Package index • scimapR

Corpus class

sm_corpus() `[`(<sm_corpus>) length(<sm_corpus>) dim(<sm_corpus>) as_tibble(<sm_corpus>) as.data.frame(<sm_corpus>) print(<sm_corpus>) format(<sm_corpus>) summary(<sm_corpus>) str(<sm_corpus>): Create an sm_corpus object
validate_sm_corpus(): Validate an sm_corpus object
sm_validate(): Validate corpus integrity
is_sm_corpus(): Test if an object is an sm_corpus
as_sm_corpus(): Coerce objects to sm_corpus
sm_save_corpus() sm_load_corpus(): Save and load an sm_corpus
sm_filter_works(): Filter works in a corpus
sm_materialise(): Materialise cached enrichment into a corpus
scimapR-stability: scimapR accessor return-type stability contract

File ingestion

sm_read_auto(): Auto-detect bibliographic file format and read
sm_read_bib(): Read BibTeX files
sm_read_cochrane(): Read Cochrane Library export files
sm_read_dimensions(): Read Dimensions CSV files
sm_read_endnote(): Read EndNote XML export files
sm_read_lens(): Read Lens.org CSV files
sm_read_openalex_json(): Read OpenAlex JSON files
sm_read_pubmed_xml(): Read PubMed XML files
sm_read_ris(): Read RIS files
sm_read_scopus(): Read Scopus CSV files
sm_read_wos(): Read Web of Science plaintext files
sm_read_zotero(): Read Zotero CSV export files

API ingestion

sm_fetch_arxiv(): Fetch works from arXiv
sm_fetch_biorxiv(): Fetch works from bioRxiv/medRxiv
sm_fetch_crossref(): Fetch works from Crossref
sm_fetch_openalex(): Fetch works from OpenAlex
sm_fetch_orcid(): Fetch works from ORCID
sm_fetch_overton(): Fetch policy citations from Overton
sm_fetch_pubmed(): Fetch works from PubMed
sm_fetch_semantic_scholar(): Fetch works from Semantic Scholar

Live refresh

sm_refresh(): Refresh stale corpus data
sm_staleness(): Check corpus staleness
sm_lock() sm_unlock(): Lock or unlock a corpus

Corpus enrichment

sm_enrich_altmetric(): Enrich corpus with Altmetric attention data
sm_enrich_concepts(): Enrich corpus with concepts from OpenAlex or MeSH
sm_enrich_opencitations(): Enrich corpus with OpenCitations citation data
sm_enrich_orcid(): Enrich corpus authors with ORCID data
sm_enrich_retraction(): Enrich corpus with retraction data
sm_enrich_ror(): Enrich corpus institutions with ROR data
sm_enrich_specter(): Enrich corpus with SPECTER embeddings
sm_enrich_unpaywall(): Enrich corpus with Unpaywall open-access data

bibliometrix interop

sm_to_bibliometrix(): Convert sm_corpus to bibliometrix format

Corpus assembly

sm_build_corpus(): Build a corpus from multiple sources
sm_bind_corpora(): Bind two corpora together
sm_dedupe(): Deduplicate corpus works by DOI

Research questions and screening

sm_question() print(<sm_question>) format(<sm_question>): Create a structured research question
is_sm_question(): Test if an object is an sm_question
sm_query(): Search works by text query
sm_corpus_for_question(): Build a corpus from a research question
sm_screen_against_question(): Screen corpus against a research question
sm_screen_regex(): Screen corpus using regex matching
sm_screen_summary(): Summarise screening decisions
sm_merge_screening_decisions(): Merge external screening decisions into corpus

Networks

sm_network_citation(): Build a direct citation network
sm_network_cocitation(): Build a co-citation network
sm_network_collab(): Build a collaboration network
sm_network_coupling(): Build a bibliographic coupling network
sm_network_coword(): Build a co-word (co-occurrence) network
sm_network_semantic(): Build a semantic similarity network

Embeddings and clustering

sm_embed_works(): Compute work embeddings using transformer models
sm_embed_save(): Save embeddings to disk
sm_embed_load(): Load embeddings from disk
sm_cluster_evolution(): Track cluster evolution over time
sm_cluster_hdbscan(): HDBSCAN clustering of works
sm_cluster_kmeans(): K-means clustering of works
sm_cluster_label(): Label clusters with representative terms
sm_cluster_leiden(): Leiden community detection

Indicators

sm_metric_collab_index(): Calculate collaboration index
sm_metric_disruption(): Calculate the CD (disruption) index
sm_metric_fnci(): Calculate Field-Normalized Citation Impact
sm_metric_g_index(): Calculate g-index
sm_metric_h_index(): Calculate h-index
sm_metric_m_index(): Calculate m-index (m-quotient)
sm_metric_novelty(): Calculate Uzzi novelty score
sm_metric_rcr(): Calculate Relative Citation Ratio
sm_metric_summary(): Robust summary of a heavy-tailed impact metric
sm_summary_authors(): Summary statistics for authors
sm_summary_period(): Summary statistics by publication period
sm_summary_sources(): Summary statistics for sources (journals)
sm_summary_works(): Summary statistics for works
sm_self_citation() print(<sm_self_citation>) summary(<sm_self_citation>): Compute self-citation from corpus reference lists

