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".

Install the latest version of this package by entering the following in R:
install.packages("fdapace")
AuthorXiongtao Dai, Pantelis Z. Hadjipantelis, Hao Ji, Hans-Georg Mueller, Jane-Ling Wang
Date of publication2017-01-25 09:02:52
MaintainerPantelis Z. Hadjipantelis <pantelis@ucdavis.edu>
LicenseBSD_3_clause + file LICENSE
Version0.3.0
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.

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

FCCor: Calculate functional correlation between two simultaneously...

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

fitted.FPCAder: Fitted functional sample from FPCAder object

FOptDes: Optimal Designs for Functional and Longitudinal Data for...

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.

Lwls2DDeriv: Two dimensional local linear kernel smoother with...

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

MakeSparseGP: Make Gaussian Process Sparse Functional Data sample

medfly25: Number of eggs laid daily from medflies

plot.FPCA: Functional Principal Component Analysis Diagnostics plot

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

WFDA: Warped Functional DAta Analysis

Wiener: Simulate standard Wiener processes (Brownian motions)

Functions

BwNN Man page
CheckData Man page
CheckOptions Man page
ConvertSupport Man page
CreateBWPlot Man page
CreateCovPlot Man page
CreateDesignPlot Man page
CreateDiagnosticsPlot Man page
CreateFuncBoxPlot Man page
CreateModeOfVarPlot Man page
CreateOutliersPlot Man page
CreatePathPlot Man page
CreateScreePlot Man page
FCCor Man page
FClust Man page
FCReg Man page
fdapace Man page
fdapace-package Man page
fitted.FPCA Man page
fitted.FPCAder Man page
FOptDes Man page
FPCA Man page
FPCAder Man page
FSVD Man page
FVPA Man page
GetCrCorYX Man page
GetCrCorYZ Man page
GetCrCovYX Man page
GetCrCovYZ Man page
GetNormalisedSample Man page
GetNormalizedSample Man page
kCFC Man page
Lwls1D Man page
Lwls2D Man page
Lwls2DDeriv Man page
MakeBWtoZscore02y Man page
MakeFPCAInputs Man page
MakeGPFunctionalData Man page
MakeHCtoZscore02y Man page
MakeLNtoZscore02y Man page
MakeSparseGP Man page
medfly25 Man page
plot.FPCA Man page
print.FPCA Man page
print.FSVD Man page
SelectK Man page
SetOptions Man page
Sparsify Man page
WFDA Man page
Wiener Man page

