Package: scimapR 0.4.0.9000

R. Heller

scimapR: Reproducible, Question-Driven, Embedding-Aware Science Mapping

A comprehensive toolkit for bibliometric and scientometric analysis, designed as a complement to the foundational 'bibliometrix' package (Aria & Cuccurullo, 2017, <doi:10.1016/j.joi.2017.08.007>). Provides unified ingestion from major bibliographic sources including 'OpenAlex', 'Crossref', 'Semantic Scholar', 'PubMed', 'arXiv', 'bioRxiv', 'ORCID', 'Overton', 'Unpaywall', 'Scopus', and 'Web of Science' exports; classical science mapping (co-citation, bibliographic coupling, co-authorship, co-word networks); modern citation indicators (CD index, Relative Citation Ratio, field-normalized scores, Uzzi novelty); embedding-based research cluster discovery; structured research-question objects with optional LLM-grounded screening; author trajectory analysis; equity and representation auditing with explicit confidence and method reporting; reproducible-by-construction corpus certificates enabling exact re-derivation of a corpus; retrieval-grounded conversational corpus exploration; and a comprehensive 'shiny' application with publication-ready figure and table export. Output is fully 'tidyverse'-compatible with tibble-based corpora, 'viridis'-themed 'ggplot2' visualizations, and 'tidygraph' network objects.

Authors:R. Heller [aut, cre]

scimapR_0.4.0.9000.tar.gz
scimapR_0.4.0.9000.zip(r-4.7-any)scimapR_0.4.0.9000.zip(r-4.6-any)scimapR_0.4.0.9000.zip(r-4.5-any)
scimapR_0.4.0.9000.tgz(r-4.6-any)scimapR_0.4.0.9000.tgz(r-4.5-any)
scimapR_0.4.0.9000.tar.gz(r-4.7-any)scimapR_0.4.0.9000.tar.gz(r-4.6-any)
scimapR_0.4.0.9000.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
scimapR/json (API)

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

Bug tracker:https://github.com/cttir/scimapr/issues

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

Datasets:

On CRAN:

Conda:

4.61 score 162 exports 52 dependencies

Last updated from:872cd1ed47. Checks:7 ERROR, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-develERROR531
source / vignettesOK295
linux-releaseERROR355
macos-releaseERROR366
macos-oldrelERROR580
windows-develERROR553
windows-releaseERROR549
windows-oldrelERROR542
wasm-releaseOK166

Exports:%>%as_sm_corpusis_sm_corpusis_sm_questionis_sm_trajectorysm_affiliation_matchsm_affiliation_methodssm_affiliation_signalssm_affiliation_summarysm_affiliation_unmatchedsm_attribute_institutionsm_audit_fundingsm_audit_gendersm_audit_geographicsm_audit_oasm_audit_summarysm_author_trajectorysm_bind_corporasm_build_corpussm_certificatesm_chatsm_chat_rendersm_citation_maturitysm_citation_windowsm_cite_corpussm_cluster_evolutionsm_cluster_hdbscansm_cluster_kmeanssm_cluster_labelsm_cluster_leidensm_concept_vocabulariessm_corpussm_corpus_for_questionsm_corpus_from_tablessm_countsm_coverage_auditsm_coverage_breakdownssm_dedupesm_didsm_diff_corporasm_embed_loadsm_embed_savesm_embed_workssm_enrich_altmetricsm_enrich_conceptssm_enrich_openalex_impactsm_enrich_opencitationssm_enrich_orcidsm_enrich_retractionsm_enrich_rorsm_enrich_spectersm_enrich_unpaywallsm_example_corpussm_example_filessm_export_covidencesm_export_csvsm_export_cytoscapesm_export_figuresm_export_gephism_export_quarto_reportsm_export_rayyansm_export_rdssm_export_tablesm_export_vosviewersm_export_zipsm_fetch_arxivsm_fetch_biorxivsm_fetch_crossrefsm_fetch_openalexsm_fetch_orcidsm_fetch_overtonsm_fetch_pubmedsm_fetch_semantic_scholarsm_field_clinical_trialssm_field_fundersm_field_pubmed_meshsm_figure_manifestsm_filter_workssm_hash_corpussm_import_rayyansm_itssm_journal_in_indexsm_link_referencessm_load_corpussm_locksm_match_typessm_materialisesm_merge_screening_decisionssm_metric_collab_indexsm_metric_disruptionsm_metric_fncism_metric_g_indexsm_metric_h_indexsm_metric_m_indexsm_metric_noveltysm_metric_rcrsm_metric_summarysm_network_citationsm_network_cocitationsm_network_collabsm_network_couplingsm_network_cowordsm_network_semanticsm_oa_statusessm_palette_qualitativesm_plot_bradfordsm_plot_citation_networksm_plot_collabsm_plot_collab_turnoversm_plot_equity_dashboardsm_plot_evolutionsm_plot_heapssm_plot_landscapesm_plot_lotkasm_plot_productionsm_plot_thematic_mapsm_plot_topsm_plot_topic_pivotssm_plot_trajectorysm_provenancesm_querysm_questionsm_read_autosm_read_bibsm_read_cochranesm_read_dimensionssm_read_endnotesm_read_lenssm_read_openalex_jsonsm_read_pubmed_xmlsm_read_rissm_read_scopussm_read_wossm_read_zoterosm_rebuild_from_certsm_reconcilesm_refreshsm_register_inputsm_researcher_profilesm_run_appsm_save_corpussm_scale_colorsm_scale_fillsm_screen_against_questionsm_screen_prismasm_screen_regexsm_screen_summarysm_self_citationsm_snapshotsm_snapshot_loadsm_stalenesssm_summary_authorssm_summary_periodsm_summary_sourcessm_summary_workssm_synthsm_themesm_to_bibliometrixsm_unlocksm_validatesm_verify_certificatevalidate_sm_corpus

