Package: fdasrvf 2.3.4

J. Derek Tucker

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]

fdasrvf_2.3.4.tar.gz
fdasrvf_2.3.4.tar.gz(r-4.5-noble)fdasrvf_2.3.4.tar.gz(r-4.4-noble)
fdasrvf_2.3.4.tgz(r-4.4-emscripten)fdasrvf_2.3.4.tgz(r-4.3-emscripten)
fdasrvf.pdf |fdasrvf.html✨
fdasrvf/json (API)
NEWS

# Install 'fdasrvf' in R:
install.packages('fdasrvf', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

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

openblascppopenmp

4.95 score 6 stars 2 packages 71 scripts 640 downloads 77 exports 83 dependencies

Last updated 24 days agofrom:1c8f3f236e. Checks:OK: 2. Indexed: no.

TargetResultDate
Doc / VignettesOKDec 06 2024
R-4.5-linux-x86_64OKDec 06 2024

Exports:align_fPCAbootTBcalc_shape_distcurve_boxplotcurve_depthcurve_distcurve_geodesiccurve_karcher_covcurve_karcher_meancurve_pair_aligncurve_principal_directionscurve_srvf_aligncurve_to_qcurve2srvfdiscrete2curvediscrete2warpingelastic_amp_change_ffelastic_change_fpcaelastic_ph_change_ffelastic.depthelastic.distanceelastic.lpcr.regressionelastic.mlpcr.regressionelastic.pcr.regressionf_plotf_to_srvffunction_group_warp_bayesgam_to_hgam_to_vgauss_modelget_distance_matrixget_hilbert_sphere_distanceget_identity_warpingget_l2_distanceget_l2_inner_productget_shape_distanceget_warping_distancegradienth_to_gamhorizFPCAinv_exp_mapinvertGammajoint_gauss_modeljointFPCAjointFPCAhkmeans_alignmultiple_align_functionsmultivariate_karcher_meanoptimum.reparamoutlier.detectionpair_align_functionspair_align_functions_bayespair_align_functions_expomappair_align_imagepcaTBplot_curveq_to_curvereparam_curvereparam_imageresamplecurvergamsample_shapesshape_CIsmooth.dataSqrtMeanSqrtMeanInverseSqrtMediansrvf_to_fsrvf2curvetime_warpingto_hilbert_spherev_to_gamvertFPCAwarp_curvewarp_f_gammawarp_q_gammawarp_srvf

Dependencies:askpassbase64encbslibcachemclicodacodetoolscolorspacecpp11crosstalkcurldata.tabledigestdoParalleldotCall64dplyrevaluatefansifarverfastmapfieldsfontawesomeforeachfsgenericsggplot2gluegtablehighrhtmltoolshtmlwidgetshttrisobanditeratorsjquerylibjsonliteknitrlabelinglaterlatticelazyevallifecyclelpSolvemagrittrmapsMASSMatrixmemoisemgcvmimemunsellmvtnormnlmeopensslpillarpkgconfigplotlypromisespurrrR6rappdirsRColorBrewerRcppRcppArmadillorlangrmarkdownsassscalesspamstringistringrsystibbletidyrtidyselecttinytextoleranceutf8vctrsviridisLitewithrxfunyaml

