fda: Functional Data Analysis

These functions were developed to support functional data analysis as described in Ramsay, J. O. and Silverman, B. W. (2005) Functional Data Analysis. New York: Springer. They were ported from earlier versions in Matlab and S-PLUS. An introduction appears in Ramsay, J. O., Hooker, Giles, and Graves, Spencer (2009) Functional Data Analysis with R and Matlab (Springer). The package includes data sets and script files working many examples including all but one of the 76 figures in this latter book. Matlab versions of the code and sample analyses are no longer distributed through CRAN, as they were when the book was published. For those, ftp from http://www.psych.mcgill.ca/misc/fda/downloads/FDAfuns/ There you find a set of .zip files containing the functions and sample analyses, as well as two .txt files giving instructions for installation and some additional information. The changes from Version 2.4.1 are fixes of bugs in density.fd and removal of functions create.polynomial.basis, polynompen, and polynomial. These were deleted because the monomial basis does the same thing and because there were errors in the code.

AuthorJ. O. Ramsay <ramsay@psych.mcgill.ca>, Hadley Wickham <h.wickham@gmail.com>, Spencer Graves <spencer.graves@prodsyse.com>, Giles Hooker <gjh27@cornell.edu>
Date of publication2014-12-16 17:59:38
MaintainerJ. O. Ramsay <ramsay@psych.mcgill.ca>
LicenseGPL (>= 2)
Version2.4.4
http://www.functionaldata.org

View on CRAN

Man pages

AmpPhaseDecomp: Decomposition for Amplitude and Phase Variation

argvalsy.swap: Swap argvals with y if the latter is simpler.

arithmetic.basisfd: Arithmatic on functional basis objects

arithmetic.fd: Arithmetic on functional data ('fd') objects

as.array3: Reshape a vector or array to have 3 dimensions.

as.fd: Convert a spline object to class 'fd'

as.POSIXct1970: as.POXIXct for number of seconds since the start of 1970.

axisIntervals: Mark Intervals on a Plot Axis

basisfd: Define a Functional Basis Object

basisfd.product: Product of two basisfd objects

bifd: Create a bivariate functional data object

bifdPar: Define a Bivariate Functional Parameter Object

bsplinepen: B-Spline Penalty Matrix

bsplineS: B-spline Basis Function Values

CanadianWeather: Canadian average annual weather cycle

cca.fd: Functional Canonical Correlation Analysis

center.fd: Center Functional Data

checkDims3: Compare dimensions and dimnames of arrays

checkLogicalInteger: Does an argument satisfy required conditions?

coef: Extract functional coefficients

cor.fd: Correlation matrix from functional data object(s)

CRAN: Test if running as CRAN

create.basis: Create Basis Set for Functional Data Analysis

create.bspline.basis: Create a B-spline Basis

create.constant.basis: Create a Constant Basis

create.exponential.basis: Create an Exponential Basis

create.fourier.basis: Create a Fourier Basis

create.monomial.basis: Create a Monomial Basis

create.polygonal.basis: Create a Polygonal Basis

create.power.basis: Create a Power Basis Object

CSTR: Continuously Stirred Tank Reactor

cycleplot.fd: Plot Cycles for a Periodic Bivariate Functional Data Object

Data2fd: Create a functional data object from data

dateAccessories: Numeric and character vectors to facilitate working with...

density.fd: Compute a Probability Density Function

deriv.fd: Compute a Derivative of a Functional Data Object

df2lambda: Convert Degrees of Freedom to a Smoothing Parameter Value

df.residual.fRegress: Degress of Freedom for Residuals from a Functional Regression