Author trajectory

sm_author_trajectory() print(<sm_trajectory>) format(<sm_trajectory>): Build an author trajectory analysis
sm_trajectory: sm_trajectory S3 class
is_sm_trajectory(): Test if an object is an sm_trajectory
sm_plot_trajectory(): Plot author trajectory
sm_plot_topic_pivots(): Plot topic pivots
sm_plot_collab_turnover(): Plot collaborator turnover

Equity and representation audit

sm_audit_funding() print(<sm_audit_funding>): Funding source audit
sm_audit_gender() print(<sm_audit_gender>): Gender representation audit
sm_audit_geographic() print(<sm_audit_geographic>): Geographic representation audit
sm_audit_oa() print(<sm_audit_oa>): Open access status audit
print(<sm_audit_summary>) sm_audit_summary(): Combined equity audit summary
sm_plot_equity_dashboard(): Plot equity dashboard

Coverage and reconciliation

sm_coverage_audit() print(<sm_coverage>) summary(<sm_coverage>) autoplot(<sm_coverage>): Audit corpus coverage against a ground-truth reference
sm_coverage_breakdowns(): Coverage breakdowns as a flat tibble
sm_journal_in_index(): Verify journal source coverage against an index by ISSN
sm_match_types(): Controlled vocabulary for coverage match types
sm_reconcile() print(<sm_reconciliation>) summary(<sm_reconciliation>) autoplot(<sm_reconciliation>): Reconcile two corpora by DOI and title

Affiliation and attribution

sm_affiliation_match(): Match author affiliations to institutions
sm_affiliation_summary(): Summarise affiliation matches
sm_affiliation_signals(): Controlled vocabulary for affiliation match signals
sm_affiliation_methods(): Controlled vocabulary for affiliation match methods
sm_attribute_institution(): Attribute matched affiliations to a controlled institution vocabulary
sm_affiliation_dict: Default affiliation-matching dictionary

Causal and policy evaluation

sm_its() print(<sm_its>) summary(<sm_its>) autoplot(<sm_its>): Interrupted time series for a corpus outcome
sm_did() print(<sm_did>) summary(<sm_did>) autoplot(<sm_did>): Difference-in-differences for a treated vs control institution set
sm_synth() print(<sm_synth>): Synthetic control for a treated institution

Counting and robust impact

sm_citation_maturity(): Flag citation-immature recent years
sm_count(): Full and fractional output / impact counting
sm_metric_summary(): Robust summary of a heavy-tailed impact metric

Reproducible reporting

sm_figure_manifest(): Build a figure caption and alt-text manifest
sm_corpus_from_tables(): Construct an sm_corpus from a relational set of tables

Conversational exploration

sm_chat() print(<sm_chat_response>): Retrieval-grounded corpus chat
sm_chat_render(): Render a chat response

Reproducibility and certificates

sm_certificate() sm_rebuild_from_cert() sm_verify_certificate() print(<sm_certificate>) print(<sm_cert_verification>): Create, rebuild from, and verify corpus certificates
sm_provenance(): Get corpus provenance
sm_hash_corpus(): Hash a corpus for reproducibility
sm_cite_corpus(): Generate citation block for a corpus
sm_snapshot() sm_snapshot_load(): Save and load corpus snapshots
sm_diff_corpora() print(<sm_corpus_diff>) superseded: Compare two corpora

Visualization

sm_theme(): scimapR plot theme
sm_scale_color() sm_scale_fill(): Viridis colour scale for scimapR
sm_palette_qualitative(): Qualitative viridis palette
autoplot(<sm_corpus>): Autoplot for sm_corpus
sm_plot_bradford(): Plot Bradford's law
sm_plot_citation_network(): Plot citation network
sm_plot_collab(): Plot collaboration map
sm_plot_collab_turnover(): Plot collaborator turnover
sm_plot_equity_dashboard(): Plot equity dashboard
sm_plot_evolution(): Plot topic evolution over time
sm_plot_heaps(): Plot Heaps' law
sm_plot_landscape(): Plot research landscape
sm_plot_lotka(): Plot Lotka's law
sm_plot_production(): Plot annual scientific production
sm_plot_thematic_map(): Plot thematic map (Callon centrality-density)
sm_plot_top(): Plot top entities
sm_plot_topic_pivots(): Plot topic pivots
sm_plot_trajectory(): Plot author trajectory

Export

sm_export_covidence(): Export corpus for Covidence
sm_export_csv(): Export corpus tables as CSV files
sm_export_cytoscape(): Export network for Cytoscape (JSON)
sm_export_figure(): Export a plot as a publication-ready figure
sm_export_gephi(): Export network for Gephi (GEXF format)
sm_export_quarto_report(): Export a Quarto report
sm_export_rayyan(): Export corpus for Rayyan
sm_export_rds(): Export corpus as RDS
sm_export_table(): Export a table as formatted XLSX or CSV
sm_export_vosviewer(): Export network for VOSviewer
sm_export_zip(): Export corpus as self-contained ZIP bundle

Systematic review bridge

sm_screen_prisma(): Generate PRISMA flow diagram
sm_import_rayyan(): Import screening decisions from Rayyan

Field-specific helpers

sm_field_clinical_trials(): Link corpus works to clinical trials
sm_field_funder(): Extract funding information
sm_field_pubmed_mesh(): Extract MeSH terms from corpus

Researcher profile

sm_researcher_profile(): Build a researcher profile

Shiny app

sm_run_app(): Launch the scimapR Shiny application

Example data

sm_example_corpus(): Generate a synthetic example corpus
sm_example_files(): Get paths to example data files
sm_example_db: Bundled example corpus