Statistical Tools for Topological Data Analysis

Tools for the statistical analysis of persistent homology and for density clustering. For that, this package provides an R interface for the efficient algorithms of the C++ libraries 'GUDHI' < http://gudhi.gforge.inria.fr/>, 'Dionysus' < http://www.mrzv.org/software/dionysus/>, and 'PHAT' < https://bitbucket.org/phat-code/phat/>. This package also implements the methods in Fasy et al. (2014) and Chazal et al. (2014) for analyzing the statistical significance of persistent homology features.


Travis BuildStatus

News

TDA: version 1.6.5

  • fixed bugs
  • update corresponding to update from R package BH 1.69
  • update to CGAL 4.13
  • added plots to examples of ripsFiltration and alphaComplexFiltration

TDA: version 1.6.4

  • remove Remotes field from Description

TDA: version 1.6.3

  • fixed bugs in alphaComplexDiag
  • added David Millman as an author
  • added tests

TDA: version 1.6.2

  • fixed bugs
  • updated Description with references and hyperlinks

TDA: version 1.6.1

  • fixed bugs
  • fixed bug in alphaShapeDiag to return correct location of representative cycles
  • computing filtrations returns coordinates of vertices when appropriate
  • resolved compile issue with gcc 8

TDA: version 1.6

  • fixed bugs
  • alphaCompelxDiag and alphaShapeDiag also returns location of representative cycles
  • for computing persistence diagrams, users can choose library GUDHI, Dionysus, and PHAT
  • several functions are added for computing filtrations from the data
  • funFiltration() function can compute the filtration from the complex and the function values
  • filtrationDiag() function can compute the persistent homology from the filtration
  • kde can use either Gaussian kernel or Epanechnikov kernel
  • when plotting diagrams, points outside diagLim are trimmed to diagLim

TDA: version 1.5.1

  • fixed CGAL library for compatibility with RcppEigen
  • registered native routines and disabled symbol search
  • resolve null pointer reference for alphaComplexDiag and alphaShapeDiag
  • alphaComplexDiag now works on 32-bit R

TDA: version 1.5

  • fixed bugs
  • dtm now takes additional tuning parameter r
  • alphaShapeDiag function is added
  • alphaComplexDiag feature
  • update boost with version 1.60.0
  • update CGAL with version 4.8
  • update GUDHI with version 1.3.0
  • in clusterTree(), sons is changed to children

TDA: version 1.4.1

  • remove alphaDiag function temporarily for installation error in Windows

TDA: version 1.4

  • fixed bugs
  • Rcpp is used in gridDiag, bottleneck & wasserstein distance, kde, kernel distance, dtm, ripsDiag, and alphaDiag
  • inputTDA.txt and outputTDA.txt are no longer used
  • kde, kernel distance, and dtm have weighted version
  • bootstrapBand, bootstrapDiagram, and maxPersistence can do weighted bootstrap
  • parallel option is possible in bootstrapDiagram
  • alphaDiag computes persistence Diagram of alpha shape in 3d
  • PHAT is available for ripsDiag
  • ripsDiag also returns location of representative cycles
  • column names for diagram is now c("dimension", "Birth", "Death")
  • In landscape(), KK is vectorized, and in silhouette(), p is vectorized

TDA: version 1.3

  • fixed bugs (memory leak in GUDHI, "1.#INF" code in Windows)
  • gridDiag now returns also location of representative cycles
  • clusterTree now returns r-Tree, lambda-Tree, alpha-Tree and kappa-Tree

TDA: version 1.2

  • fixed bugs
  • gridDiag extended to arbitrary dimension
  • PHAT can be used in gridDiag
  • GUDHI can be used in ripsDiag (requires R>=3.1.0)
  • Minor improvements for displaying the results (plot.diagram, plot.maxPersistence)

TDA: version 1.1

  • fixed bug in diag.cpp, line 421 [ fcnvalues.at(curidx) = x ]
  • ripsDiag works in 32-bit machines now (l2distance.h is bypassed)

TDA: version 1.0

  • initial release

Reference manual

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install.packages("TDA")

1.6.5 by Jisu Kim, 2 months ago


Browse source code at https://github.com/cran/TDA


Authors: Brittany T. Fasy , Jisu Kim , Fabrizio Lecci , Clement Maria , David L. Millman , Vincent Rouvreau. The included GUDHI is authored by Clement Maria , Dionysus by Dmitriy Morozov , and PHAT by Ulrich Bauer , Michael Kerber , and Jan Reininghaus.


Documentation:   PDF Manual  


GPL-3 license


Imports FNN, Rcpp, igraph, parallel, scales

Suggests testthat, lintr

Linking to BH, Rcpp, RcppEigen

System requirements: C++11, gmp


Imported by pterrace.

Suggested by archiDART.


See at CRAN