PubMatrixR

1.0.0

PubMed Pairwise Co-Occurrence Matrix Construction and Visualization

0packages depend

1.1Kdownloads / year

71.4%test coverage

13/13checks pass

Overview

About

Maintained by Enrique ToledoFirst published 2026-03-121 releasesCRAN page ↗GitHub ↗

Queries the 'NCBI' (National Center for Biotechnology Information) Entrez 'E-utilities' API to count pairwise co-occurrences between two sets of terms in 'PubMed' or 'PubMed Central'. It returns a matrix-like data frame of publication counts and can export hyperlink-enabled results in CSV or ODS format. The package also provides heatmap helpers for exploratory visualization of overlap patterns. Based on the method described in Becker et al. (2003) "PubMatrix: a tool for multiplex literature mining" doi:10.1186/1471-2105-4-61.

Install

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

install.packages("PubMatrixR", 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("ToledoEM/PubMatrixR-v2")

Development version from ToledoEM/PubMatrixR-v2. 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-pubmatrixr

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

# 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-PubMatrixR

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

Health

CRAN checks

13OK

Slowest check: 1.4 min · r-release-macos-x86_64

Code health

Yes

Tests · ratio 0.38

71.4%

Coverage · measured lines

100%

Documentation · exports

Dependencies · direct

Check history

OK2026-03-13
3 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 1,197 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

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

Downloads

1.1K

CRAN downloads in the past year

Rank #22,300 · ~3/day · ~90/mo

Releases R versions

Daily download trend is not available in this view yet.

18230 days

51290 days

1.1K1 year

Compare downloads with other packages →

Also on27 r2u28 autocran

Repository

GitHub ↗ toledoem/pubmatrixr-v2

1Stars

0Forks

0Open issues

0Open PRs

1Releases

34Commits

1Contributors

ncbi-databasepubmedrdataminingbibliometricsliterature-miningbibliometric-analysisbibliometric-visualization

34 commits · Last activity 2026-06-03 · 0% stars, 30d

Stars over time

2026-06-28 · 12026-07-07 · 1

Repository practices

Upstream repositoryBeta

2 development-tooling and community-health practices detected across 2 families in the upstream repository

Checks run against github.com/toledoem/pubmatrixr-v2 on 2026-07-19.

Continuous integration (1)

GitHub Actions

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

10 external dependencies (excludes base and recommended)

Depends (1)

R >= 4.1.0

Imports (4)

pbapply pheatmap readODS xml2

LinkingTo (0)

none

Suggests (6)

dplyr ggplot2 kableExtra knitr rmarkdown testthat (>= 3.0.0)

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

People & History

People (2)

Maintainer (1)

Enrique Toledo

Author, Maintainer

Authors (2)

Enrique Toledo

Author, Maintainer

Tyler Laird

Author

Package Timeline

1 release. R releases are shown for context.

R
R 4.6.0 released · 2026-04-24
1.0.0Latest
2026-03-12 · current release
R
R 4.5.0 released · 2025-04-11

Package metadata

First published: 2026-03-12
Total releases: 1 / 1 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 4.1.0
Download size: not tracked yet
Installed size: not tracked yet
With dependencies: not tracked yet

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