dirs: Get subdirectories

Eigen: Eigenanalysis preserving dimnames

eval.basis: Values of Basis Functions or their Derivatives

eval.bifd: Values a Two-argument Functional Data Object

evaldiag.bifd: Evaluate the Diagonal of a Bivariate Functional Data Object

eval.fd: Values of a Functional Data Object

eval.monfd: Values of a Monotone Functional Data Object

eval.penalty: Evaluate a Basis Penalty Matrix

eval.posfd: Evaluate a Positive Functional Data Object

expon: Exponential Basis Function Values

exponentiate.fd: Powers of a functional data ('fd') object

exponpen: Exponential Penalty Matrix

fbplot: Functional Boxplots

fd: Define a Functional Data Object

fd2list: Convert a univariate functional data object to s list

fdaMatlabPath: Add 'fdaM' to the Matlab path

fda-package: Functional Data Analysis in R

fdlabels: Extract plot labels and names for replicates and variables

fdPar: Define a Functional Parameter Object

file.copy2: Copy a file with a default 'to' name

fourier: Fourier Basis Function Values

fourierpen: Fourier Penalty Matrix

Fperm.fd: Permutation F-test for functional linear regression.

fRegress: Functional Regression Analysis

fRegress.CV: Computes Cross-validated Error Sum of Integrated Squared...

fRegress.stderr: Compute Standard errors of Coefficient Functions Estimated by...

Fstat.fd: F-statistic for functional linear regression.

gait: Hip and knee angle while walking

geigen: Generalized eigenanalysis

getbasismatrix: Values of Basis Functions or their Derivatives

getbasispenalty: Evaluate a Roughness Penalty Matrix

getbasisrange: Extract the range from a basis object

growth: Berkeley Growth Study data

handwrit: Cursive handwriting samples

infantGrowth: Tibia Length for One Baby

inprod: Inner products of Functional Data Objects.

inprod.Bspline: Compute Inner Products B-spline Expansions.

int2Lfd: Convert Integer to Linear Differential Operator

intensity.fd: Intensity Function for Point Process

is.basis: Confirm Object is Class "Basisfd"

is.fd: Confirm Object has Class "fd"

is.fdPar: Confirm Object has Class "fdPar"

is.fdSmooth: Confirm Object has Class "fdSmooth"

is.Lfd: Confirm Object has Class "Lfd"

knots.fd: Extract the knots from a function basis or data object

lambda2df: Convert Smoothing Parameter to Degrees of Freedom

lambda2gcv: Compute GCV Criterion

landmarkreg: Landmark Registration of Functional Observations

landmark.reg.expData: Experiment data for landmark registration and alignment

Lfd: Define a Linear Differential Operator Object

lines.fd: Add Lines from Functional Data to a Plot

linmod: Fit Fully Functional Linear Model

lip: Lip motion

lmeWinsor: Winsorized Regression with mixed effects

lmWinsor: Winsorized Regression

lmWinsor12: Support functions for lmWinsor

matplot: Plot Columns of Matrices

mean.fd: Mean of Functional Data

melanoma: melanoma 1936-1972

monfn: Evaluates a monotone function

monomial: Evaluate Monomial Basis

monomialpen: Evaluate Monomial Roughness Penalty Matrix

MontrealTemp: Montreal Daily Temperature

nondurables: Nondurable goods index

norder: Order of a B-spline

objAndNames: Add names to an object

odesolv: Numerical Solution mth Order Differential Equation System

onechild: growth in height of one 10-year-old boy

pca.fd: Functional Principal Components Analysis

pda.fd: Principal Differential Analysis

pda.overlay: Stability Analysis for Principle Differential Analysis

phaseplanePlot: Phase-plane plot

pinch: pinch force data

plot.basisfd: Plot a Basis Object

plotbeta: Plot a functional parameter object with confidence limits

plot.fd: Plot a Functional Data Object

plotfit.fd: Plot a Functional Data Object With Data

plot.Lfd: Plot a Linear Differential Operator Object

plot.lmWinsor: lmWinsor plot

plot.pca.fd: Plot Functional Principal Components

plotscores: Plot Principal Component Scores

polyg: Polygonal Basis Function Values

polygpen: Polygonal Penalty Matrix

powerbasis: Power Basis Function Values

powerpen: Power Penalty Matrix

ppBspline: Convert a B-spline function to piece-wise polynomial form

predict.fRegress: Predict method for Functional Regression

predict.lmeWinsor: Predict method for Winsorized linear model fits with mixed...

