/GenerateFunctionalData.R fdapace/R/GetCovDense.R fdapace/R/BwNN.R fdapace/R/fitted.FPCA.R fdapace/R/CreateCovPlot.R fdapace/R/CreateModeOfVarPlot.R fdapace/R/GetRawCrCovFuncScal.R fdapace/R/DesignPlotCount.R fdapace/R/CreateTrueMean.R fdapace/R/RcppExports.R fdapace/R/BinData.R fdapace/R/GetCrCorYX.R fdapace/R/GetCrCovYX.R fdapace/R/CreateOutliersPlot.R fdapace/R/SelectK.R fdapace/R/Wiener.R fdapace/R/CreateBWPlot.R fdapace/R/FCReg.R fdapace/R/BinRawCov.R fdapace/R/plot.FPCA.R fdapace/R/GetBinnedDataset.R fdapace/R/CreateBasis.R fdapace/R/TruncateObs.R fdapace/R/GetSmoothedCovarSurface.R fdapace/R/MakeHCtoZscore02y.R fdapace/R/GetCrCovYZ.R fdapace/R/kCFC.R fdapace/R/CheckOptions.R fdapace/R/SetSVDOptions.R fdapace/R/GetRawCrCovFuncFunc.R fdapace/R/GetCEScores.R fdapace/R/Minb.R fdapace/R/CheckData.R fdapace/R/GCVLwls1D1.R fdapace/R/GetUserCov.R fdapace/R/MakeResultFPCA.R fdapace/R/GetUserMeanCurve.R fdapace/R/CreateFolds.R fdapace/R/HandleNumericsAndNAN.R fdapace/R/MakeLNtoZscore02y.R fdapace/R/GetBinNum.R fdapace/R/List2Mat.R fdapace/R/MakeFPCAInputs.R fdapace/R/GetEigenAnalysisResults.R fdapace/R/pkgname.R fdapace/R/oldFCReg.R fdapace/R/GetCrCorYZ.R fdapace/R/CreateDesignPlot.R
fdapace/vignettes
fdapace/vignettes/roxygen.bib
fdapace/vignettes/Sweavel.sty
fdapace/vignettes/fdapaceVignetteKnitr.Rnw
fdapace/MD5
fdapace/build
fdapace/build/vignette.rds
fdapace/DESCRIPTION
fdapace/man
fdapace/man/print.FSVD.Rd fdapace/man/FPCA.Rd fdapace/man/FVPA.Rd fdapace/man/GetCrCovYZ.Rd fdapace/man/Wiener.Rd fdapace/man/fdapace.Rd fdapace/man/CreateDesignPlot.Rd fdapace/man/CheckData.Rd fdapace/man/Lwls2Dv1.Rd fdapace/man/Sparsify.Rd fdapace/man/MakeHCtoZscore02y.Rd fdapace/man/BwNN.Rd fdapace/man/CreateDiagnosticsPlot.Rd fdapace/man/GetCrCorYX.Rd fdapace/man/CreateFuncBoxPlot.Rd fdapace/man/MakeGPFunctionalData.Rd fdapace/man/GetCrCorYZ.Rd fdapace/man/oldFCReg.Rd fdapace/man/CreateOutliersPlot.Rd fdapace/man/CreatePathPlot.Rd fdapace/man/SelectK.Rd fdapace/man/CreateScreePlot.Rd fdapace/man/GetCrCovYX.Rd fdapace/man/kCFC.Rd fdapace/man/Lwls1D.Rd fdapace/man/FSVD.Rd fdapace/man/FCReg.Rd fdapace/man/CreateModeOfVarPlot.Rd fdapace/man/GetNormalisedSample.Rd fdapace/man/MakeLNtoZscore02y.Rd fdapace/man/print.FPCA.Rd fdapace/man/CreateCovPlot.Rd fdapace/man/Lwls2D.Rd fdapace/man/medfly25.Rd fdapace/man/ConvertSupport.Rd fdapace/man/FClust.Rd fdapace/man/fitted.FPCA.Rd fdapace/man/MakeBWtoZscore02y.Rd fdapace/man/SetOptions.Rd fdapace/man/FPCAder.Rd fdapace/man/MakeFPCAInputs.Rd fdapace/man/CreateBWPlot.Rd fdapace/man/CheckOptions.Rd
fdapace/LICENSE

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