Package: retraction 0.1.0

Ahmad Sofi-Mahmudi

retraction: Detect Retracted References in Documents and Bibliographies

Scans manuscripts, bibliographies, and reference lists for citations to retracted publications so that authors can avoid citing retracted work. 'retraction' reads bibliographic formats (BibTeX, BibLaTeX, CSL-JSON, RIS, EndNote XML) and document formats (R Markdown, Quarto, 'LaTeX', Markdown, HTML, JATS XML, Word, and PDF), extracts and normalizes identifiers, and checks them against retraction data. The default data source is the Retraction Watch database served through the 'XeraRetractionTracker' API; 'Crossref', 'OpenAlex', 'Europe PMC', 'PubMed', 'DataCite', and a preprint source ('arXiv' and 'bioRxiv' withdrawals) are available as additional sources ('OpenAlex' retraction data is itself derived from Retraction Watch). Within each source, matching proceeds from exact Digital Object Identifier (DOI) and 'PubMed' identifier lookups to fuzzy title matching, and results are returned as a tidy table with a match-quality score and an optional self-contained HTML report.

Authors:Ahmad Sofi-Mahmudi [aut, cre]

retraction_0.1.0.tar.gz
retraction_0.1.0.tar.gz(r-4.7-any)retraction_0.1.0.tar.gz(r-4.6-any)
retraction_0.1.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
retraction/json (API)

# Install 'retraction' in R:
install.packages('retraction', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/choxos/retraction/issues

Pkgdown/docs site:https://choxos.github.io

Datasets:

On CRAN:

Conda:

3.18 score 4 scripts 45 exports 21 dependencies

Last updated from:99c0a1fd6c. Checks:4 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64OK149
source / vignettesOK216
linux-release-x86_64OK156
wasm-releaseOK119

Exports:annotate_bibauthor_retractionsbadge_jsoncheck_bibcheck_doischeck_filecheck_included_studiescheck_pmccheck_preprintcheck_refscheck_zoteroclassify_timingcompare_sourcesevaluate_policyexplain_resultexport_resultexposure_scorefail_policyjournal_retractionslist_backendsmanuscript_date_ofnormalize_doinormalize_pmcidnormalize_pmidnormalize_titlepmc_articlespmc_fetch_xmlprimary_reason_bucketreason_bucketsreason_summaryrender_reportretractedretraction_addin_check_activeretraction_appretraction_cache_dirretraction_clear_cacheretraction_knit_checkretraction_mainretraction_scanretraction_snapshot_parquetretraction_syncretraction_watch_diffretraction_watch_savesnapshot_infosuggest_alternatives

Dependencies:askpassclicurlgluehttr2jsonlitelifecyclemagrittropensslpillarpkgconfigR6rappdirsrlangstringdistsystibbleutf8vctrswithrxml2

Getting started with retraction
Checking a file | Checking identifiers or a data frame | PubMed Central articles | Choosing sources | Offline mode | Identifier normalization
Rendered fromretraction.Rmdusingknitr::rmarkdown

Last update: 2026-07-10
Started: 2026-07-10

How the matching thresholds were calibrated
The labeled corpus | Result 1: the assertion gate never false-accuses | Result 2: 0.90 is the empirical sweet spot for surfacing | Conclusion | Reproducing
Rendered fromcalibration.Rmdusingknitr::rmarkdown

Last update: 2026-07-10
Started: 2026-07-10

Workflows: CI gates, reviews, monitoring, and pipelines
Gate a manuscript render | Fail CI on retracted citations | Systematic reviews | Monitor a bibliography over time | Multiple sources | Interpret and export | Offline and at scale | Reproducible pipelines with targets
Rendered fromworkflows.Rmdusingknitr::rmarkdown

Last update: 2026-07-10
Started: 2026-07-10

Readme and manuals

Help Manual

Help pageTopics
Annotate a BibTeX/BibLaTeX file, marking retracted entries.annotate_bib
Coerce a retraction result to a plain tibble.as_tibble.retraction_result
Coerce a retraction result to a data frame.as.data.frame.retraction_result
Retractions attributed to an author.author_retractions
Write a shields.io endpoint badge for a checked result.badge_json
Check a BibTeX or BibLaTeX bibliography for retracted referencescheck_bib
Check a set of DOIs or PMIDs for retractioncheck_dois
Check a document or bibliography file for retracted referencescheck_file
Check the included studies of a systematic review or meta-analysis.check_included_studies
Check the reference lists of open-access PubMed Central articlescheck_pmc
Check whether a preprint has been withdrawncheck_preprint
Check a data frame of references for retractioncheck_refs
Check a Zotero library for retracted referencescheck_zotero
Classify each citation relative to the document's date.classify_timing
Summarize cross-source (dis)agreement in a resultcompare_sources
Evaluate a checked result against a fail policyevaluate_policy
Explain the verdict for each reference in a resultexplain_result
Export a checked result to CSV, JSON, or Excel.export_result
Retraction-exposure summary, with denominator diagnostics.exposure_score
A fail policy shared by the CLI, GitHub Action, and knit gate.fail_policy
Retraction summary for a journal.journal_retractions
Names of all registered backends.list_backends
Best-effort authoring date of a manuscript file (git commit date, else mtime).manuscript_date_of
Normalize a DOI.normalize_doi
Normalize a PubMed Central identifiernormalize_pmcid
Normalize a PubMed identifier to bare digits.normalize_pmid
Normalize a title for fuzzy comparison only.normalize_title
Per-article open-access summary from a 'check_pmc()' resultpmc_articles
Retrieve open-access PMC full-text XML for a PMCIDpmc_fetch_xml
Primary (lossy) reason bucket: the first matching bucket.primary_reason_bucket
Print a retraction result.print.retraction_result
Print a systematic-review check, leading with denominators.print.retraction_review
All matching reason buckets (multi-label).reason_buckets
Tabulate primary reason buckets across a checked result.reason_summary
Render a retraction result as an HTML or Markdown reportrender_report
Subset of references flagged as retracted (or otherwise notable).retracted
RStudio addin: check retractions in the active source document.retraction_addin_check_active
Launch the retraction triage Shiny appretraction_app
Location of the retraction cache directoryretraction_cache_dir
Clear the package cacheretraction_clear_cache
Example references for demonstrating retraction checksretraction_example
Fail (or warn) a knit when the document cites retracted work.retraction_knit_check
CLI main: scan files and exit per a fail policy.retraction_main
Scan files for retracted citations.retraction_scan
Export the local snapshot to a Parquet fileretraction_snapshot_parquet
Download or update a local snapshot of the retraction corpusretraction_sync
Report references newly flagged since the saved baseline.retraction_watch_diff
Save a checked result as a named watch baseline.retraction_watch_save
Report the local snapshot's data version and freshnesssnapshot_info
Suggest alternatives to a retracted worksuggest_alternatives
Summarize a retraction result as a status tally.summary.retraction_result