Package: fda 6.1.9

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 and 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 are available by ftp from <https://www.psych.mcgill.ca/misc/fda/downloads/FDAfuns/>.

Authors:James Ramsay [aut, cre], Giles Hooker [ctb], Spencer Graves [ctb]

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NEWS

# Install 'fda' in R:

install.packages('fda', repos = c('https://jamesramsay5.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/jamesramsay5/fda/issues

Datasets:

CanadianWeather - Canadian average annual weather cycle
MontrealTemp - Montreal Daily Temperature
ReginaPrecip - Regina Daily Precipitation
daily - Canadian average annual weather cycle
day.5 - Numeric and character vectors to facilitate working with dates
dayOfYear - Numeric and character vectors to facilitate working with dates
dayOfYearShifted - Numeric and character vectors to facilitate working with dates
daysPerMonth - Numeric and character vectors to facilitate working with dates
gait - Hip and knee angle while walking
growth - Berkeley Growth Study data
handwrit - Cursive handwriting samples
handwritTime - Cursive handwriting samples
infantGrowth - Tibia Length for One Baby
lip - Lip motion
lipmarks - Lip motion
liptime - Lip motion
melanoma - Melanoma 1936-1972
monthBegin.5 - Numeric and character vectors to facilitate working with dates
monthEnd - Numeric and character vectors to facilitate working with dates
monthEnd.5 - Numeric and character vectors to facilitate working with dates
monthLetters - Numeric and character vectors to facilitate working with dates
monthMid - Numeric and character vectors to facilitate working with dates
nondurables - Nondurable goods index
pinch - Pinch force data
pinchraw - Pinch force data
pinchtime - Pinch force data
refinery - Reflux and tray level in a refinery
seabird - Sea Bird Counts
weeks - Numeric and character vectors to facilitate working with dates

On CRAN:

170 exports 2 stars 7.46 score 47 dependencies 136 dependents 34 mentions 1.8k scripts 11.2k downloads

Last updated 3 months agofrom:04f5616c6a. Checks:OK: 7. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Sep 11 2024
R-4.5-win	OK	Sep 11 2024
R-4.5-linux	OK	Sep 11 2024
R-4.4-win	OK	Sep 11 2024
R-4.4-mac	OK	Sep 11 2024
R-4.3-win	OK	Sep 11 2024
R-4.3-mac	OK	Sep 11 2024

Exports:[.fd AmpPhaseDecomp as.array3 as.fd as.POSIXct1970 axesIntervals axisIntervals basisfd bifd bifdPar boxplot.fd boxplot.fdPar boxplot.fdSmooth bsplinepen bsplineS cca.fd center.fd checkDim3 checkDims3 checkLogical checkLogicalInteger checkNumeric cor.fd covPACE CRAN create.bspline.basis create.constant.basis create.exponential.basis create.fourier.basis create.monomial.basis create.polygonal.basis create.power.basis CSTR2 CSTR2in CSTRfitLS CSTRfn CSTRres CSTRsse cumfd cycleplot.fd Data2fd density.fd deriv.fd df2lambda dirs Eigen eigen.pda eval.basis eval.bifd eval.fd eval.monfd eval.penalty eval.posfd eval.surp evaldiag.bifd expon exponentiate.fd exponpen fbplot fd fd2list fdlabels fdPar fdParcheck fourier fourierpen Fperm.fd fRegress fRegress.CV fRegress.double fRegress.fd fRegress.formula fRegress.stderr Fstat.fd geigen getbasismatrix getbasispenalty getbasisrange inprod inprod.bspline int2Lfd intensity.fd is.basis is.fd is.fdPar is.fdSmooth is.Lfd lambda2df lambda2gcv landmarkreg Lfd lines.fdSmooth linmod lnsrch matplot matplot.default mean.fd minus.fd monfn mongrad monhess monomial monomialpen norder norder.bspline objAndNames odesolv pca.fd pcaPACE pda.fd pda.overlay phaseplanePlot plot.cca.fd plot.fd plot.pca.fd plotbeta plotfit.fd plotfit.fdSmooth plotscores plus.fd polintmat polyg polygpen powerbasis powerpen ppBspline predict.basisfd predict.fd predict.fdPar predict.fdSmooth predict.fRegress project.basis quadset reconsCurves register.fd register.newfd scoresPACE sd.fd smooth.basis smooth.basis.sparse smooth.basisPar smooth.bibasis smooth.fd smooth.fdPar smooth.monotone smooth.morph smooth.pos smooth.sparse.mean smooth.surp sparse.list sparse.mat std.fd stddev.fd stdev.fd stepchk stepit surp.fit symsolve times.fd tperm.fd trapzmat var.fd varmx varmx.cca.fd varmx.pca.fd vec2Lfd wtcheck ycheck zerobasis zerofind

