R Observatory: Metrics for CooccurrenceAffinity version 2.0.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

CooccurrenceAffinity

2.0.0

Affinity in Co-Occurrence Data

0packages depend

3.6Kdownloads / year

–test coverage

13/13checks pass

Overview

About

Maintained by Kumar MainaliFirst published 2023-05-033 releasesCRAN page ↗GitHub ↗

Computes a novel metric of affinity between two entities based on their co-occurrence (using binary presence/absence data). The metric and its maximum likelihood estimator (alpha hat) were advanced in Mainali, Slud, et al, 2021 doi:10.1126/sciadv.abj9204. Four types of confidence intervals and median interval were developed in Mainali and Slud, 2022 doi:10.1101/2022.11.01.514801. The `finches` dataset is bundled with the package.

Install

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

install.packages("CooccurrenceAffinity", 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("kpmainali/CooccurrenceAffinity")

Development version from kpmainali/CooccurrenceAffinity. 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-cooccurrenceaffinity

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-CooccurrenceAffinity

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-CooccurrenceAffinity

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

Health

CRAN checks

13OK

Slowest check: 2.1 min · r-oldrel-macos-x86_64

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

5

Dependencies · direct

Check history

OK2026-08-05
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-08-01
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 1,727 wordsVignettesNopkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 100%
Return-value docs: 100%
References docs: 63%

Downloads

3.6K

CRAN downloads in the past year

Rank #11,611 · ~10/day · ~302/mo

Releases R versions

Daily download trend is not available in this view yet.

22630 days

84990 days

3.6K1 year

Compare downloads with other packages →

Also on128 r2u23 autocran

Repository

GitHub ↗ kpmainali/cooccurrenceaffinity

29Stars

1Forks

3Open issues

0Open PRs

0Releases

179Commits

1Contributors

179 commits · Last activity 2026-01-28 · -3.3% stars, 30d

Stars over time

2025-03-30 · 272026-08-10 · 29

Repository practices

Upstream repositoryBeta

Checks run against github.com/kpmainali/cooccurrenceaffinity on 2026-08-16.

No development-tooling practices detected in the upstream repository.

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

Dependencies

Declared dependencies

5 external dependencies (excludes base and recommended)

Depends (2)

R >= 4.1BiasedUrn

Imports (4)

cowplot ggplot2 plyr reshape

LinkingTo (0)

none

Suggests (0)

none

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Datasets

People & History

People (2)

Maintainer (1)

Kumar Mainali

Author, Maintainer

Authors (2)

Kumar Mainali

Author, Maintainer

Eric Slud

Author

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
2.0.0Latest
2026-02-12 · current release · diff ↗
1.0.2
2025-06-27 · diff ↗
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
1.0
2023-05-03
R
R 4.3.0 released · 2023-04-21

Package metadata

First published: 2023-05-03
Total releases: 3 / 3 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 4.1
Bundled data: 0.5 KB / 1 file
Download size: 895 KB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("CooccurrenceAffinity")

Format

Mainali, K., & Slud, E. (2026). CooccurrenceAffinity: Affinity in Co-Occurrence Data (Version 2.0.0) [Computer software]. https://doi.org/10.32614/CRAN.package.CooccurrenceAffinity

This is what citation() produces when a package has no citation file of its own. If it prints something else, use that.

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 CooccurrenceAffinity version 2.0.0 [Data set]. HJJB, LLC. Data release v2026-08-18. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-18, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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