Files

inst
inst/doc
inst/doc/fdapaceVignetteKnitr.Rnw
inst/doc/fdapaceVignetteKnitr.pdf
inst/doc/fdapaceVignetteKnitr.R
src
src/RCPPvar.cpp
src/interp2lin.cpp
src/Rmullwlsk.cpp
src/CPPlwls1d.cpp
src/RCPPmean.cpp
src/RmullwlskUniversalDeriv.cpp
src/Rcppsort.cpp
src/RmullwlskUniversal.cpp
src/RcppPseudoApprox.cpp
src/trapzRcpp.cpp
src/dropZeroElementsXYWin.cpp
src/cumtrapzRcpp.cpp
src/RmullwlskCC.cpp
src/RrotatedMullwlsk.cpp
src/GetIndCEScoresCPPnewInd.cpp
src/GetIndCEScoresCPP.cpp
src/RmullwlskCCsort2.cpp
src/RcppExports.cpp
NAMESPACE
NEWS
data
data/medfly25.RData
R
R/GetCrCovYX_old.R R/GetRawCov.R R/print.FSVD.R R/CreateFuncBoxPlot.R R/FVPA.R R/FPCAder.R R/SetOptions.R R/MakeGPFunctionalData.R R/IsRegular.R R/GetINScores.R R/FClust.R R/GetNormalisedSample.R R/GetCount.R R/FPCA.R R/GetRho.R R/Lwls1D.R R/FCCor.R R/GetBinnedCurve.R R/WFDA.R R/ConvertSupport.R R/SubsetFPCA.R R/medfly25.R R/Lwls2D.R R/GCVLwls2DV2.R R/CheckAndCreateCOPoptions.R R/GetSmoothedMeanCurve.R R/CheckSVDOptions.R R/MakeSparseGP.R R/RotateLwls2DV2.R R/FitEigenValues.R R/MakeBWtoZscore02y.R R/CVLwls1D.R R/BestDes_SR.R R/CreateScreePlot.R R/GetMinb.R R/CreateDiagnosticsPlot.R R/MCVOptRidge.R R/FSVD.R R/MapX1D.R R/GetMeanDense.R R/Sparsify.R R/SetDerOptions.R R/CreatePathPlot.R R/print.FPCA.R R/Lwls2DDeriv.R R/PC_CovE.R R/GetLogLik.R R/GenerateFunctionalData.R R/GetCovDense.R R/str.FPCA.R R/BwNN.R R/fitted.FPCA.R R/CreateCovPlot.R R/CreateModeOfVarPlot.R R/GetRawCrCovFuncScal.R R/DesignPlotCount.R R/CreateTrueMean.R R/RcppExports.R R/BinData.R R/GetCrCorYX.R R/GetCrCovYX.R R/CreateOutliersPlot.R R/SelectK.R R/Wiener.R R/CreateBWPlot.R R/FCReg.R R/BinRawCov.R R/plot.FPCA.R R/GetBinnedDataset.R R/CreateBasis.R R/TruncateObs.R R/GetSmoothedCovarSurface.R R/MakeHCtoZscore02y.R R/GetCrCovYZ.R R/kCFC.R R/CheckOptions.R R/SetSVDOptions.R R/FOptDes.R R/GetRawCrCovFuncFunc.R R/GetCEScores.R R/Minb.R R/CheckData.R R/GCVLwls1D1.R R/GetUserCov.R R/MakeResultFPCA.R R/GetUserMeanCurve.R R/CreateFolds.R R/HandleNumericsAndNAN.R R/MakeLNtoZscore02y.R R/GetBinNum.R R/List2Mat.R R/MakeFPCAInputs.R R/GetEigenAnalysisResults.R R/pkgname.R R/GetCrCorYZ.R R/BestDes_TR.R R/fitted.FPCAder.R R/CreateDesignPlot.R
vignettes
vignettes/roxygen.bib
vignettes/Sweavel.sty
vignettes/fdapaceVignetteKnitr.Rnw
MD5
build
build/vignette.rds
DESCRIPTION
man
man/print.FSVD.Rd man/FPCA.Rd man/FVPA.Rd man/GetCrCovYZ.Rd man/Wiener.Rd man/fdapace.Rd man/CreateDesignPlot.Rd man/CheckData.Rd man/plot.FPCA.Rd man/Sparsify.Rd man/MakeHCtoZscore02y.Rd man/BwNN.Rd man/GetCrCorYX.Rd man/CreateFuncBoxPlot.Rd man/MakeGPFunctionalData.Rd man/WFDA.Rd man/GetCrCorYZ.Rd man/CreateOutliersPlot.Rd man/CreatePathPlot.Rd man/SelectK.Rd man/CreateScreePlot.Rd man/GetCrCovYX.Rd man/kCFC.Rd man/Lwls1D.Rd man/FSVD.Rd man/FCReg.Rd man/fitted.FPCAder.Rd man/CreateModeOfVarPlot.Rd man/FCCor.Rd man/GetNormalisedSample.Rd man/MakeSparseGP.Rd man/MakeLNtoZscore02y.Rd man/print.FPCA.Rd man/CreateCovPlot.Rd man/Lwls2D.Rd man/medfly25.Rd man/ConvertSupport.Rd man/FClust.Rd man/fitted.FPCA.Rd man/FOptDes.Rd man/MakeBWtoZscore02y.Rd man/Lwls2DDeriv.Rd man/SetOptions.Rd man/FPCAder.Rd man/MakeFPCAInputs.Rd man/CreateBWPlot.Rd man/CheckOptions.Rd
LICENSE

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