Package: CiteSource 0.2.1

Trevor Riley

CiteSource: Data-Driven Search Strategy Development and Evidence Synthesis Reporting

Deduplicates bibliographic citations from multiple sources while preserving customizable metadata, supporting data-driven search strategy development and evidence synthesis reporting. Search results can be analyzed using plots and tables, and imported or exported in 'RIS' and 'CSV' formats. An interactive 'shiny' application is included for exploratory use.

Authors:Trevor Riley [aut, cre], Kaitlyn Hair [aut], Lukas Wallrich [aut], Matthew Grainger [aut], Sarah Young [aut], Chris Pritchard [aut], Neal Haddaway [aut], Martin Westgate [cph], Eliza Grames [cph], Kaitlyn Hair [cph], CAMARADES Group [cph]

CiteSource_0.2.1.tar.gz
CiteSource_0.2.1.tar.gz(r-4.7-any)CiteSource_0.2.1.tar.gz(r-4.6-any)
CiteSource_0.2.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
CiteSource/json (API)
NEWS

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

Bug tracker:https://github.com/eshackathon/citesource/issues

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

On CRAN:

Conda:

3.48 score 12 scripts 30 exports 110 dependencies

Last updated from:e95e069ea9. Checks:4 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64OK201
source / vignettesOK200
linux-release-x86_64OK243
wasm-releaseOK156

Exports:calculate_detailed_recordscalculate_initial_recordscalculate_phase_countcalculate_phase_recordscalculate_record_countscitation_summary_tablecompare_sourcescount_uniquecreate_detailed_record_tablecreate_initial_record_tablecreate_precision_sensitivity_tablededup_citationsdedup_citations_add_manualdedup_citations_add_sourcesdedup_logexport_bibexport_csvexport_dedup_candidatesexport_risplot_contributionsplot_source_overlap_heatmapplot_source_overlap_upsetread_citationsrecord_countsrecord_level_tablereimport_csvreimport_dedup_candidatesreimport_risrun_shinyrunShiny

Dependencies:base64encbigDbitbit64bitopsblobbslibcachemclassclicodetoolscommonmarkcpp11crosstalkcurldata.tableDBIdiagramdigestdplyrDTe1071evaluateevdfarverfastmapfffontawesomeforcatsfsfuturefuture.applygenericsggnewscaleggplot2globalsgluegridExtragtgtablehighrhtmltoolshtmlwidgetsigraphipredisobandjquerylibjsonlitejuicyjuiceKernSmoothknitrlabelinglaterlatticelavalazyevallifecyclelistenvlitedownmagrittrmarkdownMASSMatrixmemoisemimennetnumDerivotelparallellypillarpkgconfigplyrprodlimprogressrpromisesproxypurrrR6rappdirsRColorBrewerRcppreactablereactRRecordLinkagerlangrmarkdownrpartRSQLiteS7sassscalesshapeSQUAREMstringistringrsurvivaltibbletidyrtidyselecttinytexUpSetRutf8V8vctrsviridisLitewithrxfunxml2xtableyaml

Assessing Usefulness of Databases for Evidence Synthesis

Rendered fromcitesource_vignette_db-pre-screen_validation.Rmdusingknitr::rmarkdownon Jun 16 2026.

Last update: 2026-06-16
Started: 2026-06-16

Benchmark Testing

Rendered fromcitesource_new_benchmark_testing.Rmdusingknitr::rmarkdownon Jun 16 2026.

Last update: 2026-06-16
Started: 2026-06-16

Comparing Database Topic Coverage

Rendered fromcitesource_vignette_db-topic-coverage.Rmdusingknitr::rmarkdownon Jun 16 2026.

Last update: 2026-06-16
Started: 2026-06-16

Comparing Search Strings

Rendered fromcitesource_search_string_comparison.Rmdusingknitr::rmarkdownon Jun 16 2026.

Last update: 2026-06-16
Started: 2026-06-16

Source Analysis Across Screening Phases

Rendered fromcitesource_analysis_across_screening_phases.Rmdusingknitr::rmarkdownon Jun 16 2026.

Last update: 2026-06-16
Started: 2026-06-16

Readme and manuals

Help Manual

Help pageTopics
CiteSource: A package to compare sources of citation recordsCiteSource-package CiteSource
Calculate Detailed Record Countscalculate_detailed_records
Calculate Initial Records Unique Citationscalculate_initial_records
Calculate phase counts, precision, and recallcalculate_phase_count
Calculate Phase Counts with Precision and Recallcalculate_phase_records
Calculate record counts function Calculate and combine counts of distinct records, imported records, and unique records for each databasecalculate_record_counts
Contribution summary tablecitation_summary_table
Compare duplicate citations across sources, labels, and stringscompare_sources
Count number of unique and non-unique citations from different sources, labels, and stringscount_unique
Create a Detailed Record Tablecreate_detailed_record_table
Initial Record Tablecreate_initial_record_table
Count and Precision/Sensitivity Tablecreate_precision_sensitivity_table
Deduplicate citationsdedup_citations
Add manually identified duplicate pairs to a deduplicated datasetdedup_citations_add_manual
Add new citations to a previously deduplicated set and re-deduplicatededup_citations_add_sources
Build a provenance log of all merged duplicate pairsdedup_log
Detect file formatting informationdetect_ detect_delimiter detect_lookup detect_parser detect_year
Export deduplicated citations to .bib fileexport_bib
Export deduplicated citations with source data as CSV fileexport_csv
Export manual-review candidate pairs to a CSV fileexport_dedup_candidates
Export data frame to RIS fileexport_ris
Bind two or more data frames with different columnsmerge_columns
Parse bibliographic text in a variety of formatsparse_ parse_bibtex parse_csv parse_pubmed parse_ris parse_tsv
Create a bar chart that compares source contributions over stagesplot_contributions
Create a heatmap matrix showing the overlap between sourcesplot_source_overlap_heatmap
Create an UpSetR upset plot showing the overlap between sourcesplot_source_overlap_upset
Import citations from fileread_citations
Record counts function Calculate and combine counts of distinct records and imported records for each databaserecord_counts
Record-level tablerecord_level_table
Reimport a CSV-file exported from CiteSourcereimport_csv
Reimport manual-review candidate pairs exported from CiteSourcereimport_dedup_candidates
Reimport a RIS-file exported from CiteSourcereimport_ris
A wrapper function to run Shiny Apps from 'CiteSource'.runShiny run_shiny
Import bibliographic search resultsread_ref synthesisr_read_refs
Export data to a bibliographic formatwrite_bib write_refs write_ris