Dependencies:askpassbitbit64clicliprcpp11crayoncurldigestdplyrfarverfsgenericsggplot2gluegtablehmshttr2igraphisobandjsonlitelabelinglatticelifecyclemagrittrMatrixopensslpillarpkgconfigprettyunitsprogresspurrrR6RColorBrewerreadrrlangS7scalesstringistringrsystibbletidygraphtidyrtidyselecttzdbutf8vctrsviridisLitevroomwithrxml2

Building a Corpus from Files and APIs
Bring your own relational data (recommended) | Materialising cached enrichment | File ingestion | Combining multiple sources | Auto-detection | API fetching | Deduplication | Validation
Rendered fromingestion.Rmdusingknitr::rmarkdown

Last update: 2026-11-04
Started: 2026-05-09

Embeddings and Cluster Discovery
Semantic research landscape | Clustering | HDBSCAN | Visualise the landscape | Cluster labels (TF-IDF) | Thematic map | Advanced: Python-based embeddings
Rendered fromembeddings-and-clusters.Rmdusingknitr::rmarkdown

Last update: 2026-11-04
Started: 2026-05-09

Equity Audit, Trajectory Analysis, and Corpus Chat
Equity and representation audit | Geographic audit | Open access audit | Equity dashboard | Epistemic humility | Author trajectory analysis | LLM-grounded corpus chat
Rendered fromequity-trajectory-and-chat.Rmdusingknitr::rmarkdown

Last update: 2026-11-04
Started: 2026-05-09

Getting Started with scimapR
What is scimapR? | Quick start | Exploring the corpus | Visualisation | Networks and large graphs | Filtering | Next steps
Rendered fromscimapR.Rmdusingknitr::rmarkdown

Last update: 2026-11-04
Started: 2026-05-09

Modern Citation Indicators
Beyond the h-index | Classical indices | CD index (disruption) | Relative Citation Ratio | Field-Normalized Citation Impact | Uzzi novelty | Summary tables | Self-citation and self-corrected indices | References
Rendered frommodern-indicators.Rmdusingknitr::rmarkdown

Last update: 2026-11-04
Started: 2026-05-09

Question-Driven Reviews
Research questions as objects | Building a corpus from a question | Screening | Regex-based (deterministic) | LLM-grounded screening | Screening summary | PRISMA flow | Export for Rayyan/Covidence
Rendered fromquestion-driven-reviews.Rmdusingknitr::rmarkdown

Last update: 2026-11-04
Started: 2026-05-09

Relationship to bibliometrix
Acknowledgement | When to use which? | Round-trip interop | scimapR to bibliometrix | bibliometrix to scimapR | Round-trip preservation | Engine delegation | Citation guidance
Rendered fromrelationship-to-bibliometrix.Rmdusingknitr::rmarkdown

Last update: 2026-11-04
Started: 2026-05-09

Reproducibility and Corpus Certificates
Why certificates? | Provenance tracking | Corpus hashing | Creating a certificate | Verifying a certificate | Local input files | Saving and loading | Snapshot and diff | Citation | Locking a corpus
Rendered fromreproducibility-and-certificates.Rmdusingknitr::rmarkdown

Last update: 2026-11-04
Started: 2026-05-09

Research-management analytics: coverage, attribution, and policy evaluation
A reproducible starting corpus | 1. Coverage auditing | 2. Affiliation capture and attribution | 3. Policy evaluation | 4. Counting and robust impact | 5. Reproducible reporting
Rendered fromresearch-management-analytics.Rmdusingknitr::rmarkdown

