Package: fdasrvf 2.4.3

fdasrvf: Elastic Functional Data Analysis

Performs alignment, PCA, and modeling of multidimensional and unidimensional functions using the square-root velocity framework (Srivastava et al., 2011 <doi:10.48550/arXiv.1103.3817> and Tucker et al., 2014 <doi:10.1016/j.csda.2012.12.001>). This framework allows for elastic analysis of functional data through phase and amplitude separation.

Authors:J. Derek Tucker [aut, cre], Aymeric Stamm [ctb]

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fdasrvf.pdf |fdasrvf.html✨
fdasrvf/json (API)
NEWS

# Install 'fdasrvf' in R:

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

Bug tracker:https://github.com/jdtuck/fdasrvf_r/issues

Uses libs:

openblas– Optimized BLAS
c++– GNU Standard C++ Library v3
openmp– GCC OpenMP (GOMP) support library

Datasets:

beta - MPEG7 Curve Dataset
growth_vel - Berkeley Growth Velocity Dataset
im - Example Image Data set
simu_data - Simulated two Gaussian Dataset
simu_warp - Aligned Simulated two Gaussian Dataset
simu_warp_median - Aligned Simulated two Gaussian Dataset using Median
toy_data - Distributed Gaussian Peak Dataset
toy_warp - Aligned Distributed Gaussian Peak Dataset

On CRAN:

openblas cpp openmp

8.02 score 14 stars 4 packages 100 scripts 1.2k downloads 84 exports 81 dependencies

Last updated from:435fe7af07. Checks:13 OK. Indexed: yes.

Target	Result	Time
linux-devel-arm64	OK	234
linux-devel-x86_64	OK	234
source / vignettes	OK	246
linux-release-arm64	OK	215
linux-release-x86_64	OK	236
macos-release-arm64	OK	223
macos-release-x86_64	OK	472
macos-oldrel-arm64	OK	274
macos-oldrel-x86_64	OK	539
windows-devel	OK	252
windows-release	OK	272
windows-oldrel	OK	247
wasm-release	OK	164

Exports:align_fPCA bootTB calc_shape_dist curve_boxplot curve_depth curve_dist curve_geodesic curve_pair_align curve_to_q curve2srvf discrete2curve discrete2warping elastic_amp_change_ff elastic_change_fpca elastic_ph_change_ff elastic.depth elastic.distance elastic.lpcr.regression elastic.mlpcr.regression elastic.pcr.regression f_plot f_to_srvf function_group_warp_bayes gam_to_h gam_to_psi gam_to_v gauss_model get_curve_centroid get_distance_matrix get_hilbert_sphere_distance get_identity_warping get_l2_distance get_l2_inner_product get_l2_norm get_shape_distance get_warping_distance gradient h_to_gam horizFPCA horizFPNS inv_exp_map invertGamma joint_gauss_model jointFPCA jointFPCAh kmeans_align multiple_align_functions multiple_align_multivariate multivariate_karcher_cov multivariate_karcher_mean multivariate_pca optimum.reparam outlier.detection pair_align_functions pair_align_functions_bayes pair_align_functions_expomap pair_align_image pcaTB plot_curve ppd psi_to_gam q_to_curve reparam_curve reparam_image resamplecurve rgam rotation_pca sample_shapes shape_CI smooth.data SqrtMean SqrtMeanInverse SqrtMedian srvf_to_f srvf2curve time_warping to_hilbert_sphere v_to_curve v_to_gam vertFPCA warp_curve warp_f_gamma warp_q_gamma warp_srvf

Dependencies:askpass base64enc bslib cachem cli coda codetools cpp11 crosstalk curl data.table digest doParallel dotCall64 dplyr evaluate farver fastmap fields fontawesome foreach fs generics ggplot2 glue gtable highr htmltools htmlwidgets httr isoband iterators jquerylib jsonlite knitr labeling later lattice lazyeval lifecycle lpSolve magrittr maps MASS Matrix memoise mime minpack.lm mvtnorm openssl otel pillar pkgconfig plotly promises purrr R6 rappdirs RColorBrewer Rcpp RcppArmadillo rlang rmarkdown S7 sass scales spam stringi stringr sys tibble tidyr tidyselect tinytex tolerance utf8 vctrs viridisLite withr xfun yaml

