Package: TDA 1.9.1

TDA: 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' <https://project.inria.fr/gudhi/software/>, 'Dionysus' <https://www.mrzv.org/software/dionysus/>, and 'PHAT' <https://bitbucket.org/phat-code/phat/>. This package also implements the methods in Fasy et al. (2014) <doi:10.1214/14-AOS1252> and Chazal et al. (2014) <doi:10.1145/2582112.2582128> for analyzing the statistical significance of persistent homology features.

Authors:Brittany T. Fasy, Jisu Kim, Fabrizio Lecci, Clement Maria, David L. Millman, Vincent Rouvreau.

TDA_1.9.1.tar.gz
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TDA.pdf |TDA.html
TDA/json (API)
NEWS

# Install 'TDA' in R:
install.packages('TDA', repos = c('https://jkim82133.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Uses libs:
  • gmp– Multiprecision arithmetic library
  • c++– GNU Standard C++ Library v3

On CRAN:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

7.21 score 9 stars 6 packages 202 scripts 491 downloads 55 mentions 38 exports 23 dependencies

Last updated 10 months agofrom:b32c360cc0. Checks:OK: 1 NOTE: 8. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 26 2024
R-4.5-win-x86_64NOTEOct 26 2024
R-4.5-linux-x86_64NOTEOct 26 2024
R-4.4-win-x86_64NOTEOct 26 2024
R-4.4-mac-x86_64NOTEOct 26 2024
R-4.4-mac-aarch64NOTEOct 26 2024
R-4.3-win-x86_64NOTEOct 26 2024
R-4.3-mac-x86_64NOTEOct 26 2024
R-4.3-mac-aarch64NOTEOct 26 2024

Exports:alphaComplexDiagalphaComplexFiltrationalphaShapeDiagalphaShapeFiltrationbootstrapBandbootstrapDiagrambottleneckcircleUnifclusterTreedistFctdtmfiltrationDiagfunFiltrationgridDiaggridFiltrationhausdIntervalkdekernelDistknnDElandscapemaxPersistencemultipBootstrapplot.clusterTreeplot.diagramplot.maxPersistenceprint.clusterTreeprint.diagramprint.maxPersistenceprint.summary.diagramprint.summary.maxPersistenceripsDiagripsFiltrationsilhouettesphereUnifsummary.diagramsummary.maxPersistencetorusUnifwasserstein

Dependencies:BHclicolorspacecpp11farverFNNglueigraphlabelinglatticelifecyclemagrittrMatrixmunsellpkgconfigR6RColorBrewerRcppRcppEigenrlangscalesvctrsviridisLite

Introduction to TDA

Rendered fromarticle.Rnwusingutils::Sweaveon Oct 26 2024.

Last update: 2021-03-11
Started: 2014-08-01

Readme and manuals

Help Manual

Help pageTopics
Statistical Tools for Topological Data AnalysisTDA-package TDA
Alpha Complex Persistence DiagramalphaComplexDiag
Alpha Complex FiltrationalphaComplexFiltration
Persistence Diagram of Alpha Shape in 3dalphaShapeDiag
Alpha Shape Filtration in 3dalphaShapeFiltration
Bootstrap Confidence BandbootstrapBand
Bootstrapped Confidence Set for a Persistence Diagram, using the Bottleneck Distance (or the Wasserstein distance).bootstrapDiagram
Bottleneck distance between two persistence diagramsbottleneck
Uniform Sample From The CirclecircleUnif
Density clustering: the cluster treeclusterTree print.clusterTree
Distance functiondistFct
Distance to Measure Functiondtm
Persistence Diagram of FiltrationfiltrationDiag
Filtration from function valuesfunFiltration
Persistence Diagram of a function over a GridgridDiag
Persistence Diagram of a function over a GridgridFiltration
Subsampling Confidence Interval for the Hausdorff Distance between a Manifold and a SamplehausdInterval
Kernel Density Estimator over a Grid of Pointskde
Kernel distance over a Grid of PointskernelDist
k Nearest Neighbors Density Estimator over a Grid of PointsknnDE
The Persistence Landscape Functionlandscape
Maximal Persistence MethodmaxPersistence print.maxPersistence print.summary.maxPersistence summary.maxPersistence
Multiplier Bootstrap for Persistence Landscapes and SilhouettesmultipBootstrap
Plots the Cluster Treeplot.clusterTree
Plot the Persistence Diagramplot.diagram
Summary plot for the maxPersistence functionplot.maxPersistence
Rips Persistence DiagramripsDiag
Rips FiltrationripsFiltration
The Persistence Silhouette Functionsilhouette
Uniform Sample From The Sphere S^dsphereUnif
'print' and 'summary' for 'diagram'print.diagram print.summary.diagram summary.diagram
Uniform Sample From The 3D TorustorusUnif
Wasserstein distance between two persistence diagramswasserstein