Dependencies:ash bitops cli cluster colorspace deSolve fansi farver fds FNN ggplot2 glue gtable hdrcde isoband kernlab KernSmooth ks labeling lattice lifecycle locfit magrittr MASS Matrix mclust mgcv multicool munsell mvtnorm nlme pcaPP pillar pkgconfig pracma R6 rainbow RColorBrewer Rcpp RCurl rlang scales tibble utf8 vctrs viridisLite withr

BasisBasics

Rendered fromBasisBasics.Rmdusingknitr::rmarkdownon Sep 11 2024.

Last update: 2023-05-24
Started: 2022-04-19

monotoneFunctions

Jim Ramsay

Rendered frommonotoneFunctions.Rmdusingknitr::rmarkdownon Sep 11 2024.

Last update: 2023-05-24
Started: 2022-04-19

SplineFunctions

Jim Ramsay

Rendered fromsplineFunctions.Rmdusingknitr::rmarkdownon Sep 11 2024.

Last update: 2023-05-24
Started: 2022-04-19

Help page	Topics
Decomposition for Amplitude and Phase Variation	AmpPhaseDecomp
Arithmatic on functional basis objects	==.basisfd arithmetic.basisfd
Arithmetic on functional data ('fd') objects	*.fd +.fd -.fd arithmetic.fd minus.fd plus.fd times.fd
Reshape a vector or array to have 3 dimensions.	as.array3
Convert a spline object to class 'fd'	as.fd as.fd.fdSmooth as.fd.function as.fd.smooth.spline
'as.POXIXct' for number of seconds since the start of 1970.	as.POSIXct1970
Mark Intervals on a Plot Axis	axesIntervals axisIntervals
Product of two basisfd objects	*.basisfd basisfd.product
Create a bivariate functional data object	bifd
Define a Bivariate Functional Parameter Object	bifdPar
B-Spline Penalty Matrix	bsplinepen
B-spline Basis Function Values	bsplineS
Canadian average annual weather cycle	CanadianWeather daily
Functional Canonical Correlation Analysis	cca.fd
Center Functional Data	center.fd
Compare dimensions and dimnames of arrays	checkDim3 checkDims3
Does an argument satisfy required conditions?	checkLogical checkLogicalInteger checkNumeric
Extract functional coefficients	coef.fd coef.fdPar coef.fdSmooth coefficients.fd coefficients.fdPar coefficients.fdSmooth
Correlation matrix from functional data object(s)	cor.fd
Estimate of the covariance surface	covPACE
Test if running as CRAN	CRAN
Create Basis Set for Functional Data Analysis	create.basis
Create a B-spline Basis	create.bspline.basis
Create a Constant Basis	create.constant.basis
Create an Exponential Basis	create.exponential.basis
Create a Fourier Basis	create.fourier.basis
Create a Monomial Basis	create.monomial.basis
Create a Polygonal Basis	create.polygonal.basis
Create a Power Basis Object	create.power.basis
Continuously Stirred Tank Reactor	CSTR CSTR2 CSTR2in CSTRfitLS CSTRfn CSTRres CSTRsse
Compute a Cumulative Distribution Functional Data Object	cumfd
Plot Cycles for a Periodic Bivariate Functional Data Object	cycleplot.fd
Create smooth functions that fit scatterplot data.	Data2fd
Numeric and character vectors to facilitate working with dates	dateAccessories day.5 dayOfYear dayOfYearShifted daysPerMonth monthAccessories monthBegin.5 monthEnd monthEnd.5 monthLetters monthMid weeks
Compute a Probability Density Function	density.fd
Compute a Derivative of a Functional Data Object	deriv.fd
Degrees of Freedom for Residuals from a Functional Regression	df.residual.fRegress
Convert Degrees of Freedom to a Smoothing Parameter Value	df2lambda
Get subdirectories	dirs
Eigenanalysis preserving dimnames	Eigen
Stability Analysis for Principle Differential Analysis	eigen.pda
Predicting electricity demand in Adelaide from temperature	ElectricDemand
Values of Basis Functions or their Derivatives	eval.basis predict.basisfd
Values a Two-argument Functional Data Object	eval.bifd
Values of a Functional Data Object	eval.fd fitted.fdSmooth predict.fd predict.fdPar predict.fdSmooth residuals.fdSmooth
Values of a Monotone Functional Data Object	eval.monfd fitted.monfd predict.monfd residuals.monfd