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Group-wise function alignment and PCA Extractions	align_fPCA
MPEG7 Curve Dataset	beta
Tolerance Bound Calculation using Bootstrap Sampling	bootTB
Functional Boxplot	boxplot.ampbox boxplot.curvebox boxplot.fdawarp boxplot.phbox
Elastic Shape Distance	calc_shape_dist
Curve Boxplot	curve_boxplot
Calculates elastic depth for a set of curves	curve_depth
Distance Matrix Computation	curve_dist
Form geodesic between two curves	curve_geodesic
Pairwise align two curves	curve_pair_align
Curve to SRVF Space	curve_to_q
Converts a curve to its SRVF representation	curve2srvf
Converts a curve from matrix to functional data object	discrete2curve
Converts a warping function from vector to functional data object	discrete2warping
Elastic Amplitude Changepoint Detection	elastic_amp_change_ff
Elastic Changepoint Detection	elastic_change_fpca
Elastic Phase Changepoint Detection	elastic_ph_change_ff
Calculates elastic depth	elastic.depth
Calculates two elastic distance	elastic.distance
Elastic Logistic Regression	elastic.logistic
Elastic logistic Principal Component Regression	elastic.lpcr.regression
Elastic Multinomial Logistic Regression	elastic.mlogistic
Elastic Multinomial logistic Principal Component Regression	elastic.mlpcr.regression
Elastic Linear Principal Component Regression	elastic.pcr.regression
Elastic Prediction from Regression Models	elastic.prediction
Elastic Linear Regression	elastic.regression
Plot functional data	f_plot
Transformation to SRVF Space	f_to_srvf
Elastic Functional Data Analysis	fdasrvf-package fdasrvf
Bayesian Group Warping	function_group_warp_bayes
Bayesian Karcher Mean Calculation	function_mean_bayes
map warping function to tangent space at identity	gam_to_h
map warping function to Hilbert Sphere	gam_to_psi
map warping function to tangent space at identity	gam_to_v
Gaussian model of functional data	gauss_model
Computes the centroid of a curve	get_curve_centroid
Computes the distance matrix between a set of shapes.	get_distance_matrix
Computes the geodesic distance between two SRVFs on the Hilbert sphere	get_hilbert_sphere_distance
Computes the identity warping function	get_identity_warping
Computes the L^2 distance between two SRVFs	get_l2_distance
Computes the L^2 inner product between two SRVFs	get_l2_inner_product
Computes the L^2 norm of an SRVF	get_l2_norm
Computes the distance between two shapes	get_shape_distance
Computes the distance between two warping functions	get_warping_distance
Gradient using finite differences	gradient
Berkeley Growth Velocity Dataset	growth_vel
map shooting vector to warping function at identity	h_to_gam
Horizontal Functional Principal Component Analysis	horizFPCA
Horizontal Functional Principal Component Analysis	horizFPNS
Example Image Data set	im
map square root of warping function to tangent space	inv_exp_map
Invert Warping Function	invertGamma
Gaussian model of functional data using joint Model	joint_gauss_model
Joint Vertical and Horizontal Functional Principal Component Analysis	jointFPCA
Joint Vertical and Horizontal Functional Principal Component Analysis	jointFPCAh
K-Means Clustering and Alignment	kmeans_align
Long Run Covariance Matrix Estimation for Multivariate Time Series	LongRunCovMatrix
Group-wise function alignment to specified mean	multiple_align_functions
Group-wise multivariate function alignment to specified mean	multiple_align_multivariate
Curve Karcher Covariance	multivariate_karcher_cov
Karcher Mean of Multivariate Functional Data	multivariate_karcher_mean
Curve PCA	multivariate_pca
Align two functions	optimum.reparam
Outlier Detection	outlier.detection
Align two functions	pair_align_functions
Align two functions	pair_align_functions_bayes
Align two functions using geometric properties of warping functions	pair_align_functions_expomap
Pairwise align two images This function aligns to images using the q-map framework	pair_align_image
Tolerance Bound Calculation using Elastic Functional PCA	pcaTB
Plot Curve	plot_curve
Compute Peak Persistence Diagram	ppd
Elastic Prediction for curve PCA	predict.curve_pca
Elastic Prediction for functional PCA	predict.hfpca
Elastic Prediction for functional PCA	predict.jfpca
Elastic Prediction for functional PCA	predict.jfpcah
Elastic Prediction for functional logistic PCR Model	predict.lpcr
Elastic Prediction for functional multinomial logistic PCR Model	predict.mlpcr
Elastic Prediction for functional PCR Model	predict.pcr
Elastic Prediction for functional PCA	predict.vfpca
map Hilbert sphere to warping function	psi_to_gam
Convert to curve space	q_to_curve
Align two curves	reparam_curve
Find optimum reparameterization between two images	reparam_image
Resample Curve	resamplecurve
Random Warping	rgam
Rotation Principal Component Analysis	rotation_pca
Sample shapes from model	sample_shapes
Shape Confidence Interval Calculation using Bootstrap Sampling	shape_CI
Simulated two Gaussian Dataset	simu_data
Aligned Simulated two Gaussian Dataset	simu_warp
Aligned Simulated two Gaussian Dataset using Median	simu_warp_median
Smooth Functions	smooth.data
SRVF transform of warping functions	SqrtMean
SRVF transform of warping functions	SqrtMeanInverse
SRVF transform of warping functions	SqrtMedian
Transformation from SRSF Space	srvf_to_f
Converts from SRVF to curve representation	srvf2curve
Alignment of univariate functional data	time_warping
Projects an SRVF onto the Hilbert sphere	to_hilbert_sphere
Distributed Gaussian Peak Dataset	toy_data
Aligned Distributed Gaussian Peak Dataset	toy_warp
map shooting vector to curve at mean	v_to_curve
map shooting vector to warping function at identity	v_to_gam
Vertical Functional Principal Component Analysis	vertFPCA
Applies a warping function to a given curve	warp_curve
Warp Function	warp_f_gamma
Warp SRSF	warp_q_gamma
Applies a warping function to a given SRVF	warp_srvf