fdapace: Functional Data Analysis and Empirical Dynamics

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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".

Author
Xiongtao Dai, Pantelis Z. Hadjipantelis, Hao Ji, Hans-Georg Mueller, Jane-Ling Wang
Date of publication
2016-07-15 10:19:26
Maintainer
Pantelis Z. Hadjipantelis <pantelis@ucdavis.edu>
License
BSD_3_clause + file LICENSE
Version
0.2.5
URLs

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