Evaluate a Basis Penalty Matrix	eval.penalty
Evaluate a Positive Functional Data Object	eval.posfd fitted.posfd predict.posfd residuals.posfd
Values of a Functional Data Object Defining Surprisal Curves.	eval.surp
Evaluate the Diagonal of a Bivariate Functional Data Object	evaldiag.bifd
Exponential Basis Function Values	expon
Powers of a functional data ('fd') object	exponentiate.fd ^.fd
Exponential Penalty Matrix	exponpen
Functional Boxplots	boxplot.fd boxplot.fdPar boxplot.fdSmooth fbplot
Convert a univariate functional data object to a list	fd2list
Functions for statistical analyses of functions	fda
Extract plot labels and names for replicates and variables	fdlabels
Define a Functional Parameter Object	fdPar
Convert 'fd' or 'basisfd' Objects to 'fdPar' Objects	fdParcheck
Fourier Basis Function Values	fourier
Fourier Penalty Matrix	fourierpen
Permutation F-test for functional linear regression.	Fperm.fd
Functional Regression Analysis	fRegress fRegress.character fRegress.double fRegress.fd fRegress.formula
Computes Cross-validated Error Sum of Integrated Squared Errors for a Functional Regression Model	fRegress.CV
Compute Standard errors of Coefficient Functions Estimated by Functional Regression Analysis	fRegress.stderr
F-statistic for functional linear regression.	Fstat.fd
Hip and knee angle while walking	gait
Generalized eigenanalysis	geigen
Values of Basis Functions or their Derivatives	getbasismatrix
Evaluate a Roughness Penalty Matrix	getbasispenalty
Extract the range from a basis object	getbasisrange
Berkeley Growth Study data	growth
Cursive handwriting samples	handwrit handwritTime
Tibia Length for One Baby	infantGrowth
Inner products of Functional Data Objects.	inprod
Compute Inner Products B-spline Expansions.	inprod.bspline
Convert Integer to Linear Differential Operator	int2Lfd
Intensity Function for Point Process	intensity.fd
Confirm Object is Class "Basisfd"	is.basis
Confirm that two objects of class "Basisfd" are identical	is.eqbasis
Confirm Object has Class "fd"	is.fd
Confirm Object has Class "fdPar"	is.fdPar
Confirm Object has Class "fdSmooth"	is.fdSmooth
Confirm Object has Class "Lfd"	is.Lfd
Extract the knots from a function basis or data object	knots.basisfd knots.fd knots.fdSmooth
Convert Smoothing Parameter to Degrees of Freedom	lambda2df
Compute GCV Criterion	lambda2gcv
Landmark Registration of Functional Observations with Differing Ranges	landmarkreg
Define a Linear Differential Operator Object	Lfd
Add Lines from Functional Data to a Plot	lines.fd lines.fdSmooth
Fit Fully Functional Linear Model	linmod
Lip motion	lip lipmarks liptime
Search along a line for a minimum within an optimisation algorithm.	lnsrch
Plot Columns of Matrices	matplot matplot.Date matplot.default matplot.POSIXct
Mean of Functional Data	mean.fd
melanoma 1936-1972	melanoma
Evaluate the a monotone function	monfn
Evaluate the gradient of a monotone function	mongrad
Evaluate the Hessian matrix of a monotone function	monhess
Evaluate Monomial Basis	monomial
Evaluate Monomial Roughness Penalty Matrix	monomialpen
Montreal Daily Temperature	MontrealTemp
Nondurable goods index	nondurables
Order of a B-spline	norder norder.basisfd norder.bspline norder.default norder.fd
Add names to an object	objAndNames
Numerical Solution mth Order Differential Equation System	odesolv
Functional Principal Components Analysis	pca.fd
Estimate the functional principal components	pcaPACE
Principal Differential Analysis	pda.fd
Stability Analysis for Principle Differential Analysis	pda.overlay
Phase-plane plot	phaseplanePlot
pinch force data	pinch pinchraw pinchtime
Plot a Basis Object	plot.basisfd
Plot Functional Canonical Correlation Weight Functions	plot.cca.fd
Plot a Functional Data Object	plot.fd plot.fdPar plot.fdSmooth
Plot a Linear Differential Operator Object	plot.Lfd
