Package: phutil 0.0.2.9000

Aymeric Stamm

phutil: Persistence Homology Utilities

A low-level package for hosting persistence data. It is part of the 'TDAverse' suite of packages, which is designed to provide a collection of packages for enabling machine learning and data science tasks using persistent homology. Implements a class for hosting persistence data, a number of coercers from and to already existing and used data structures from other packages and functions to compute distances between persistence diagrams. A formal definition and study of bottleneck and Wasserstein distances can be found in Bubenik, Scott and Stanley (2023) <doi:10.1007/s41468-022-00103-8>. Their implementation in 'phutil' relies on the 'C++' Hera library developed by Kerber, Morozov and Nigmetov (2017) <doi:10.1145/3064175>.

Authors:Aymeric Stamm [aut, cre], Jason Cory Brunson [aut], Michael Kerber [ctb], Dmitriy Morozov [ctb], Arnur Nigmetov [ctb]

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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
phutil/json (API)

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

Bug tracker:https://github.com/tdaverse/phutil/issues

Pkgdown/docs site:https://tdaverse.github.io

Uses libs:
  • c++– GNU Standard C++ Library v3
  • openmp– GCC OpenMP (GOMP) support library
Datasets:

On CRAN:

Conda:

quartocppopenmp

6.16 score 2 packages 30 scripts 578 downloads 10 exports 4 dependencies

Last updated from:c9bb2ebe0e. Checks:13 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-arm64OK160
linux-devel-x86_64OK149
source / vignettesOK267
linux-release-arm64OK152
linux-release-x86_64OK156
macos-release-arm64OK171
macos-release-x86_64OK294
macos-oldrel-arm64OK141
macos-oldrel-x86_64OK281
windows-develOK197
windows-releaseOK157
windows-oldrelOK145
wasm-releaseOK161

Exports:as_diagramas_persistenceas_persistence_setbottleneck_distancebottleneck_pairwise_distancesget_pairskantorovich_distancekantorovich_pairwise_distanceswasserstein_distancewasserstein_pairwise_distances

Dependencies:BHclicpp11rlang

Validation and Benchmark of Wasserstein Distances
Definitions | Validation | Distances between nontrivial diagrams | Distances from the trivial diagram | Benchmarks | References
Rendered fromvalidation-benchmark.qmdusingquarto::html

Last update: 2025-09-01
Started: 2025-04-27

The persistence class
Structure of the class | Supported inputs
Rendered frompersistence-class.qmdusingquarto::html

Last update: 2025-05-02
Started: 2025-05-02

Readme and manuals

Help Manual

Help pageTopics
A sample of persistence diagrams from the arch spiralarch_spirals
Distances between two persistence diagramsbottleneck_distance distances kantorovich_distance wasserstein_distance
Toy Data: Noisy circlenoisy_circle noisy_circle_points noisy_circle_ripserr noisy_circle_tda_rips
Pairwise distances within a set of persistence diagramsbottleneck_pairwise_distances kantorovich_pairwise_distances pairwise-distances wasserstein_pairwise_distances
An 'S3' class for storing persistence dataas.data.frame.persistence as.matrix.persistence as_diagram as_diagram.persistence as_diagram.PHom as_persistence as_persistence.data.frame as_persistence.diagram as_persistence.hclust as_persistence.list as_persistence.matrix as_persistence.persistence as_persistence.PHom format.persistence get_pairs persistence print.persistence
Toy Data: A sample of persistence diagramspersistence_sample
An 'S3' class object for storing sets of persistence diagramsas_persistence_set format.persistence_set persistence-set print.persistence_set
A sample of persistence diagrams from the trefoiltrefoils