predict.lmWinsor: Predict method for Winsorized linear model fits

project.basis: Approximate Functional Data Using a Basis

quadset: Quadrature points and weights for Simpson's rule

readHMD: Download data from the Human Mortality Database (HMD)

refinery: Reflux and tray level in a refinery

ReginaPrecip: Regina Daily Precipitation

register.fd: Register Functional Data Objects Using a Continuous Criterion

register.fd0: Correct for initial position error between functional data...

register.newfd: Register Functional Data Objects with Pre-Computed Warping...

resid.fRegress: Residuals from a Functional Regression

sd: Standard Deviation of Functional Data

seabird: Sea Bird Counts

smooth.basis: Construct a functional data object by smoothing data using a...

smooth.basisPar: Smooth Data Using a Directly Specified Roughness Penalty

smooth.bibasis: Smooth a discrete surface over a rectangular lattice

smooth.fd: Smooth a Functional Data Object Using an Indirectly Specified...

smooth.fdPar: Smooth a functional data object using a directly specified...

smooth.monotone: Monotone Smoothing of Data

smooth.morph: Estimates a Smooth Warping Function

smooth.pos: Smooth Data with a Positive Function

StatSciChinese: Statistical Science in Chinese

sum.fd: Sum of Functional Data

summary.basisfd: Summarize a Functional Data Object

summary.bifd: Summarize a Bivariate Functional Data Object

summary.fd: Summarize a Functional Data Object

summary.fdPar: Summarize a Functional Parameter Object

summary.Lfd: Summarize a Linear Differential Operator Object

svd2: singular value decomposition with automatic error handling

symsolve: solve(A, B) where A is symmetric

TaylorSpline: Taylor representation of a B-Spline

tperm.fd: Permutation t-test for two groups of functional data objects.

var.fd: Variance, Covariance, and Correlation Surfaces for Functional...

varmx: Rotate a Matrix of Component Loadings using the VARIMAX...

varmx.cca.fd: Rotation of Functional Canonical Components with VARIMAX

varmx.pca.fd: Rotation of Functional Principal Components with VARIMAX...

vec2Lfd: Make a Linear Differential Operator Object from a Vector

wtcheck: Check a vector of weights

zerofind: Does the range of the input contain 0?

