CiteSource 0.2.1

New features

• Incremental deduplication: dedup_citations_add_sources() adds new citations to a previously deduplicated set and deduplicates across both, preserving prior automatic and manual merge decisions and the original record_ids provenance. For the same data it yields the same unique set as deduplicating everything from scratch. Exposed in the Shiny app — re-upload a deduplicated set, add new citation files, and “Find duplicates” merges them in. Works in manual = TRUE mode to surface new candidate pairs for review.
• Deferred manual deduplication: run automatic dedup now and complete manual review later. export_dedup_candidates() / reimport_dedup_candidates() persist and restore the $manual_dedup candidate pairs, and export_csv() gains a manual_dedup_complete flag (written as a column, read back by reimport_csv()) so downstream steps know whether review is still pending. Re-import, mark result == "match", and merge with dedup_citations_add_manual().
• Shiny app: re-importing a deduplicated set now shows a read-only source overview (records per source, and per label/string) on the upload page so you can see what is already in the set before adding more; the re-upload input accepts a candidate-pairs CSV and several files at once.

Bug fixes

• reimport_csv() now reads all columns as character, matching the canonical (all-character) types produced by dedup_citations(). This is required so a reimported set can re-enter dedup_citations_add_manual() (and incremental re-deduplication) without column-type clashes.
• Shiny app: the re-upload (re-import) input no longer errors when more than one file is selected; each file is routed by content (deduplicated set vs. candidate-pairs CSV vs. RIS).

Documentation

• In-app User Guide and README updated to document incremental and deferred deduplication; the file upload page labels were clarified.

CiteSource 0.2.0

Breaking changes

• Requires R >= 4.1.0 (native pipe and across() syntax used throughout).

New features

• read_citations() now warns when cite_label values are outside the standard vocabulary (search, screened, final), since phase-analysis functions depend on those exact strings.

Bug fixes

• calculate_phase_records(): n_distinct() called as a terminal pipe no longer throws an error; fixed by replacing with summarise() |> pull().
• calculate_initial_records() / calculate_detailed_records(): separator regex in separate_rows() changed from "," to ",\\s*" so sources with spaces after commas are split correctly.
• generate_apa_reference(): NA DOI values no longer cause an error in str_detect(); handled with case_when(is.na(doi) ~ NA_character_, ...).
• Shiny app — summaryPrecTab: n_unique was referenced without the rv$ prefix, causing a scope error; fixed.
• Shiny app — manual_dedup_dt: columnDefs targets now computed as 0-based integer indices rather than column name strings, matching the DT API.
• count_unique() / compare_sources(): added !is.na() guard alongside != "" so NA values in cite_source, cite_label, cite_string no longer cause filter or pivot errors.
• Shiny app — rv$pairs_to_check[,1:36] subsetting removed; full data frame passed directly.

Performance

• generate_apa_citation() and generate_apa_reference(): all rowwise() calls replaced with purrr::map2_chr() and purrr::pmap_chr(), avoiding per-row dplyr group overhead.
• Shiny app: compare_sources() is now computed once in a shared reactive and consumed by both the heatmap and upset plot, halving the work on each render.
• Shiny app: multi-value column filtering replaced from per-row sapply + str_split to vectorized strsplit + vapply via a file-scope helper .filter_multivalue_col.

CRAN / dependency changes

• ASySD deduplication functions vendored directly into R/asys_dedup.R (GPL-3, with attribution to CAMARADES / Kaitlyn Hair); the GitHub-only ASySD package is no longer a dependency.
• Remotes: field removed from DESCRIPTION.
• New imports: cli, igraph, parallelly, RecordLinkage, utf8.
• Removed from imports: ASySD, plogr.
• Added to Suggests: bslib.
• .onLoad side effects removed; shiny.maxRequestSize is no longer set at package load time.
• %>% re-export removed; use the native |> pipe.

Deprecations

• record_counts() → calculate_initial_records()
• calculate_record_counts() → calculate_detailed_records()
• calculate_phase_count() → calculate_phase_records()
• record_counts_table() → create_initial_record_table()
• record_summary_table() → create_summary_record_table()
• precision_sensitivity_table() → create_phase_record_table()

All deprecated functions remain callable with a .Deprecated() warning pointing to their replacements.

Internal

• Google Analytics injection simplified: URL-path reactive detection replaced by a file-scope CITESOURCE_ENV environment variable check evaluated once at app startup.

CiteSource 0.0.1

• Added a NEWS.md file to track changes to the package.

• Added dependency on latest version of the ASySD R package

• Simplified dedup function arguments (now specified within call to ASySD)

• Integrated new dedup function into R shiny app

CiteSource 0.1.1

• Added new functions which allow creation of tables and plots based on deduplicated (reimported) data.

• Updated shiny functionality, look and feel, and documentation

• Added new vignettes