R Observatory: Metrics for puremoe version 1.1.0

Balamuta, James Joseph

puremoe

1.1.0

Integrated Retrieval and Analysis of 'PubMed', 'NIH', and 'NLM' Literature Data

0packages depend

3.5Kdownloads / year

39.3%test coverage

13/13checks pass

Overview

About

Maintained by Jason TimmFirst published 2024-04-196 releasesCRAN page ↗GitHub ↗

Retrieve and analyze biomedical literature from 'PubMed' and the wider 'NIH'/'NLM' data stack through a single, PMID-centered interface. A PubMed search resolves to a set of PMIDs, which can be used to retrieve article metadata and abstracts, author affiliations, 'iCite' citation data and links, 'PubTator3' entity and relation annotations, and open-access full text from 'PMC'. A local analysis layer operates on the retrieved tables, supporting corpus expansion through citation links, citation network construction, sentence-level entity co-occurrence, inspection of relation evidence, and 'MeSH' descriptor keyness.

Install

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

install.packages("puremoe", 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("jaytimm/puremoe")

Development version from jaytimm/puremoe. 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-puremoe

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-puremoe

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-puremoe

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

Health

CRAN checks

13OK

Slowest check: 1.8 min · r-oldrel-windows-x86_64

Code health

Yes

Tests · ratio 0.20

39.3%

Coverage · measured lines

100%

Documentation · exports

12

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
OK2026-06-24
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-23
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-06-21
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Show 8 earlier snapshots

ERROR2026-06-20
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-06-08
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-07
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-06-04
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-03
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-05-28
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-05-20
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 585 wordsVignettesNopkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 0%
Documented parameters: 99%
Return-value docs: 100%
References docs: 0%

Downloads

3.5K

CRAN downloads in the past year

Rank #8,650 · ~10/day · ~291/mo

Releases R versions

Daily download trend is not available in this view yet.

11030 days

1.1K90 days

3.5K1 year

Compare downloads with other packages →

Also on125 r2u

Repository

GitHub ↗ jaytimm/puremoe

4Stars

0Forks

2Open issues

0Open PRs

0Releases

79Commits

1Contributors

pubmed-centralpubmed-parser

79 commits · Last activity 2026-06-24 · 0% stars, 30d

Stars over time

2024-05-17 · 22026-07-07 · 4

Repository practices

Upstream repositoryBeta

3 development-tooling and community-health practices detected across 3 families in the upstream repository

Checks run against github.com/jaytimm/puremoe on 2026-08-03.

Continuous integration (1)

GitHub Actions

Reproducibility and dev environment (1)

data-raw/

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

14 external dependencies (excludes base and recommended)

Depends (1)

R >= 3.5

Imports (12)

rentrez textshape xml2 data.table httr pbapply jsonlite rappdirs textpressparalleltoolsutils

LinkingTo (0)

none

Suggests (5)

knitr rmarkdown DT dplyr testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

People & History

People (1)

Maintainer (1)

Jason Timm

Author, Maintainer

Authors (1)

Jason Timm

Author, Maintainer

Package Timeline

6 releases. Pick two to compare their code metrics. R releases are shown for context.

1.1.0Latest
2026-06-24 · current release · diff ↗
R
R 4.6.0 released · 2026-04-24
1.0.4
2026-04-21 · diff ↗
1.0.3
2026-01-27 · diff ↗
R
R 4.5.0 released · 2025-04-11
1.0.2
2024-10-15 · diff ↗
1.0.1
2024-05-13 · diff ↗
R
R 4.4.0 released · 2024-04-24
1.0.0
2024-04-19
R
R 4.3.0 released · 2023-04-21

Package metadata

First published: 2024-04-19
Total releases: 6 / 2 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 3.5
Bundled data: 359 KB / 1 file
Download size: 24 KB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Start here. This is the citation for the package itself.

citation("puremoe")

CRAN DOI

https://doi.org/10.32614/CRAN.package.puremoe

BibTeX, derived from DESCRIPTION

@Manual{puremoe,
  title  = {puremoe: Integrated Retrieval and Analysis of 'PubMed', 'NIH', and 'NLM'
Literature Data},
  author = {Timm, Jason},
  year   = {2026},
  note   = {R package version 1.1.0},
  doi    = {10.32614/CRAN.package.puremoe},
  url    = {https://CRAN.R-project.org/package=puremoe}
}

Derived from the package DESCRIPTION, not from a citation file the authors wrote. If they publish one later, prefer it.

This is the citation for the package. It is not a citation for the R Observatory.

Cite this page

Use this when the claim is about a measurement on this page.

BibTeX

@misc{robservatorypuremoe,
  author    = {Balamuta, James Joseph},
  title     = {{R} {Observatory}: Metrics for {puremoe} version 1.1.0},
  year      = {2026},
  publisher = {HJJB, LLC},
  url       = {https://r-observatory.thecoatlessprofessor.com/packages/puremoe},
  note      = {Data set. Data release v2026-08-05}
}

APA

Balamuta, J. J. (2026). R Observatory: Metrics for puremoe version 1.1.0 [Data set]. HJJB, LLC. Data release v2026-08-05. https://r-observatory.thecoatlessprofessor.com/packages/puremoe

RIS

TY  - DATA
AU  - Balamuta, James Joseph
TI  - R Observatory: Metrics for puremoe version 1.1.0
PY  - 2026
PB  - HJJB, LLC
N1  - Data release v2026-08-05
UR  - https://r-observatory.thecoatlessprofessor.com/packages/puremoe
ER  -

In prose

These package metrics were obtained from the R Observatory (Balamuta, 2026), data release v2026-08-05, https://r-observatory.thecoatlessprofessor.com/packages/puremoe.

Bound to data release v2026-08-05, which is what makes the numbers on this page reproducible. See how to cite.

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