NEWS

CiteSource 1.0.0

First stable release, following acceptance on CRAN.

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.

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.

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.

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).

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

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.

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.

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.

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.

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

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

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