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retraction 0.1.0

First release. retraction scans manuscripts, bibliographies, and reference lists for citations to retracted publications, so authors can find and remove citations to retracted work before submitting. It reads a wide range of document and bibliography formats, extracts and normalizes identifiers, checks them against retraction data, and returns a tidy, scored report.

Checking documents and bibliographies

• check_file() detects the format of a file and checks every reference it contains. Bibliography formats: BibTeX and BibLaTeX (.bib), CSL-JSON (.json), RIS (.ris), and EndNote XML. Document formats: JATS XML, Word (.docx), PDF, and R Markdown, Quarto, LaTeX, Markdown, plain text, and HTML (.Rmd, .qmd, .tex, .md, .txt, .html), from which DOIs are scraped from the text.
• check_bib() checks a bibliography file when you want to name the input explicitly.
• check_dois() checks a vector of DOIs or PMIDs directly.
• check_refs() checks a data frame of references, with identifier and title columns auto-detected.
• check_pmc() accepts a PMID, PMCID, DOI, title, or whole reference string, resolves it to a PubMed Central article, reports whether the open-access full text is available, and if so checks the article’s reference list for retractions. pmc_articles() returns the per-article open-access summary, and pmc_fetch_xml() retrieves the open-access JATS XML directly.
• normalize_doi(), normalize_pmid(), normalize_pmcid(), and normalize_title() clean and canonicalize identifiers so equivalent forms match.

Sources and reconciliation

• Retraction data comes from pluggable sources: "xera" (Retraction Watch via the XeraRetractionTracker API, the default), "crossref", "openalex", "europepmc", "ncbi" (PubMed), "datacite", and "preprint" (arXiv and bioRxiv withdrawals). list_backends() lists them; sources = "all" queries every one.
• Any check_*() call can query several sources at once. The highest-priority match sets the verdict, every confirming source is recorded, and a disagreement flag is raised when sources do not agree.
• The Crossref source now recognizes corrections and expressions of concern (via update-to), not only retractions.

Matching

• Matching runs a strict cascade: exact DOI, then PMID (matched directly against the Retraction Watch corpus, falling back to OpenAlex only to obtain a DOI for the other sources), then fuzzy title matching for references without an identifier. PMID matching no longer requires OpenAlex and also works offline.
• Exact identifier matches are asserted with high confidence; fuzzy matches are reported as possible so you can verify them. A citation of a retraction notice is not flagged, and a work that was later reinstated is reported as reinstated.
• Title normalization now folds accents, ligatures, full-width forms, and non-Latin scripts (via stringi), so non-English titles match more reliably.

More inputs, scale, and interfaces

• check_zotero() scans a Zotero library directly from its database.
• check_preprint() reports whether an arXiv or bioRxiv preprint was withdrawn.
• retraction_app() launches a Shiny triage app to upload a file and browse results interactively.
• The HTML report is now sortable and filterable in the browser (self-contained, no external assets).
• Offline matching uses an in-memory hash index for O(1) DOI lookups; retraction_snapshot_parquet() exports the corpus for arrow-based analysis; and checking parallelizes across references when a future plan is set.

Offline snapshot

• retraction_sync() downloads a local snapshot of the retraction corpus for bulk checking, privacy, and offline use. Updates are incremental, adding new retractions rather than re-downloading everything.
• retraction_cache_dir() reports where the snapshot lives, and retraction_clear_cache() removes it. Offline mode is fully local by default; an optional notice (options(retraction.check_freshness = TRUE)) warns when the snapshot has fallen behind the live database.

Results and reports

• A check returns a retraction_result: a tidy tibble, one row per reference, with the retraction status, an is_retracted flag, a match confidence, the retraction date, the reason, and which sources confirmed it. It has print(), summary(), as.data.frame(), and as_tibble() methods, and retracted() returns just the flagged rows.
• render_report() writes a self-contained HTML report, or a Markdown report with format = "md".
• A bundled example, retraction_example, lets examples and tests run without network access.

Interpreting results

• explain_result() gives a plain-language sentence per reference: what matched, on which identifier, at what confidence, which sources confirmed, and any disagreement.
• compare_sources() returns the rows where the selected sources disagreed.
• exposure_score() summarizes a document’s retraction exposure with proper denominators (checked, unchecked, possible), not a bare flagged rate.
• classify_timing() labels each citation relative to the document’s date (conservatively, document_after_retraction, unless you supply per-citation dates), to distinguish work cited before vs after its retraction.
• snapshot_info() reports which retraction-database version an offline check ran against; badge_json() writes a shields.io endpoint for a README badge.

Monitoring and systematic reviews

• retraction_watch_save() / retraction_watch_diff() register a bibliography and later report references that have become retracted since, keyed on normalized identifiers so re-ordering does not confuse the diff.
• check_included_studies() checks a review’s included-study identifiers, deduplicating and reporting checked/unchecked/retracted counts, since a retracted included trial can invalidate a pooled estimate.

Workflow integration

• retraction_scan() and retraction_main() power a command-line check that exits non-zero per a fail_policy() (flagged, possible, unchecked, error) and fails closed: a missing file or a fetch error is an error, never a silently clean pass.
• retraction_knit_check() gates a knitr/Quarto render on retracted citations.
• An RStudio addin checks the active document; a ready-made GitHub Action (inst/actions/action.yml) fails CI on retracted citations.
• check_dois(), check_refs(), check_file(), and check_bib() gain strict = TRUE, which errors when a reference could not be checked (and, for check_file(), when the file is missing or yields no references) rather than returning a clean-looking result.

Export, annotation, and queries

• export_result() writes CSV, JSON, or Excel; annotate_bib() writes a bibliography back out with retracted entries marked (idempotently).
• suggest_alternatives() returns the records the corpus links to a retracted work (a correction or reinstatement) to help decide what to cite instead.
• author_retractions() and journal_retractions() query the corpus by author or journal; primary_reason_bucket() / reason_buckets() group free-text retraction reasons into a coarse taxonomy.
• Title matching adds a strict title_exact tier: an exact title, year, and first author (with a short-title guard) is asserted rather than only flagged as “possible”.

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
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