R Observatory: Metrics for TDApplied version 3.0.4

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

TDApplied

3.0.4Package record

Machine Learning and Inference for Topological Data Analysis

0packages depend

7Kdownloads / year

13.2%test coverage

13/13flavors OK

Overview

About

Maintained by Shael BrownCRAN page ↗GitHub ↗Issues ↗Declared funder: Dr. Reza Farivar

Topological data analysis is a powerful tool for finding non-linear global structure in whole datasets. The main tool of topological data analysis is persistent homology, which computes a topological shape descriptor of a dataset called a persistence diagram. 'TDApplied' provides useful and efficient methods for analyzing groups of persistence diagrams with machine learning and statistical inference, and these functions can also interface with other data science packages to form flexible and integrated topological data analysis pipelines.

Changes in 3.0.4

fixed distance exponentiation and group permuting in permutation test
added permutation model inference procedure
added universal null and enclosing radius functions

From NEWS.md in the release

Install

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

install.packages("TDApplied", 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("shaelebrown/TDApplied")

Development version from shaelebrown/TDApplied. 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-tdapplied

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled. We list this channel from recorded r2u download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

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-TDApplied

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-TDApplied

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed). We list this channel from recorded autoCRAN download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

Health

CRAN checks

13OK

CRAN check page ↗

Slowest check: 15.4 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-10-01
ERROR12 OK, 1 ERROR2026-09-30
OK13 OK2026-09-08
ERROR12 OK, 1 ERROR2026-09-07
OK13 OK2026-08-05

Show 5 earlier changesHide 5 earlier changes

NOTE12 OK, 1 NOTE2026-08-01
OK12 OK2026-04-25
NOTE11 OK, 3 NOTE2026-04-22
ERROR11 OK, 2 NOTE, 1 ERROR2026-04-16
NOTE11 OK, 3 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 3.0.4

READMEYes · 753 wordsVignettesYes · 5 · evaluation depends on the environmentNEWSYes · 100% structured · mentions 3.0.4Citation fileNoWebsitenot declared in DESCRIPTION

Help pages: 28 (2 internal)includes a package overview page
Examples that run: 91%21 run in a plain check · 2 never run
Exported functions with examples: 100%
Documented parameters: 93%
Return-value docs: 96%
Help pages citing references: 46%

Vignettes (5)

How these are measured

Downloads

7K

CRAN downloads in the past year

Rank #6,343 · ~19/day · ~580/mo

Releases R versions

Daily download trend is not available in this view yet.

45330 days

1.3K90 days

7K1 year

Compare downloads with other packages →

Also on396 r2u5 autocran

How downloads are counted

Repository

shaelebrown/tdapplied ↗Account: shaelebrown

18Stars

2Forks

0Open issues

0Open PRs

1Releases

446Commits

4Commit identities

License file reads as GPL-3.0 · 446 commits · Last activity 2024-10-28 · 0% stars, 30d

Responsiveness

How these are sampled

PRs merged (all time): 100%
Median days to close, 50 most recently updated closed issues: 5
Median days to close, 50 most recently updated closed PRs: 1

Stars over time

2025-06-05 · 162026-07-07 · 18

How these are measured

PracticesBeta

4 development-tooling and community-health practices detected across 3 families in the upstream repository

Checks run against github.com/shaelebrown/tdapplied on 2026-10-18.

Docs source (1)

README.Rmd

CRAN release process (2)

cran-comments.mdCRAN-SUBMISSION

Lint, format, editor (1)

RStudio project

How this is detected·Detection ruleset v3 (2026-09-26)

Dependencies

Declared dependencies

16 external dependencies (excludes base and recommended)

Installing TDApplied adds 9 packages (6 with compiled code, 5.4 MB of source tarballs). Heaviest: Rcpp 1.8 MB, RcppArmadillo 1.0 MB, kernlab 1.0 MB.

Depends (1)

R >= 3.5.0

Imports (12)

paralleldoParallel foreach clue rdist parallelly kernlab iteratorsmethodsstatsutilsRcpp

LinkingTo (1)

Rcpp

Suggests (7)

rmarkdown knitr testthat TDAstats reticulate TDA igraph

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

How these are counted

Code & Tests

People & History

People (2)

Shael Brown

Author, Maintainer since 0.1.0 (2022)

Dr. Reza Farivar

Author, Funder

Releases (13)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
R
R 4.5.0 released · 2025-04-11
3.0.4Latest
record
2024-10-29 · current release · diff ↗ ·
added 3 exports
enclosing_radius, permutation_model_inference, universal_null
R
R 4.4.0 released · 2024-04-24
3.0.3
record
2024-03-13 · diff ↗
unarchivedReturned to CRAN
2024-01-21
3.0.2
record
2024-01-21 · diff ↗ ·
removed 1 export
analyze_representatives
archivedRemoved from CRAN
2023-12-18
issues were not corrected in multiple re-submissions
3.0.0
record
2023-12-07 · diff ↗ ·
added 3 exports
analyze_representatives, plot_vr_graph, vr_graphs
R
R 4.3.0 released · 2023-04-21
2.0.4
record
2023-01-25 · diff ↗
2.0.3
record
2023-01-15 · diff ↗
2.0.2
record
2023-01-12 · diff ↗
2.0.1
record
2022-12-23 · diff ↗
2.0.0
record
2022-11-08 · diff ↗ ·
added 4 exports
PyH, bootstrap_persistence_thresholds, import_ripser, plot_diagram
0.1.3
record
2022-10-02 · diff ↗

Show 6 earlier eventsHide 6 earlier events

unarchivedReturned to CRAN
2022-09-26
0.1.2
record
2022-09-26 · diff ↗
archivedRemoved from CRAN
2022-09-04
issues were not corrected in time
0.1.1
record
2022-08-29 · diff ↗
0.1.0
record
2022-08-15
R
R 4.2.0 released · 2022-04-22

Package metadata

First published: 2022-08-15
Total releases: 13 / 4 yrs
License: GPL (>= 3) OSI
Minimum R: ≥ 3.5.0
Download size: 4.8 MB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("TDApplied")

Format

Brown, S., & Farivar, D. R. (2024). TDApplied: Machine Learning and Inference for Topological Data Analysis (Version 3.0.4) [Computer software]. https://doi.org/10.32614/CRAN.package.TDApplied

This package has no citation file, so citation() returns this entry built from DESCRIPTION.

Cite the R Observatory

For a number measured here: a download total, a coverage figure, an archival date.

Format

APA

Balamuta, J. J. (2026). R Observatory: Metrics for TDApplied version 3.0.4 [Data set]. HJJB, LLC. Data release v2026-10-21. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-21, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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