Files in this package

fda
fda/TODO
fda/inst
fda/inst/scripts
fda/inst/scripts/fda-ch07.R
fda/inst/scripts/fdarm-ch01.R
fda/inst/scripts/fda-ch08.R
fda/inst/scripts/afda-ch07.R
fda/inst/scripts/fdarm-ch02.R
fda/inst/scripts/afda-ch02.R
fda/inst/scripts/afda-ch04.R
fda/inst/scripts/fdarm-ch03.R
fda/inst/scripts/afda-ch01.R
fda/inst/scripts/fdarm-ch04.R
fda/inst/scripts/fdarm-ch09.R
fda/inst/scripts/fda-ch01.R
fda/inst/scripts/fdarm-ch06.R
fda/inst/scripts/afda-ch06.R
fda/inst/scripts/fdarm-ch07.R
fda/inst/scripts/fda-ch13.R
fda/inst/scripts/afda-ch03.R
fda/inst/scripts/fdarm-ch11.R
fda/inst/scripts/fda-ch17.R
fda/inst/scripts/fda-ch03.R
fda/inst/scripts/fdarm-ch08.R
fda/inst/scripts/fdarm-ch05.R
fda/inst/scripts/fdarm-ch10.R
fda/inst/scripts/fda-ch02.R
fda/inst/scripts/afda-ch05.R
fda/inst/Matlab
fda/inst/Matlab/README
fda/NAMESPACE
fda/demo
fda/demo/melanoma.R
fda/demo/handwrit.pda.R
fda/demo/create.test.R
fda/demo/weatherstats.R
fda/demo/canadian-weather.R
fda/demo/fdarm.R
fda/demo/handwrit.R
fda/demo/gait.R
fda/demo/weathersetup.R
fda/demo/weatherlm.R
fda/demo/growthsetup.R
fda/demo/growthsmooth.R
fda/demo/weathersmooth.R
fda/demo/weatherPCA.R
fda/demo/00Index
fda/demo/lip.R
fda/demo/growth.R
fda/demo/goodsindex.R
fda/demo/examples.R
fda/demo/weatherANOVA.R
fda/demo/pinch.R
fda/demo/refinery.R
fda/demo/growthreg.R
fda/CHANGELOG
fda/NEWS
fda/data
fda/data/infantGrowth.rda
fda/data/melanoma.rda
fda/data/MontrealTemp.rda
fda/data/onechild.rda
fda/data/dateAccessories.rda
fda/data/growth.rda
fda/data/pinchraw.rda
fda/data/pinch.rda
fda/data/handwrit.rda
fda/data/daily.rda
fda/data/ReginaPrecip.rda
fda/data/landmark.reg.expData.rda
fda/data/gait.rda
fda/data/CanadianWeather.rda
fda/data/seabird.rda
fda/data/nondurables.rda
fda/data/refinery.rda
fda/data/StatSciChinese.rda
fda/data/lip.rda
fda/R
fda/R/Eigen.R fda/R/register.fd0.R fda/R/exponpen.R fda/R/phaseplanePlot.R fda/R/smooth.pos.R fda/R/cor.fd.R fda/R/monomial.R fda/R/smooth.fd.R fda/R/plotfit.fd.R fda/R/landmarkreg.R fda/R/stddev.fd.R fda/R/predict.fRegress.R fda/R/monomialpen.R fda/R/fRegress.R fda/R/is.fdSmooth.R fda/R/std.fd.R fda/R/derivs.R fda/R/smooth.fdPar.R fda/R/fRegress.numeric.R fda/R/eval.bifd.R fda/R/objAndNames.R fda/R/is.diag.R fda/R/varmx.cca.fd.R fda/R/expon.R fda/R/create.constant.basis.R fda/R/readHMD.R fda/R/create.bspline.basis.R fda/R/int2Lfd.R fda/R/fdParcheck.R fda/R/register.fd.R fda/R/is.fd.R fda/R/eval.fd.R fda/R/eval.basis.R fda/R/plotbeta.R fda/R/varmx.R fda/R/fourierpen.R fda/R/getbasisrange.R fda/R/fourier.R fda/R/polintmat.R fda/R/intensity.fd.R fda/R/smooth.basis.R fda/R/is.Lfd.R fda/R/argcheck.R fda/R/CSTRfn.R fda/R/fd2list.R fda/R/density.fd.R fda/R/as.POSIXct1970.R fda/R/create.exponential.basis.R fda/R/powerbasis.R fda/R/deriv.fd.R fda/R/fdPar.R fda/R/linmod.R fda/R/project.basis.R fda/R/smooth.bibasis.R fda/R/matplot.R fda/R/create.fourier.basis.R fda/R/as.fd.R fda/R/fRegress.stderr.R fda/R/center.fd.R fda/R/fRegress.formula.R fda/R/axisIntervals.R fda/R/bifd.R fda/R/mongrad.R