Readme and manuals

Help Manual

Help pageTopics
Group-wise function alignment and PCA Extractionsalign_fPCA
MPEG7 Curve Datasetbeta
Tolerance Bound Calculation using Bootstrap SamplingbootTB
Functional Boxplotboxplot.ampbox boxplot.curvebox boxplot.fdawarp boxplot.phbox
Elastic Shape Distancecalc_shape_dist
Curve Boxplotcurve_boxplot
Calculates elastic depth for a set of curvescurve_depth
Distance Matrix Computationcurve_dist
Form geodesic between two curvescurve_geodesic
Curve Karcher Covariancecurve_karcher_cov
Karcher Mean of Curvescurve_karcher_mean
Pairwise align two curvescurve_pair_align
Curve PCAcurve_principal_directions
Align Curvescurve_srvf_align
Curve to SRVF Spacecurve_to_q
Converts a curve to its SRVF representationcurve2srvf
Converts a curve from matrix to functional data objectdiscrete2curve
Converts a warping function from vector to functional data objectdiscrete2warping
Elastic Amplitude Changepoint Detectionelastic_amp_change_ff
Elastic Changepoint Detectionelastic_change_fpca
Elastic Phase Changepoint Detectionelastic_ph_change_ff
Calculates elastic depthelastic.depth
Calculates two elastic distanceelastic.distance
Elastic Logistic Regressionelastic.logistic
Elastic logistic Principal Component Regressionelastic.lpcr.regression
Elastic Multinomial Logistic Regressionelastic.mlogistic
Elastic Multinomial logistic Principal Component Regressionelastic.mlpcr.regression
Elastic Linear Principal Component Regressionelastic.pcr.regression
Elastic Prediction from Regression Modelselastic.prediction
Elastic Linear Regressionelastic.regression
Plot functional dataf_plot
Transformation to SRVF Spacef_to_srvf
Elastic Functional Data Analysisfdasrvf-package fdasrvf
Bayesian Group Warpingfunction_group_warp_bayes
Bayesian Karcher Mean Calculationfunction_mean_bayes
map warping function to tangent space at identitygam_to_h
map warping function to tangent space at identitygam_to_v
Gaussian model of functional datagauss_model
Computes the distance matrix between a set of shapes.get_distance_matrix
Computes the geodesic distance between two SRVFs on the Hilbert sphereget_hilbert_sphere_distance
Computes the identity warping functionget_identity_warping
Computes the L^2 distance between two SRVFsget_l2_distance
Computes the L^2 inner product between two SRVFsget_l2_inner_product
Computes the distance between two shapesget_shape_distance
Computes the distance between two warping functionsget_warping_distance
Gradient using finite differencesgradient
Berkeley Growth Velocity Datasetgrowth_vel
map shooting vector to warping function at identityh_to_gam
Horizontal Functional Principal Component AnalysishorizFPCA
Example Image Data setim
map square root of warping function to tangent spaceinv_exp_map
Invert Warping FunctioninvertGamma
Gaussian model of functional data using joint Modeljoint_gauss_model
Joint Vertical and Horizontal Functional Principal Component AnalysisjointFPCA
Joint Vertical and Horizontal Functional Principal Component AnalysisjointFPCAh
K-Means Clustering and Alignmentkmeans_align
Long Run Covariance Matrix Estimation for Multivariate Time SeriesLongRunCovMatrix
Group-wise function alignment to specified meanmultiple_align_functions
Karcher Mean of Multivariate Functional Datamultivariate_karcher_mean
Align two functionsoptimum.reparam
Outlier Detectionoutlier.detection
Align two functionspair_align_functions
Align two functionspair_align_functions_bayes
Align two functions using geometric properties of warping functionspair_align_functions_expomap
Pairwise align two images This function aligns to images using the q-map frameworkpair_align_image
Tolerance Bound Calculation using Elastic Functional PCApcaTB
Plot Curveplot_curve
Elastic Prediction for functional PCApredict.hfpca
Elastic Prediction for functional PCApredict.jfpca
Elastic Prediction for functional PCApredict.jfpcah
Elastic Prediction for functional logistic PCR Modelpredict.lpcr
Elastic Prediction for functional multinomial logistic PCR Modelpredict.mlpcr
Elastic Prediction for functional PCR Modelpredict.pcr
Elastic Prediction for functional PCApredict.vfpca
Convert to curve spaceq_to_curve
Align two curvesreparam_curve
Find optimum reparameterization between two imagesreparam_image
Resample Curveresamplecurve
Random Warpingrgam
Sample shapes from modelsample_shapes
Shape Confidence Interval Calculation using Bootstrap Samplingshape_CI
Simulated two Gaussian Datasetsimu_data
Aligned Simulated two Gaussian Datasetsimu_warp
Aligned Simulated two Gaussian Dataset using Mediansimu_warp_median
Smooth Functionssmooth.data
SRVF transform of warping functionsSqrtMean
SRVF transform of warping functionsSqrtMeanInverse
SRVF transform of warping functionsSqrtMedian
Transformation from SRSF Spacesrvf_to_f
Converts from SRVF to curve representationsrvf2curve
Alignment of univariate functional datatime_warping
Projects an SRVF onto the Hilbert sphereto_hilbert_sphere
Distributed Gaussian Peak Datasettoy_data
Aligned Distributed Gaussian Peak Datasettoy_warp
map shooting vector to warping function at identityv_to_gam
Vertical Functional Principal Component AnalysisvertFPCA
Applies a warping function to a given curvewarp_curve
Warp Functionwarp_f_gamma
Warp SRSFwarp_q_gamma
Applies a warping function to a given SRVFwarp_srvf