CiteSource 0.2.0 (CRAN Submission Ready)

.Rbuildignore

@@ -1,3 +1,4 @@
+^\.claude
 ^renv$
 ^renv\.lock$
 ^.*\.Rproj$
@@ -8,4 +9,14 @@
 ^_pkgdown.yml$
 ^cran-comments\.md$
 ^\.httr-oauth$
-^docs$
+^CITATION\.cff$
+^REQUIREMENTS.*$
+^vignettes/working_example_data$
+^vignettes/benchmark_data$
+^vignettes/vignette_exports$
+^vignettes/new_stage_data$
+^vignettes/new_benchmark_data$
+^vignettes/topic_data$
+^vignettes/valid_data$
+^tests/shinytest$
+^CRAN-SUBMISSION$

.github/workflows/document-and-deploy-manual.yml

@@ -84,7 +84,7 @@ jobs:
             pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)"
 
       - name: Deploy to GitHub pages 🚀
-        if: ${{ github.ref_name }} == 'main' || ${{ github.ref_name }} == 'master'
+        if: ${{ github.ref_name == 'main' || github.ref_name == 'master' }}
         uses: JamesIves/github-pages-deploy-action@v4
         with:
           clean: true

.github/workflows/document-and-deploy.yml

@@ -24,7 +24,7 @@ jobs:
       - name: Set up R Dependencies
         uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages: devtools, plogr, roxygen2, remotes, rsconnect, pkgdown
+          extra-packages: devtools, roxygen2, remotes, rsconnect, pkgdown
 
       - name: Create documentation
         run: |
@@ -36,28 +36,28 @@ jobs:
             roxygen2::roxygenise();
             try(devtools::build_manual())
           "
-        
+
       - name: commit
         run: |
           git config --local user.email "actions@github.com"
           git config --local user.name "GitHub Actions"
           git add -f man/\* NAMESPACE
           git commit -m 'Documentation' || echo "No changes to commit"
           git push origin || echo "No changes to commit"
-    
+
       - name: Deploy latest from dev
         if: github.ref == 'refs/heads/dev'
         env:
           GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
           RENV_CONFIG_SNAPSHOT_VALIDATE: "false"
         run: |
           R -e "
-            remotes::install_github('ESHackathon/CiteSource', force = TRUE);
-            rsconnect::setAccountInfo(name=${{secrets.SHINY_LUKAS_ACCOUNT}}, token=${{secrets.SHINY_LUKAS_TOKEN}}, secret=${{secrets.SHINY_LUKAS_SECRET}}); 
+            renv::install('ESHackathon/CiteSource@dev');
+            rsconnect::setAccountInfo(name=${{secrets.SHINY_LUKAS_ACCOUNT}}, token=${{secrets.SHINY_LUKAS_TOKEN}}, secret=${{secrets.SHINY_LUKAS_SECRET}});
             rsconnect::deployApp(
               appName = 'CiteSource_latest',
               appDir = './inst/shiny-app/CiteSource',
-              forceUpdate = TRUE)"   
+              forceUpdate = TRUE)"
 
       - name: Deploy stable version from main
         if: github.ref == 'refs/heads/main'
@@ -66,25 +66,25 @@ jobs:
           RENV_CONFIG_SNAPSHOT_VALIDATE: "false"
         run: |
           R -e "
-            remotes::install_github('ESHackathon/CiteSource', force = TRUE);
-            rsconnect::setAccountInfo(name=${{secrets.SHINY_LUKAS_ACCOUNT}}, token=${{secrets.SHINY_LUKAS_TOKEN}}, secret=${{secrets.SHINY_LUKAS_SECRET}}); 
+            renv::install('ESHackathon/CiteSource');
+            rsconnect::setAccountInfo(name=${{secrets.SHINY_LUKAS_ACCOUNT}}, token=${{secrets.SHINY_LUKAS_TOKEN}}, secret=${{secrets.SHINY_LUKAS_SECRET}});
             rsconnect::deployApp(
               appName = 'CiteSource',
               appDir = './inst/shiny-app/CiteSource',
-              forceUpdate = TRUE)"   
+              forceUpdate = TRUE)"
 
       - name: Create pkgdown
         env:
           GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
         run: |
           R -e "
-            if (!require(CiteSource)) remotes::install_github('ESHackathon/CiteSource', force = TRUE);
+            devtools::install(dependencies = FALSE, upgrade = FALSE);
             pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)"
-      
+
       - name: Deploy to GitHub pages 🚀
-        if: ${{ github.ref_name }} == 'main'
+        if: ${{ github.ref_name == 'main' }}
         uses: JamesIves/github-pages-deploy-action@v4
         with:
           clean: true
           branch: gh-pages
-          folder: docs      
+          folder: docs

