PubMatrixR: PubMed Pairwise Co-Occurrence Matrix Construction and Visualization
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>.
| Version: | 1.0.0 |
| Depends: | R (≥ 4.1.0) |
| Imports: | pbapply, pheatmap, readODS, xml2 |
| Suggests: | dplyr, ggplot2, kableExtra, knitr, rmarkdown, testthat (≥ 3.0.0) |
| Published: | 2026-03-12 |
| DOI: | 10.32614/CRAN.package.PubMatrixR |
| Author: | Tyler Laird [aut],
Enrique Toledo 
[aut, cre] |
| Maintainer: | Enrique Toledo <enriquetoledo at gmail.com> |
| BugReports: | https://github.com/ToledoEM/PubMatrixR-v2/issues |
| License: | MIT + file LICENSE |
| URL: | https://github.com/ToledoEM/PubMatrixR-v2 |
| NeedsCompilation: | no |
| Citation: | PubMatrixR citation info |
| Materials: | README, NEWS |
| CRAN checks: | PubMatrixR results |
Documentation:
| Reference manual: | PubMatrixR.html , PubMatrixR.pdf |
| Vignettes: |
PubMatrixR: Literature Co-occurrence Analysis (source, R code) |
Downloads:
| Package source: | PubMatrixR_1.0.0.tar.gz |
| Windows binaries: | r-devel: PubMatrixR_1.0.0.zip, r-release: not available, r-oldrel: PubMatrixR_1.0.0.zip |
| macOS binaries: | r-release (arm64): PubMatrixR_1.0.0.tgz, r-oldrel (arm64): PubMatrixR_1.0.0.tgz, r-release (x86_64): PubMatrixR_1.0.0.tgz, r-oldrel (x86_64): PubMatrixR_1.0.0.tgz |
Linking:
Please use the canonical form https://CRAN.R-project.org/package=PubMatrixR to link to this page.