Elastic Functional Data Analysis MATLAB code
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DP
basis
bayesian
bspline_tools
data
gropt
minFunc
mlogit_warp
util
.gitignore
Basis_Normal_A.m
Contents.m
Find_Best_Rotation.m
Find_Rotation_and_Seed_unique.m
Gram_Schmidt.m
InnerProd_Q.m
L2norm.m
Parallel_Transport_C.m
Path_Plot.m
ProgressBar.m
ProjectC.m
Project_Tangent.m
README.md
ReSampleCurve.m
ShiftF.m
SqrtMean.m
SqrtMeanInverse.m
SqrtMedian.m
Translation_Boxplot.m
align_fPCA.m
ampbox.m
bootstrap_tol.m
calculateCentroid.m
cumsimps.m
cumtrapzmid.m
curve_to_q.m
elastic_distance.m
elastic_logistic.m
elastic_lpcr_regression.m
elastic_mlogistic.m
elastic_mlpcr_regression.m
elastic_pcr_regression.m
elastic_regression.m
exp_map.m
f_to_srvf.m
fdacurve.m
fdahpca.m
fdajpca.m
fdakma.m
fdavpca.m
fdawarp.m
geodesic_sphere_Full.m
inner_product.m
inv_exp_map.m
invertGamma.m
optimum_reparam.m
outlier_detection.m
pairwise_align.m
pairwise_align_bayes.m
pairwise_align_curves.m
phbox.m
progress.m
q_to_curve.m
randomGamma.m
rgam.m
setup.m
setup_paths.m
simps.m
simul_align.m
simul_gam.m
smooth_data.m
srvf_to_f.m
updateParallel.m
varycolor.m
warp_curve_gamma.m
warp_f_gamma.m
warp_q_gamma.m

README.md

MATLAB FileExchange

fdasrvf

MATLAB library for elastic functional data analysis

A MATLAB package for functional data analysis using the square root velocity framework which performs pair-wise and group-wise alignment as well as modeling using functional component analysis

Installation


  1. Download zip or tar.gz of package or clone repository
  2. Run setup.m to setup paths and compile MEX functions NOTE: Armadillo c++ library required for bayesian code.

References

Tucker, J. D. 2014, Functional Component Analysis and Regression using Elastic Methods. Ph.D. Thesis, Florida State University.

Robinson, D. T. 2012, Function Data Analysis and Partial Shape Matching in the Square Root Velocity Framework. Ph.D. Thesis, Florida State University.

Huang, W. 2014, Optimization Algorithms on Riemannian Manifolds with Applications. Ph.D. Thesis, Florida State University.

Srivastava, A., Wu, W., Kurtek, S., Klassen, E. and Marron, J. S. (2011). Registration of Functional Data Using Fisher-Rao Metric. arXiv:1103.3817v2 [math.ST].

Tucker, J. D., Wu, W. and Srivastava, A. (2013). Generative models for functional data using phase and amplitude separation. Computational Statistics and Data Analysis 61, 50-66.

J. D. Tucker, W. Wu, and A. Srivastava, ``Phase-Amplitude Separation of Proteomics Data Using Extended Fisher-Rao Metric," Electronic Journal of Statistics, Vol 8, no. 2. pp 1724-1733, 2014.

J. D. Tucker, W. Wu, and A. Srivastava, "Analysis of signals under compositional noise With applications to SONAR data," IEEE Journal of Oceanic Engineering, Vol 29, no. 2. pp 318-330, Apr 2014.

Srivastava, A., Klassen, E., Joshi, S., Jermyn, I., (2011). Shape analysis of elastic curves in euclidean spaces. Pattern Analysis and Machine Intelligence, IEEE Transactions on 33 (7), 1415-1428.

S. Kurtek, A. Srivastava, and W. Wu. Signal estimation under random time-warpings and nonlinear signal alignment. In Proceedings of Neural Information Processing Systems (NIPS), 2011.

Wen Huang, Kyle A. Gallivan, Anuj Srivastava, Pierre-Antoine Absil. "Riemannian Optimization for Elastic Shape Analysis", Short version, The 21st International Symposium on Mathematical Theory of Networks and Systems (MTNS 2014).

W. Xie, S. Kurtek, K. Bharath, and Y. Sun, A geometric approach to visualization of variability in functional data, Journal of American Statistical Association 112 (2017), pp. 979-993.

Lu, Y., R. Herbei, and S. Kurtek, 2017: Bayesian registration of functions with a Gaussian process prior. Journal of Computational and Graphical Statistics, 26, no. 4, 894–904.

Lee, S. and S. Jung, 2017: Combined analysis of amplitude and phase variations in functional data. arXiv:1603.01775 [stat.ME], 1–21.

J. D. Tucker, J. R. Lewis, and A. Srivastava, “Elastic Functional Principal Component Regression,” Statistical Analysis and Data Mining, 10.1002/sam.11399, 2018.