.gitignore

@@ -3,5 +3,10 @@
 .RData
 .Ruserdata
 .DS_Store
+.claude/
+guide/
+CLAUDE.md
 inst/doc
 .httr-oauth
+CITESOURCE_V020_CHANGES.md
+custom_dedup_notes.md

CITATION.cff

@@ -20,7 +20,8 @@ authors:
     given-names: "Matthew J."
     orcid: "https://orcid.org/0000-0001-8426-6495"
 title: "CiteSource: An R Package for Data-Driven Search Strategy Development and Enhanced Evidence Synthesis Reporting"
-version: 0.1.1
+version: 0.2.0
+date-released: 2026-05-13
 doi: TBD 
 url: "https://github.com/ESHackathon/CiteSource"
 preferred-citation:

CRAN-SUBMISSION

@@ -0,0 +1,3 @@
+Version: 0.2.0
+Date: 2026-05-20 13:12:58 UTC
+SHA: 728bc0a1274a64087c45193e90721cf19d4905d0

DESCRIPTION

@@ -1,9 +1,9 @@
 Package: CiteSource
-Title: An R package for data-driven search strategy development and enhanced evidence synthesis reporting
-Version: 0.1.1
-Date: 2023-06-22
+Title: Data-Driven Search Strategy Development and Evidence Synthesis Reporting
+Version: 0.2.0
+Date: 2026-05-11
 Authors@R: c(
-    person("Trevor", "Riley", , "trevor.riley@noaa.gov", role = c("aut", "cre"),
+    person("Trevor", "Riley", , "tnriley@gmail.com", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0002-6834-9802")),
     person("Kaitlyn", "Hair", , "kaitlyn.hair@ed.ac.uk", role = "aut",
            comment = c(ORCID = "0000-0003-0180-7343")),
@@ -18,58 +18,58 @@ Authors@R: c(
     person("Neal", "Haddaway", , "nealhaddaway@gmail.com", role = "aut",
            comment = c(ORCID = "0000-0003-3902-2234")),
     person("Martin", "Westgate", role = "cph", comment = "Author of included synthesisr fragments"),
-    person("Eliza", "Grames", role = "cph", comment = "Author of included synthesisr fragments")      
+    person("Eliza", "Grames", role = "cph", comment = "Author of included synthesisr fragments"),
+    person("Kaitlyn", "Hair", role = "cph", comment = "Author of included ASySD deduplication code"),
+    person("CAMARADES Group", role = "cph", comment = "Authors of ASySD (github.com/camaradesuk/ASySD)")
   )
-Description: This package was developed in order to provide researchers the ability to 
-             examine the utility and efficacy of literature resources and search 
-             methodologies. The package provides users with the ability to deduplicate
-             references while maintaining customizable metadata. The resulting data 
-             can be analyzed using predeveloped plots and tables, including a summary 
-             table. Users are also able to export and reimport data in .ris, and csv. 
-             files. The package includes a shiny application for interactive use.
+Description: Tools for data-driven search strategy development and evidence
+             synthesis reporting. Researchers can deduplicate references while
+             maintaining customizable metadata, analyze results using
+             plots and tables, and import or export data in 'RIS' and 'CSV' formats.
+             An interactive 'shiny' application is included for exploratory use.
 License: GPL (>= 3)
 URL: https://www.eshackathon.org/CiteSource
 BugReports: https://github.com/ESHackathon/CiteSource/issues
-Imports: 
-    ASySD (>= 0.3.0),
+Imports:
     dplyr,
     DT,
     forcats,
     ggnewscale,
     ggplot2,
     glue,
     gt,
-    progress,
+    igraph,
+    parallelly,
     purrr,
+    RecordLinkage,
     rlang,
     scales,
     stringr,
     tibble,
     tidyr,
     tidyselect,
-    UpSetR
-Suggests: 
+    UpSetR,
+    utf8
+Suggests:
+    bslib,
     htmltools,
+    jsonlite,
     knitr,
     networkD3,
     plotly,
+    progressr,
     rmarkdown,
     shiny,
     shinyalert,
-    shinyjs,
-    progressr,
     shinybusy,
+    shinyjs,
     shinyWidgets,
-    testthat (>= 3.0.0),
-    plogr
-VignetteBuilder: 
+    testthat (>= 3.0.0)
+VignetteBuilder:
     knitr
 Config/testthat/edition: 3
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.2.3
-Depends: 
-    R (>= 3.5.0)
-Remotes:
-    camaradesuk/ASySD,
-    plogr=url::https://cran.r-project.org/src/contrib/Archive/plogr/plogr_0.2.0.tar.gz
+Depends:
+    R (>= 4.1.0)
+Config/roxygen2/version: 8.0.0