Plot Functional Principal Components	plot.pca.fd
Plot Principle Differential Analysis Components	plot.pda.fd
Plot a functional parameter object with confidence limits	plotbeta
Plot a Functional Data Object With Data	plotfit.fd plotfit.fdSmooth
Plot Principal Component Scores	plotscores
Polynomial extrapolation for a converging sequence of one or more values	polintmat
Polygonal Basis Function Values	polyg
Polygonal Penalty Matrix	polygpen
Power Basis Function Values	powerbasis
Power Penalty Matrix	powerpen
Convert a B-spline function to piece-wise polynomial form	ppBspline
Predict method for Functional Regression	predict.fRegress
Approximate Functional Data Using a Basis	project.basis
Quadrature points and weights for Simpson's rule	quadset
Reconstruct data curves using functional principal components	reconsCurves
Reflux and tray level in a refinery	refinery
Regina Daily Precipitation	ReginaPrecip
Register Functional Data Objects Using a Continuous Criterion	register.fd
Register Functional Data Objects with Pre-Computed Warping Functions	register.newfd
Estimates of functional Principal Component scores through PACE	scoresPACE
Standard Deviation of Functional Data	sd.fd std.fd stddev.fd stdev.fd
Sea Bird Counts	seabird
Construct a functional data object by smoothing data using a roughness penalty	smooth.basis smooth.basis1 smooth.basis2 smooth.basis3
Construct a functional data object by smoothing data using a roughness penalty	smooth.basis.sparse
Smooth Data Using a Directly Specified Roughness Penalty	smooth.basisPar
Smooth a discrete surface over a rectangular lattice	smooth.bibasis
Smooth a Functional Data Object Using an Indirectly Specified Roughness Penalty	smooth.fd
Smooth a functional data object using a directly specified roughness penalty	smooth.fdPar
Monotone Smoothing of Data	smooth.monotone
Estimates a Smooth Warping Function Mapping an Interval into Another	smooth.morph
Smooth Data with a Positive Function	smooth.pos
Smooth the mean function of sparse data	smooth.sparse.mean
Fit data with surprisal smoothing.	smooth.surp
Creates a list of sparse data from a matrix	sparse.list
Creates a matrix of sparse data with NAs out of a list	sparse.mat
Check a step size value for being within parameter limits.	stepchk
Compute a new step size for a linear search within an optimization algorithm.	stepit
Sum of Functional Data	sum.fd
Summarize a Functional Data Object	summary.basisfd
Summarize a Bivariate Functional Data Object	summary.bifd
Summarize a Functional Data Object	summary.fd
Summarize a Functional Parameter Object	summary.fdPar
Summarize a Linear Differential Operator Object	summary.Lfd
Evaluate the fit of surprisal curves to binned psychometric data.	surp.fit
solve(A, B) where A is symmetric	symsolve
Permutation t-test for two groups of functional data objects.	tperm.fd
Approximate the functional inner product of two functional data objects using the trapezpoidal rule over a fine mesh of value.	trapzmat
Variance, Covariance, and Correlation Surfaces for Functional Data Object(s)	var.fd
Rotate a Matrix of Component Loadings using the VARIMAX Criterion	varmx
Rotation of Functional Canonical Components with VARIMAX	varmx.cca.fd
Rotation of Functional Principal Components with VARIMAX Criterion	varmx.pca.fd
Make a Linear Differential Operator Object from a Vector	vec2Lfd
Check a vector of weights	wtcheck
Check Data Arrays for Smoothing Functions	ycheck
Orthonormal Matrix with Columns Summing to Zero	zerobasis
Does the range of the input contain 0?	zerofind

Package: fda 6.1.9

fda: Functional Data Analysis

BasisBasics

monotoneFunctions

SplineFunctions

Citation

Development and contributors

Readme and manuals

Help Manual

Usage by other packages (reverse dependencies)