Package: CiteSource 1.0.0

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_1.0.0.tar.gz
CiteSource_1.0.0.zip(r-4.7-any)CiteSource_1.0.0.zip(r-4.6-any)CiteSource_1.0.0.zip(r-4.5-any)
CiteSource_1.0.0.tgz(r-4.6-any)CiteSource_1.0.0.tgz(r-4.5-any)
CiteSource_1.0.0.tar.gz(r-4.7-any)CiteSource_1.0.0.tar.gz(r-4.6-any)
CiteSource_1.0.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
CiteSource/json (API)

# Install 'CiteSource' in R:
install.packages('CiteSource', repos = c('https://eshackathon.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:

evidence-basedevidence-synthesisliterature-reviewsystematic-mappingsystematic-review

8.00 score 30 stars 33 scripts 390 downloads 30 exports 110 dependencies

Last updated from:fa9f98753a. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-develOK217
source / vignettesOK231
linux-releaseOK177
macos-releaseOK203
macos-oldrelOK269
windows-develOK136
windows-releaseOK163
windows-oldrelOK162
wasm-releaseOK136

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
About this vignette | Installation and setup | Import files from multiple sources | Deduplication and source information | Plot heatmap to compare source overlap | Heatmap by number of records | Heatmap by percentage of records | Plot an upset plot to compare source overlap | Bar plots of unique and shared records | Analyzing unique contributions | Record-level table | Search summary table | Exporting for further analysis | In summary
Rendered fromcitesource_vignette_db-pre-screen_validation.Rmdusingknitr::rmarkdown

Last update: 2026-06-17
Started: 2023-01-23

Benchmark Testing
About this vignette | Installation and setup | Import citation files | Assign custom metadata | Deduplicate and create data tables | Review internal duplication | Compare overlap with an upset plot | Review benchmark coverage with a record-level table | Detailed source contribution table | Exporting for further analysis
Rendered fromcitesource_new_benchmark_testing.Rmdusingknitr::rmarkdown

Last update: 2026-06-17
Started: 2024-08-14

Comparing Database Topic Coverage
About this vignette | Installation and setup | Import files from multiple sources | Deduplication and source information | Plot heatmap to compare source overlap | Heatmap by number of records | Heatmap by percentage of records | Plot an upset plot to compare source overlap | Bar plots of unique and shared records | Analyzing unique contributions | Analyze journal titles | Analyze publication years | Exporting for further analysis | In summary
Rendered fromcitesource_vignette_db-topic-coverage.Rmdusingknitr::rmarkdown

Last update: 2026-06-17
Started: 2022-12-09

Comparing Search Strings
About this vignette | Installation and setup | Import citation files | Assign metadata using all three fields | Deduplicate and create comparison data | Review initial record counts | Visualize overlap between strings | Upset plot by string | Heatmap by string | Compare string contributions | Benchmark coverage by string | Detailed contribution table by string | When to use cite_string vs cite_source
Rendered fromcitesource_search_string_comparison.Rmdusingknitr::rmarkdown

Last update: 2026-06-17
Started: 2026-06-17

Source Analysis Across Screening Phases
About this vignette | 1. Installation and setup | 2. Import citation files | 3. Assign custom metadata | 4. Deduplicate and create data tables | 5. Review internal duplication | 6. Analyze overlap across sources | Heatmaps | Upset plot | 7. Analyze records across screening phases | 8. Analyze data with tables | Detailed record table | Precision and sensitivity table | 9. Record-level table | 10. Exporting for further analysis
Rendered fromcitesource_analysis_across_screening_phases.Rmdusingknitr::rmarkdown

Last update: 2026-06-17
Started: 2026-06-17

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