Package: PubMatrixR
Title: PubMed Pairwise Co-Occurrence Matrix Construction and
        Visualization
Version: 1.0.1
Authors@R: c(
    person(given = "Tyler", family = "Laird",
      email = "tylerscottlaird@gmail.com", role = "aut"),
    person(given = "Enrique", family = "Toledo",
      email = "enriquetoledo@gmail.com", role = c("aut", "cre"),
      comment = c(ORCID = "0000-0002-1460-4708"))
  )
Description: 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>.
Depends: R (>= 4.1.0)
License: MIT + file LICENSE
Encoding: UTF-8
URL: https://github.com/ToledoEM/PubMatrixR-v2,
        https://toledoem.github.io/pubmatrixr/
BugReports: https://github.com/ToledoEM/PubMatrixR-v2/issues
Imports: pbapply, pheatmap, readODS, xml2
Suggests: covr, dplyr, ggplot2, kableExtra, knitr, rmarkdown, testthat
        (>= 3.0.0), withr
VignetteBuilder: knitr
Config/testthat/edition: 3
Config/roxygen2/version: 8.1.0
Config/pak/sysreqs: libicu-dev libxml2-dev
Repository: https://toledoem.r-universe.dev
Date/Publication: 2026-08-20 16:57:01 UTC
RemoteUrl: https://github.com/toledoem/pubmatrixr-v2
RemoteRef: HEAD
RemoteSha: fddd355d74d6d5b2f37728224eee7b4cc99f3497
NeedsCompilation: no
Packaged: 2026-09-19 09:11:15 UTC; root
Author: Tyler Laird [aut],
  Enrique Toledo [aut, cre] (ORCID:
    <https://orcid.org/0000-0002-1460-4708>)
Maintainer: Enrique Toledo <enriquetoledo@gmail.com>