phutil

0.0.2

Persistence Homology Utilities

2packages depend

6.2Kdownloads / year

90.6%test coverage

12/13checks pass

Overview

About

Maintained by Aymeric StammFirst published 2025-05-153 releasesCRAN page ↗GitHub ↗

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.

Install

R (CRAN)pak (dev)Ubuntu (r2u)Fedora (COPR)openSUSE (OBS)

install.packages("phutil", repos = "https://cloud.r-project.org/")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

if (!requireNamespace("pak", quietly = TRUE))
  install.packages("pak", repos = "https://cloud.r-project.org/")
pak::pak("tdaverse/phutil")

Development version from tdaverse/phutil. Installs pak first if it is not already available.

Release

# enable cranapt (r2u) if it is not already set up, then install
grep -rqs r2u.stat.illinois.edu /etc/apt/sources.list /etc/apt/sources.list.d/ \
  || curl -fsSL https://raw.githubusercontent.com/eddelbuettel/r2u/master/inst/scripts/add_cranapt_noble.sh | sudo bash
sudo apt install -y r-cran-phutil

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled.

bspm (used by r2u) also needs make: sudo apt install make

# enable the iucar/cran COPR if it is not already present, then install
ls /etc/yum.repos.d/*iucar*cran*.repo >/dev/null 2>&1 \
  || sudo dnf copr enable -y iucar/cran
sudo dnf install -y R-CRAN-phutil

RPMs from the iucar/cran COPR, rebuilt from CRAN.

For install.packages() integration in R, also: sudo dnf install R-CoprManager

# add the autoCRAN OBS repo (Tumbleweed) if it is missing, then install
zypper -q lr | grep -qi autoCRAN \
  || sudo zypper addrepo https://download.opensuse.org/repositories/devel:/languages:/R:/autoCRAN/openSUSE_Tumbleweed/devel:languages:R:autoCRAN.repo
sudo zypper install -y R-phutil

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed).

Health

CRAN checks

1NOTE12OK

Failing flavors

NOTE r-devel-linux-x86_64-debian-gcc

Slowest check: 3.0 min · r-oldrel-windows-x86_64

Code health

Yes

Tests · ratio 0.00

90.6%

Coverage · measured lines

100%

Documentation · exports

Dependencies · direct

Check history

NOTE2026-08-01
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-05-11
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
WARNING2026-05-10
12 OK · 0 NOTE · 1 WARNING · 0 ERROR · 0 FAILURE
OK2026-04-20
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-18
13 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE

Show 1 earlier snapshots

OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 705 wordsVignettesNopkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 93%
Return-value docs: 100%
References docs: 0%

Downloads

6.2K

CRAN downloads in the past year

Rank #7,109 · ~17/day · ~518/mo

Releases R versions

Daily download trend is not available in this view yet.

25730 days

1.4K90 days

6.2K1 year

Compare downloads with other packages →

Also on430 r2u3 autocran

Repository

GitHub ↗ tdaverse/phutil

0Stars

1Forks

12Open issues

2Open PRs

2Releases

252Commits

3Contributors

252 commits · Last activity 2026-07-10

Forks over time

2025-04-15 · 12026-07-07 · 1

Repository practices

Upstream repositoryBeta

6 development-tooling and community-health practices detected across 6 families in the upstream repository

Checks run against github.com/tdaverse/phutil on 2026-07-31.

Continuous integration (1)

GitHub Actions

Reproducibility and dev environment (1)

data-raw/

CRAN release process (1)

cran-comments.md

Docs source (1)

README.Rmd

Show all practices

Lint, format, editor (1)

RStudio project

Coverage (1)

Codecov

How this is detected·Detection ruleset v1 (2026-07-18)

Dependencies

Declared dependencies

11 external dependencies (excludes base and recommended)

Depends (1)

R >= 3.5

Imports (2)

cli rlang

LinkingTo (2)

BH cpp11

Suggests (7)

knitr microbenchmark quarto TDA tdaunif tinysnapshot tinytest

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

2direct

0indirect

rgph inphr

Code & Tests

Datasets

People & History

People (5)

Maintainer (1)

Aymeric Stamm

Author, Maintainer

Authors (2)

Aymeric Stamm

Author, Maintainer

Jason Cory Brunson

Author

Contributors (3)

Michael Kerber

Contributor

Dmitriy Morozov

Contributor

Arnur Nigmetov

Contributor

Package Timeline

3 releases. Pick two to compare their code metrics. R releases are shown for context.

R
R 4.6.0 released · 2026-04-24
0.0.2Latest
2026-04-17 · current release · diff ↗
0.0.1-2
2026-04-15 · diff ↗
0.0.1
2026-03-10
R
R 4.5.0 released · 2025-04-11

Package metadata

First published: 2025-05-15
Total releases: 3 / 1 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 3.5
Bundled data: 171 KB / 6 files
Download size: 402 KB
Installed size: not tracked yet
With dependencies: not tracked yet

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