NAMESPACE

@@ -1,7 +1,6 @@
 # Generated by roxygen2: do not edit by hand
 
 S3method(as.data.frame,bibliography)
-export("%>%")
 export(calculate_detailed_records)
 export(calculate_initial_records)
 export(calculate_phase_count)
@@ -15,37 +14,103 @@ export(create_initial_record_table)
 export(create_precision_sensitivity_table)
 export(dedup_citations)
 export(dedup_citations_add_manual)
+export(dedup_log)
 export(export_bib)
 export(export_csv)
 export(export_ris)
 export(plot_contributions)
 export(plot_source_overlap_heatmap)
 export(plot_source_overlap_upset)
-export(precision_sensitivity_table)
 export(read_citations)
 export(record_counts)
-export(record_counts_table)
 export(record_level_table)
-export(record_summary_table)
 export(reimport_csv)
 export(reimport_ris)
 export(runShiny)
 export(run_shiny)
-import(dplyr)
-import(gt)
-import(rlang)
-import(scales)
-import(tidyr)
-importFrom(dplyr,"%>%")
+importFrom(RecordLinkage,compare.dedup)
+importFrom(RecordLinkage,jarowinkler)
+importFrom(dplyr,across)
+importFrom(dplyr,all_of)
+importFrom(dplyr,anti_join)
+importFrom(dplyr,any_of)
+importFrom(dplyr,arrange)
+importFrom(dplyr,bind_cols)
+importFrom(dplyr,bind_rows)
+importFrom(dplyr,case_when)
+importFrom(dplyr,coalesce)
+importFrom(dplyr,desc)
+importFrom(dplyr,distinct)
+importFrom(dplyr,everything)
+importFrom(dplyr,filter)
+importFrom(dplyr,first)
+importFrom(dplyr,group_by)
+importFrom(dplyr,if_else)
+importFrom(dplyr,last_col)
+importFrom(dplyr,left_join)
+importFrom(dplyr,matches)
+importFrom(dplyr,mutate)
+importFrom(dplyr,n)
+importFrom(dplyr,n_distinct)
+importFrom(dplyr,na_if)
+importFrom(dplyr,pull)
+importFrom(dplyr,relocate)
+importFrom(dplyr,rename)
+importFrom(dplyr,rename_with)
+importFrom(dplyr,right_join)
+importFrom(dplyr,row_number)
+importFrom(dplyr,rowwise)
+importFrom(dplyr,select)
+importFrom(dplyr,slice_head)
+importFrom(dplyr,starts_with)
+importFrom(dplyr,summarise)
+importFrom(dplyr,transmute)
+importFrom(dplyr,ungroup)
+importFrom(gt,cell_borders)
+importFrom(gt,cell_text)
+importFrom(gt,cells_body)
 importFrom(gt,cells_column_labels)
+importFrom(gt,cells_column_spanners)
+importFrom(gt,cols_align)
 importFrom(gt,cols_label)
+importFrom(gt,fmt_number)
+importFrom(gt,fmt_percent)
 importFrom(gt,gt)
+importFrom(gt,md)
+importFrom(gt,px)
+importFrom(gt,sub_missing)
 importFrom(gt,tab_footnote)
 importFrom(gt,tab_header)
+importFrom(gt,tab_options)
+importFrom(gt,tab_source_note)
+importFrom(gt,tab_spanner_delim)
+importFrom(gt,tab_style)
+importFrom(igraph,components)
+importFrom(igraph,graph_from_data_frame)
+importFrom(parallelly,availableCores)
 importFrom(rlang,":=")
 importFrom(rlang,.data)
+importFrom(rlang,as_name)
+importFrom(rlang,enquo)
+importFrom(rlang,inform)
+importFrom(rlang,is_installed)
+importFrom(rlang,quo_is_null)
+importFrom(rlang,sym)
+importFrom(scales,percent)
+importFrom(scales,trans_format)
+importFrom(stats,na.omit)
 importFrom(stats,xtabs)
+importFrom(tidyr,fill)
+importFrom(tidyr,pivot_longer)
+importFrom(tidyr,pivot_wider)
+importFrom(tidyr,replace_na)
+importFrom(tidyr,separate)
+importFrom(tidyr,separate_rows)
+importFrom(tidyr,unite)
+importFrom(tidyselect,where)
+importFrom(utf8,utf8_encode)
 importFrom(utils,head)
+importFrom(utils,menu)
 importFrom(utils,read.table)
 importFrom(utils,tail)
 importFrom(utils,write.table)