Changes in version 1.0.0                        

First stable release, following acceptance on CRAN.

Bug fixes

  - compare_sources() now honors include_references: when TRUE, the
    bibliographic columns are joined back onto the source/label/string
    indicator matrix, matching the behavior of count_unique().
    Previously the argument was silently ignored and only indicator
    columns were returned.
  - calculate_detailed_records(): the Total row's Distinct Records now
    respects labels_to_include. It previously used the unfiltered input,
    making the Total inconsistent with the filtered per-source rows and
    overstating distinct records when labels were restricted.

Improvements

  - create_detailed_record_table() and
    create_precision_sensitivity_table() redesigned for readability:
    related columns are grouped under spanner headers, the
    contribution/uniqueness percentages have clearer labels, Precision
    and Recall are formatted as percentages, and the Total row is
    visually distinguished as a summary.

                 Changes in version 0.2.1 (2026-06-16)                  

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.

                        Changes in version 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.

                        Changes in version 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

                        Changes in version 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