Last update: 2026-11-04
Started: 2026-06-01

Readme and manuals

Help Manual

Help pageTopics
Coerce objects to sm_corpusas_sm_corpus as_sm_corpus.bibliometrixDB as_sm_corpus.data.frame as_sm_corpus.list as_sm_corpus.sm_corpus
Autoplot for sm_corpusautoplot.sm_corpus
Test if an object is an sm_corpusis_sm_corpus
Test if an object is an sm_questionis_sm_question
Test if an object is an sm_trajectoryis_sm_trajectory
Combined equity audit summaryprint.sm_audit_summary sm_audit_summary
Default affiliation-matching dictionarysm_affiliation_dict
Match author affiliations to institutionssm_affiliation_match
Controlled vocabulary for affiliation match methodssm_affiliation_methods
Controlled vocabulary for affiliation match signalssm_affiliation_signals
Summarise affiliation matchessm_affiliation_summary
List affiliation strings that matched no institutionsm_affiliation_unmatched
Attribute matched affiliations to a controlled institution vocabularysm_attribute_institution
Funding source auditprint.sm_audit_funding sm_audit_funding
Gender representation auditprint.sm_audit_gender sm_audit_gender
Geographic representation auditprint.sm_audit_geographic sm_audit_geographic
Open access status auditprint.sm_audit_oa sm_audit_oa
Build an author trajectory analysisformat.sm_trajectory print.sm_trajectory sm_author_trajectory
Bind two corpora togethersm_bind_corpora
Build a corpus from multiple sourcessm_build_corpus
Create, rebuild from, and verify corpus certificatesprint.sm_certificate print.sm_cert_verification sm_certificate sm_rebuild_from_cert sm_verify_certificate
Retrieval-grounded corpus chatprint.sm_chat_response sm_chat
Render a chat responsesm_chat_render
Flag citation-immature recent yearssm_citation_maturity
Citations within a fixed window after publicationsm_citation_window
Generate citation block for a corpussm_cite_corpus
Track cluster evolution over timesm_cluster_evolution
HDBSCAN clustering of workssm_cluster_hdbscan
K-means clustering of workssm_cluster_kmeans
Label clusters with representative termssm_cluster_label
Leiden community detectionsm_cluster_leiden
Controlled vocabulary for concept vocabulariessm_concept_vocabularies
Create an sm_corpus objectas.data.frame.sm_corpus as_tibble.sm_corpus dim.sm_corpus format.sm_corpus length.sm_corpus print.sm_corpus sm_corpus str.sm_corpus summary.sm_corpus [.sm_corpus
Build a corpus from a research questionsm_corpus_for_question
Construct an sm_corpus from a relational set of tablessm_corpus_from_tables
Full and fractional output / impact countingsm_count
Audit corpus coverage against a ground-truth referenceautoplot.sm_coverage print.sm_coverage sm_coverage_audit summary.sm_coverage
Coverage breakdowns as a flat tibblesm_coverage_breakdowns
Deduplicate corpus works by selected columnssm_dedupe
Difference-in-differences for a treated vs control institution setautoplot.sm_did print.sm_did sm_did summary.sm_did
Compare two corporaprint.sm_corpus_diff sm_diff_corpora
Load embeddings from disksm_embed_load
Save embeddings to disksm_embed_save
Compute work embeddings using transformer modelssm_embed_works
Enrich corpus with Altmetric attention datasm_enrich_altmetric
Enrich corpus with concepts from OpenAlex or MeSHsm_enrich_concepts
Add OpenAlex impact fields to any corpussm_enrich_openalex_impact
Enrich corpus with OpenCitations citation datasm_enrich_opencitations
Enrich corpus authors with ORCID datasm_enrich_orcid
Enrich corpus with retraction datasm_enrich_retraction
Enrich corpus institutions with ROR datasm_enrich_ror
Enrich corpus with SPECTER embeddingssm_enrich_specter
Enrich corpus with Unpaywall open-access datasm_enrich_unpaywall
Generate a synthetic example corpussm_example_corpus
Bundled example corpussm_example_db
Get paths to example data filessm_example_files
Export corpus for Covidencesm_export_covidence
Export corpus tables as CSV filessm_export_csv
Export network for Cytoscape (JSON)sm_export_cytoscape
Export a plot as a publication-ready figuresm_export_figure
Export network for Gephi (GEXF format)sm_export_gephi
Export a Quarto reportsm_export_quarto_report
Export corpus for Rayyansm_export_rayyan
Export corpus as RDSsm_export_rds
Export a table as formatted XLSX or CSVsm_export_table
Export network for VOSviewersm_export_vosviewer
Export corpus as self-contained ZIP bundlesm_export_zip
Fetch works from arXivsm_fetch_arxiv
Fetch works from bioRxiv/medRxivsm_fetch_biorxiv
Fetch works from Crossrefsm_fetch_crossref
