JATSdecoder

1.3.1

A Metadata and Text Extraction and Manipulation Tool Set

1packages depend

4.5Kdownloads / year

–test coverage

13/13checks pass

Overview

About

Maintained by Ingmar BöschenFirst published 2022-09-308 releasesCRAN page ↗GitHub ↗

Provides a function collection to extract metadata, sectioned text and study characteristics from scientific articles in 'NISO-JATS' format. Articles in PDF format can be converted to 'NISO-JATS' with the 'Content ExtRactor and MINEr' ('CERMINE', https://github.com/CeON/CERMINE). For convenience, two functions bundle the extraction heuristics: JATSdecoder() converts 'NISO-JATS'-tagged XML files to a structured list with elements title, author, journal, history, 'DOI', abstract, sectioned text and reference list. study.character() extracts multiple study characteristics like number of included studies, statistical methods used, alpha error, power, statistical results, correction method for multiple testing, software used. The function get.stats() extracts all statistical results from text and recomputes p-values for many standard test statistics. It performs a consistency check of the reported with the recalculated p-values. An estimation of the involved sample size is performed based on textual reports within the abstract and the reported degrees of freedom within statistical results. In addition, the package contains some useful functions to process text (text2sentences(), text2num(), ngram(), strsplit2(), grep2()). See Böschen, I. (2021) doi:10.1007/s11192-021-04162-z Böschen, I. (2021) doi:10.1038/s41598-021-98782-3, Böschen, I. (2023) doi:10.1038/s41598-022-27085-y, and Böschen, I. (2024) doi:10.48550/arXiv.2408.07948.

Install

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

install.packages("JATSdecoder", 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("ingmarboeschen/JATSdecoder")

Development version from ingmarboeschen/JATSdecoder. 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-jatsdecoder

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-JATSdecoder

RPMs from the iucar/cran COPR, rebuilt from CRAN.

For install.packages() integration in R, also: sudo dnf install R-CoprManager

Health

CRAN checks

13OK

Slowest check: 2.3 min · r-devel-linux-x86_64-fedora-clang

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

Dependencies · direct

Check history

OK2026-04-06
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-04
13 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMENoVignettesNopkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 97%
Documented parameters: 99%
Return-value docs: 100%
References docs: 11%

Downloads

4.5K

CRAN downloads in the past year

Rank #8,424 · ~12/day · ~371/mo

Releases R versions

Daily download trend is not available in this view yet.

25730 days

1.2K90 days

4.5K1 year

Compare downloads with other packages →

Also on145 r2u

Repository

GitHub ↗ ingmarboeschen/jatsdecoder

22Stars

3Forks

0Open issues

0Open PRs

3Releases

385Commits

1Contributors

text-extractiontext-miningniso-jatsxml-filespubmedcentralrcermine

License GPL-3.0 · 385 commits · Last activity 2026-04-10 · +4.8% stars, 30d

Stars over time

2025-06-19 · 172026-07-07 · 22

Repository practices

Upstream repositoryBeta

1 development-tooling and community-health practice detected across 1 family in the upstream repository

Checks run against github.com/ingmarboeschen/jatsdecoder on 2026-07-30.

Governance and community (1)

Issue templates

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

Dependencies

Declared dependencies

2 external dependencies (excludes base and recommended)

Depends (1)

R >= 3.1.1

Imports (4)

utilsstatsNLP openNLP

LinkingTo (0)

none

Suggests (0)

none

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

1direct

0indirect

tableParser

Code & Tests

People & History

People (1)

Maintainer (1)

Ingmar Böschen

Author, Maintainer

Authors (1)

Ingmar Böschen

Author, Maintainer

Package Timeline

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

R
R 4.6.0 released · 2026-04-24
1.3.1Latest
2026-04-09 · current release · diff ↗
1.3.0
2026-02-16 · diff ↗
1.2.2
2026-01-08 · diff ↗
1.2.1
2025-07-29 · diff ↗
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
1.2.0
2023-10-12 · diff ↗
R
R 4.3.0 released · 2023-04-21
1.1.2
2023-02-27 · diff ↗
1.1.1
2022-10-21 · diff ↗
1.1
2022-09-30
R
R 4.2.0 released · 2022-04-22

Package metadata

First published: 2022-09-30
Total releases: 8 / 4 yrs
License: GPL-3 OSI
Minimum R: ≥ 3.1.1
Download size: 229 KB
Installed size: not tracked yet
With dependencies: not tracked yet

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