fda: Functional Data Analysis

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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.

Author
J. 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 publication
2016-02-17 23:31:54
Maintainer
J. O. Ramsay <ramsay@psych.mcgill.ca>
License
GPL (>= 2)
Version
2.4.5
URLs

View on R-Forge

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