Fetch works from OpenAlexsm_fetch_openalex
Fetch works from ORCIDsm_fetch_orcid
Fetch policy citations from Overtonsm_fetch_overton
Fetch works from PubMedsm_fetch_pubmed
Fetch works from Semantic Scholarsm_fetch_semantic_scholar
Link corpus works to clinical trialssm_field_clinical_trials
Extract funding informationsm_field_funder
Extract MeSH terms from corpussm_field_pubmed_mesh
Build a figure caption and alt-text manifestsm_figure_manifest
Filter works in a corpussm_filter_works
Hash a corpus for reproducibilitysm_hash_corpus
Import screening decisions from Rayyansm_import_rayyan
Interrupted time series for a corpus outcomeautoplot.sm_its print.sm_its sm_its summary.sm_its
Verify journal source coverage against an index by ISSNsm_journal_in_index
Link cited references to works in a corpussm_link_references
Lock or unlock a corpussm_lock sm_unlock
Controlled vocabulary for coverage match typessm_match_types
Materialise cached enrichment into a corpussm_materialise
Merge external screening decisions into corpussm_merge_screening_decisions
Calculate collaboration indexsm_metric_collab_index
Calculate the CD (disruption) indexsm_metric_disruption
Calculate Field-Normalized Citation Impactsm_metric_fnci
Calculate g-indexsm_metric_g_index
Calculate h-indexsm_metric_h_index
Calculate m-index (m-quotient)sm_metric_m_index
Calculate Uzzi novelty scoresm_metric_novelty
Calculate Relative Citation Ratiosm_metric_rcr
Robust summary of a heavy-tailed impact metricsm_metric_summary
Build a direct citation networksm_network_citation
Build a co-citation networksm_network_cocitation
Build a collaboration networksm_network_collab
Build a bibliographic coupling networksm_network_coupling
Build a co-word (co-occurrence) networksm_network_coword
Build a semantic similarity networksm_network_semantic
Controlled vocabulary for open-access statusessm_oa_statuses
Qualitative viridis palettesm_palette_qualitative
Plot Bradford's lawsm_plot_bradford
Plot citation networksm_plot_citation_network
Plot collaboration mapsm_plot_collab
Plot collaborator turnoversm_plot_collab_turnover
Plot equity dashboardsm_plot_equity_dashboard
Plot topic evolution over timesm_plot_evolution
Plot Heaps' lawsm_plot_heaps
Plot research landscapesm_plot_landscape
Plot Lotka's lawsm_plot_lotka
Plot annual scientific productionsm_plot_production
Plot thematic map (Callon centrality-density)sm_plot_thematic_map
Plot top entitiessm_plot_top
Plot topic pivotssm_plot_topic_pivots
Plot author trajectorysm_plot_trajectory
Get corpus provenancesm_provenance
Search works by text querysm_query
Create a structured research questionformat.sm_question print.sm_question sm_question
Auto-detect bibliographic file format and readsm_read_auto
Read BibTeX filessm_read_bib
Read Cochrane Library export filessm_read_cochrane
Read Dimensions CSV filessm_read_dimensions
Read EndNote XML export filessm_read_endnote
Read Lens.org CSV filessm_read_lens
Read OpenAlex JSON filessm_read_openalex_json
Read PubMed XML filessm_read_pubmed_xml
Read RIS filessm_read_ris
Read Scopus CSV filessm_read_scopus
Read Web of Science export filessm_read_wos
Read Zotero CSV export filessm_read_zotero
Reconcile two corpora by DOI and titleautoplot.sm_reconciliation print.sm_reconciliation sm_reconcile summary.sm_reconciliation
Refresh stale corpus datasm_refresh
Register a local input file of a corpussm_register_input
Build a researcher profilesm_researcher_profile
Launch the scimapR Shiny applicationsm_run_app
Save and load an sm_corpussm_load_corpus sm_save_corpus
Viridis colour scale for scimapRsm_scale_color sm_scale_fill
Screen corpus against a research questionsm_screen_against_question
Generate PRISMA flow diagramsm_screen_prisma
Screen corpus using regex matchingsm_screen_regex
Summarise screening decisionssm_screen_summary
Compute self-citation from corpus reference listsprint.sm_self_citation sm_self_citation summary.sm_self_citation
Save and load corpus snapshotssm_snapshot sm_snapshot_load
Check corpus stalenesssm_staleness
Summary statistics for authorssm_summary_authors
Summary statistics by publication periodsm_summary_period
Summary statistics for sources (journals)sm_summary_sources
Summary statistics for workssm_summary_works
Synthetic control for a treated institutionprint.sm_synth sm_synth
scimapR plot themesm_theme
Convert sm_corpus to bibliometrix formatsm_to_bibliometrix
sm_trajectory S3 classsm_trajectory
Validate corpus integritysm_validate
Validate an sm_corpus objectvalidate_sm_corpus