Definitions | Validation | Distances between nontrivial diagrams | Distances from the trivial diagram | Benchmarks | References
Package: phutil 0.0.3.9000
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:
phutil_0.0.3.9000.tar.gz
phutil_0.0.3.9000.zip(r-4.7-x86_64)phutil_0.0.3.9000.zip(r-4.7-arm64)phutil_0.0.3.9000.zip(r-4.6-x86_64)phutil_0.0.3.9000.zip(r-4.6-arm64)phutil_0.0.3.9000.zip(r-4.5-x86_64)
phutil_0.0.3.9000.tgz(r-4.6-x86_64)phutil_0.0.3.9000.tgz(r-4.6-arm64)phutil_0.0.3.9000.tgz(r-4.5-x86_64)phutil_0.0.3.9000.tgz(r-4.5-arm64)
phutil_0.0.3.9000.tar.gz(r-4.7-arm64)phutil_0.0.3.9000.tar.gz(r-4.7-x86_64)phutil_0.0.3.9000.tar.gz(r-4.6-arm64)phutil_0.0.3.9000.tar.gz(r-4.6-x86_64)
phutil_0.0.3.9000.tgz(r-4.6-emscripten)
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
Datasets:
- arch_spirals - A sample of persistence diagrams from the arch spiral
- noisy_circle_points - Toy Data: Noisy circle
- noisy_circle_ripserr - Toy Data: Noisy circle
- noisy_circle_tda_rips - Toy Data: Noisy circle
- persistence_sample - Toy Data: A sample of persistence diagrams
- trefoils - A sample of persistence diagrams from the trefoil
Last updated from:39d259f99a. Checks:15 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-arm64 | OK | 152 | ||
| linux-devel-x86_64 | OK | 151 | ||
| source / vignettes | OK | 218 | ||
| linux-release-arm64 | OK | 115 | ||
| linux-release-x86_64 | OK | 178 | ||
| macos-release-arm64 | OK | 192 | ||
| macos-release-x86_64 | OK | 244 | ||
| macos-oldrel-arm64 | OK | 180 | ||
| macos-oldrel-x86_64 | OK | 248 | ||
| windows-devel-arm64 | OK | 389 | ||
| windows-devel-x86_64 | OK | 287 | ||
| windows-release-arm64 | OK | 364 | ||
| windows-release-x86_64 | OK | 145 | ||
| windows-oldrel-x86_64 | OK | 157 | ||
| wasm-release | OK | 116 |
Exports:as_diagramas_persistenceas_persistence_setbottleneck_distancebottleneck_pairwise_distancesget_pairskantorovich_distancekantorovich_pairwise_distanceswasserstein_distancewasserstein_pairwise_distances
Validation and Benchmark of Wasserstein Distances
Last update: 2025-09-01
Started: 2025-04-27
The persistence class
Structure of the class | Supported inputs
Last update: 2025-05-02
Started: 2025-05-02
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| A sample of persistence diagrams from the arch spiral | arch_spirals |
| Distances between two persistence diagrams | bottleneck_distance distances kantorovich_distance wasserstein_distance |
| Toy Data: Noisy circle | noisy_circle noisy_circle_points noisy_circle_ripserr noisy_circle_tda_rips |
| Pairwise distances within a set of persistence diagrams | bottleneck_pairwise_distances kantorovich_pairwise_distances pairwise-distances wasserstein_pairwise_distances |
| An 'S3' class for storing persistence data | as.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 diagrams | persistence_sample |
| An 'S3' class object for storing sets of persistence diagrams | as_persistence_set format.persistence_set persistence-set print.persistence_set |
| A sample of persistence diagrams from the trefoil | trefoils |