fda/R/pda.overlay.r
fda/R/monhess.R fda/R/checkDims3.R fda/R/isotone.R fda/R/varmx.pca.fd.R fda/R/is.eqbasis.R fda/R/stepchk.R fda/R/pda.fd.R fda/R/AmpPhaseDecomp.R fda/R/eval.penalty.R fda/R/vec2Lfd.R fda/R/as.array3.R fda/R/wtcheck.R fda/R/TaylorSpline.R fda/R/quadset.R fda/R/polygpen.R fda/R/Fperm.fd.R fda/R/CSTR2.R fda/R/polyg.R fda/R/zerobasis.R fda/R/coef.R fda/R/evaldiag.bifd.R fda/R/rangechk.R fda/R/ycheck.R fda/R/plotreg.fd.R fda/R/stepit.R fda/R/ppBspline.R fda/R/plot.basisfd.R fda/R/var.fd.R fda/R/argvalsy.swap.R fda/R/checkLogicalInteger.R fda/R/create.power.basis.R fda/R/smooth.monotone.R fda/R/boxplot.fd.R fda/R/bsplineS.R fda/R/ppderiv.R fda/R/fd.R fda/R/eval.posfd.R fda/R/CSTRres.R fda/R/inprod.R fda/R/inprod.bspline.R fda/R/lines.fd.R fda/R/predict.lmeWinsor.R fda/R/plot.pca.fd.R fda/R/lmeWinsor.R fda/R/CRAN.R fda/R/fdlabels.R fda/R/trapzmat.R fda/R/subscript.R fda/R/lambda2gcv.R fda/R/Fstat.fd.R fda/R/norder.R fda/R/dirs.R fda/R/create.bspline.irregular.R fda/R/svd2.R fda/R/plot.pda.fd.R fda/R/eigen.pda.R fda/R/fbplot.R fda/R/is.integerLfd.R fda/R/CSTRfitLS.R fda/R/cca.fd.R fda/R/create.monomial.basis.R fda/R/getbasispenalty.R fda/R/Lfd.R fda/R/fRegressArgCheck.R fda/R/geigen.R fda/R/polyprod.R fda/R/df.residual.fRegress.R fda/R/lmWinsor.R fda/R/pca.fd.R fda/R/derivchk.R fda/R/bsplinepen.R fda/R/odesolv.R fda/R/cycleplot.fd.R fda/R/smooth.morph.R fda/R/register.newfd.R fda/R/knots.fd.R fda/R/symsolve.R fda/R/lambda2df.R fda/R/create.polygonal.basis.R fda/R/predict.lmWinsor.R fda/R/smooth.basis1.R fda/R/plot.fd.R fda/R/exponentiate.fd.R fda/R/fRegress.fdPar.R fda/R/basisfd.R fda/R/plotscores.R fda/R/file.copy2.R fda/R/getbasismatrix.R fda/R/fRegress.CV.R fda/R/tperm.fd.R fda/R/is.fdPar.R fda/R/monfn.R fda/R/Data2fd.R fda/R/CSTR2in.R fda/R/smooth.basisPar.R fda/R/plot.cca.fd.R fda/R/bifdPar.R fda/R/is.basis.R fda/R/eval.monfd.R fda/R/fdaMatlabPath.R fda/R/df2lambda.R fda/R/powerpen.R fda/R/plot.lmWinsor.R
fda/MD5
fda/DESCRIPTION
fda/man
fda/man/axisIntervals.Rd fda/man/cca.fd.Rd fda/man/resid.fRegress.Rd fda/man/linmod.Rd fda/man/register.fd0.Rd fda/man/norder.Rd fda/man/lines.fd.Rd fda/man/onechild.Rd fda/man/int2Lfd.Rd fda/man/zerofind.Rd fda/man/predict.lmWinsor.Rd fda/man/arithmetic.fd.Rd fda/man/create.exponential.basis.Rd fda/man/eval.basis.Rd fda/man/wtcheck.Rd fda/man/fda-package.Rd fda/man/register.fd.Rd fda/man/handwrit.Rd fda/man/create.polygonal.basis.Rd fda/man/Lfd.Rd fda/man/CRAN.Rd fda/man/create.bspline.basis.Rd fda/man/polyg.Rd fda/man/plotfit.fd.Rd
fda/man/plotreg.fd.rd
fda/man/is.Lfd.Rd fda/man/smooth.fd.Rd
fda/man/is.eqbasis.rd
