Package: TDA 1.9.4

TDA: Statistical Tools for Topological Data Analysis

Tools for Topological Data Analysis. The package focuses on statistical analysis of persistent homology and 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 methods from Fasy et al. (2014) <doi:10.1214/14-AOS1252> and Chazal et al. (2015) <doi:10.20382/jocg.v6i2a8> for analyzing the statistical significance of persistent homology features.

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

TDA_1.9.4.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'))

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.

gmp cpp

7.18 score 9 stars 5 packages 204 scripts 1.1k downloads 55 mentions 38 exports 23 dependencies

Last updated 1 months agofrom:0e300018d1. Checks:1 OK, 11 NOTE. Indexed: yes.

Target	Result	Latest binary
Doc / Vignettes	OK	Mar 04 2025
R-4.5-win-x86_64	NOTE	Mar 04 2025
R-4.5-mac-x86_64	NOTE	Mar 04 2025
R-4.5-mac-aarch64	NOTE	Mar 04 2025
R-4.5-linux-x86_64	NOTE	Mar 04 2025
R-4.4-win-x86_64	NOTE	Mar 04 2025
R-4.4-mac-x86_64	NOTE	Mar 04 2025
R-4.4-mac-aarch64	NOTE	Mar 04 2025
R-4.4-linux-x86_64	NOTE	Mar 04 2025
R-4.3-win-x86_64	NOTE	Mar 04 2025
R-4.3-mac-x86_64	NOTE	Mar 04 2025
R-4.3-mac-aarch64	NOTE	Mar 04 2025

Exports:alphaComplexDiag alphaComplexFiltration alphaShapeDiag alphaShapeFiltration bootstrapBand bootstrapDiagram bottleneck circleUnif clusterTree distFct dtm filtrationDiag funFiltration gridDiag gridFiltration hausdInterval kde kernelDist knnDE landscape maxPersistence multipBootstrap plot.clusterTree plot.diagram plot.maxPersistence print.clusterTree print.diagram print.maxPersistence print.summary.diagram print.summary.maxPersistence ripsDiag ripsFiltration silhouette sphereUnif summary.diagram summary.maxPersistence torusUnif wasserstein

Dependencies:BH cli colorspace cpp11 farver FNN glue igraph labeling lattice lifecycle magrittr Matrix munsell pkgconfig R6 RColorBrewer Rcpp RcppEigen rlang scales vctrs viridisLite

Introduction to TDA

Rendered fromarticle.Rnwusingutils::Sweaveon Mar 04 2025.

Last update: 2025-02-02
Started: 2014-08-01

Citation

Readme and manuals

Help Manual

Help page	Topics
Statistical Tools for Topological Data Analysis	TDA-package TDA
Alpha Complex Persistence Diagram	alphaComplexDiag
Alpha Complex Filtration	alphaComplexFiltration
Persistence Diagram of Alpha Shape in 3d	alphaShapeDiag
Alpha Shape Filtration in 3d	alphaShapeFiltration
Bootstrap Confidence Band	bootstrapBand
Bootstrapped Confidence Set for a Persistence Diagram, using the Bottleneck Distance (or the Wasserstein distance).	bootstrapDiagram
Bottleneck distance between two persistence diagrams	bottleneck
Uniform Sample From The Circle	circleUnif
Density clustering: the cluster tree	clusterTree print.clusterTree
Distance function	distFct
Distance to Measure Function	dtm
Persistence Diagram of Filtration	filtrationDiag
Filtration from function values	funFiltration
Persistence Diagram of a function over a Grid	gridDiag
Persistence Diagram of a function over a Grid	gridFiltration
Subsampling Confidence Interval for the Hausdorff Distance between a Manifold and a Sample	hausdInterval
Kernel Density Estimator over a Grid of Points	kde
Kernel distance over a Grid of Points	kernelDist
k Nearest Neighbors Density Estimator over a Grid of Points	knnDE
The Persistence Landscape Function	landscape
Maximal Persistence Method	maxPersistence print.maxPersistence print.summary.maxPersistence summary.maxPersistence
Multiplier Bootstrap for Persistence Landscapes and Silhouettes	multipBootstrap
Plots the Cluster Tree	plot.clusterTree
Plot the Persistence Diagram	plot.diagram
Summary plot for the maxPersistence function	plot.maxPersistence
Rips Persistence Diagram	ripsDiag
Rips Filtration	ripsFiltration
The Persistence Silhouette Function	silhouette
Uniform Sample From The Sphere S^d	sphereUnif
'print' and 'summary' for 'diagram'	print.diagram print.summary.diagram summary.diagram
Uniform Sample From The 3D Torus	torusUnif
Wasserstein distance between two persistence diagrams	wasserstein