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”.