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
NeedsCompilation: no
Packaged: 2026-08-20 12:01:28 UTC; enrique
Author: Tyler Laird [aut],
  Enrique Toledo [aut, cre] (ORCID:
    <https://orcid.org/0000-0002-1460-4708>)
Maintainer: Enrique Toledo <enriquetoledo@gmail.com>
Repository: CRAN
Date/Publication: 2026-08-21 05:46:09 UTC
Built: R 4.5.3; ; 2026-08-26 01:28:36 UTC; windows