fda/man/expon.Rd fda/man/StatSciChinese.Rd fda/man/basisfd.Rd fda/man/polygpen.Rd fda/man/argvalsy.swap.Rd fda/man/create.fourier.basis.Rd fda/man/fbplot.Rd fda/man/bifd.Rd fda/man/geigen.Rd fda/man/refinery.Rd fda/man/arithmetic.basisfd.Rd fda/man/lip.Rd fda/man/varmx.Rd fda/man/Data2fd.Rd fda/man/pda.overlay.Rd fda/man/sd.Rd fda/man/summary.basisfd.Rd fda/man/plotscores.Rd fda/man/dirs.Rd fda/man/eval.fd.Rd fda/man/plot.Lfd.Rd fda/man/project.basis.Rd fda/man/cycleplot.fd.Rd fda/man/readHMD.Rd fda/man/evaldiag.bifd.Rd fda/man/eval.monfd.Rd fda/man/landmarkreg.Rd fda/man/fRegress.CV.Rd fda/man/ppBspline.Rd fda/man/smooth.fdPar.Rd fda/man/svd2.Rd fda/man/CanadianWeather.Rd fda/man/center.fd.Rd fda/man/summary.fd.Rd fda/man/odesolv.Rd fda/man/knots.fd.Rd fda/man/TaylorSpline.Rd fda/man/matplot.Rd fda/man/plot.basisfd.Rd fda/man/is.fdSmooth.Rd fda/man/exponpen.Rd fda/man/quadset.Rd
fda/man/eigen.pda.rd
fda/man/smooth.bibasis.Rd fda/man/var.fd.Rd fda/man/create.constant.basis.Rd fda/man/is.fd.Rd fda/man/monomial.Rd fda/man/eval.posfd.Rd fda/man/fdPar.Rd fda/man/pda.fd.Rd fda/man/inprod.Bspline.Rd fda/man/file.copy2.Rd fda/man/bifdPar.Rd fda/man/as.fd.Rd fda/man/fd.Rd fda/man/as.POSIXct1970.Rd fda/man/inprod.Rd fda/man/powerpen.Rd fda/man/create.monomial.basis.Rd fda/man/summary.Lfd.Rd fda/man/intensity.fd.Rd fda/man/varmx.cca.fd.Rd fda/man/summary.bifd.Rd fda/man/checkLogicalInteger.Rd
fda/man/plot.cca.fd.rd
fda/man/landmark.reg.expData.Rd fda/man/fRegress.stderr.Rd fda/man/nondurables.Rd fda/man/smooth.monotone.Rd fda/man/sum.fd.Rd fda/man/monfn.Rd fda/man/eval.penalty.Rd fda/man/fdlabels.Rd fda/man/growth.Rd fda/man/lambda2df.Rd fda/man/lmWinsor12.Rd fda/man/summary.fdPar.Rd fda/man/is.basis.Rd fda/man/pca.fd.Rd fda/man/AmpPhaseDecomp.Rd fda/man/create.basis.Rd fda/man/smooth.basis.Rd fda/man/seabird.Rd fda/man/register.newfd.Rd fda/man/smooth.morph.Rd fda/man/eval.bifd.Rd fda/man/Eigen.Rd fda/man/cor.fd.Rd fda/man/fd2list.Rd fda/man/powerbasis.Rd fda/man/fdaMatlabPath.Rd fda/man/as.array3.Rd fda/man/getbasisrange.Rd fda/man/plot.fd.Rd fda/man/exponentiate.fd.Rd fda/man/fourierpen.Rd fda/man/deriv.fd.Rd fda/man/lmWinsor.Rd fda/man/varmx.pca.fd.Rd fda/man/phaseplanePlot.Rd fda/man/lmeWinsor.Rd fda/man/dateAccessories.Rd fda/man/lambda2gcv.Rd fda/man/smooth.pos.Rd fda/man/CSTR.Rd fda/man/density.fd.Rd fda/man/monomialpen.Rd fda/man/infantGrowth.Rd fda/man/predict.lmeWinsor.Rd fda/man/gait.Rd fda/man/MontrealTemp.Rd fda/man/df.residual.fRegress.Rd fda/man/bsplineS.Rd fda/man/mean.fd.Rd fda/man/plot.pca.fd.Rd fda/man/is.fdPar.Rd fda/man/checkDims3.Rd fda/man/tperm.fd.Rd fda/man/df2lambda.Rd fda/man/objAndNames.Rd fda/man/plot.lmWinsor.Rd fda/man/vec2Lfd.Rd fda/man/plotbeta.Rd
fda/man/plot.pda.fd.rd
fda/man/create.power.basis.Rd fda/man/basisfd.product.Rd fda/man/symsolve.Rd fda/man/bsplinepen.Rd fda/man/Fstat.fd.Rd fda/man/fRegress.Rd fda/man/melanoma.Rd fda/man/Fperm.fd.Rd fda/man/getbasismatrix.Rd fda/man/coef.Rd fda/man/smooth.basisPar.Rd fda/man/getbasispenalty.Rd fda/man/ReginaPrecip.Rd fda/man/fourier.Rd fda/man/predict.fRegress.Rd fda/man/pinch.Rd

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

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