NEWS.md

In bibnets: Importing, Constructing, and Exporting Bibliometric Networks

bibnets 0.6.0

Breaking changes

• The example dataset open_alex_gold_open_access_learning_analytics is renamed to learning_analytics. Update data(...) calls accordingly.

New features

• id argument on every network builder. author_network(), keyword_network(), reference_network(), document_network(), source_network(), country_network(), institution_network(), conetwork(), local_citations(), and historiograph() gain an id argument that names the work-identifier column (the rows of the works x entities matrix). This completes the custom-column workflow introduced in 0.5.0, which had given every entity field a self-naming argument but still required the works column to be named id.
• id = NULL (default): use an existing id column when present, otherwise fall back to row numbers (each row is one document). A custom data frame with no identifier column now builds without error.
• id = "paper_id": use any named column as the identifier.

The new argument sits at the end of each signature, so existing positional calls are unaffected. If id names a column other than "id" while the data already has a distinct "id" column, the call errors rather than silently overwriting that column (which might itself be an entity field).

Bug fixes

• split_field() (and therefore every builder) now coerces a factor entity column to character before splitting, instead of failing with "non-character argument". Hand-built data frames with stringsAsFactors = TRUE now work like character columns.

Generic reader: map columns by entity name

• read_biblio(format = "generic", ...) now takes entity-named arguments — authors, keywords, references, countries, affiliations, and journal — each naming the source column to map onto that standard field. Multi-valued fields are split on sep into the standard list-column; journal is kept scalar. This mirrors the network-builder vocabulary, so the same field names are used end to end:

r read_biblio("my.csv", format = "generic", id = "paper_id", authors = "Author Names", keywords = "Tags", sep = ",")

list_cols is retained for splitting any further columns in place (keeping their original names). Naming any of these columns (or id) implies format = "generic", so passing format is optional:

r read_biblio("my.csv", id = "paper_id", authors = "Author Names", sep = ",")

Deprecations

• The generic reader's actors argument is deprecated — the columns it named were never only "actors". Use the entity arguments above (or list_cols for arbitrary columns). actors still works, mapped to list_cols, with a deprecation warning.

bibnets 0.5.1

Documentation

• The README now documents the custom column/separator network-builder arguments introduced in 0.5.0: a "Custom Columns and Separators" section covers the entity-named column arguments (authors, keywords, references, journal, countries, affiliations), sep, references_sep, and strip_quotes, with a per-builder default-argument table. The deprecated keyword_network(field = ) example was updated to the keywords = form.
• No user-facing code changes.

bibnets 0.5.0

New features

• Custom data sets, any column name, any separator. Every network builder now takes a self-describing column argument plus sep, so a non-standard CSV works in a single call without renaming columns or pre-splitting strings:
• author_network(d, authors = "Author Names", sep = ",")
• keyword_network(d, keywords = "Tags", sep = ",")
• reference_network(d, references = "Cited Refs", sep = ",")
• document_network(d, references = "Cited Refs", sep = ",")
• source_network(d, journal = "Source title")
• country_network(d, countries = "Nations", sep = ",")
• institution_network(d, affiliations = "Orgs", sep = ",")
• local_citations() and historiograph() gain references + sep.

sep accepts any delimiter (",", "|", " and ", ...) and applies to the named entity column. The new arguments sit at the end of each signature, so existing positional calls are unaffected.

• references_sep — author_network(), country_network(), institution_network(), and source_network() gain a references_sep argument (default ";") so the references column used for coupling can have its own separator, independent of the entity sep. (Reference strings often contain internal commas, which is why it is separate.)

• strip_quotes — every builder gains a strip_quotes argument (default TRUE) that removes surrounding quote characters (straight ", doubled "", and curly quotes) from each entity, so a quoted CSV value like "Alice" or ""Alice"" is treated as Alice. Set strip_quotes = FALSE to keep quotes as part of the label. Applies to both freshly-split strings and entities supplied in a list-column.

• parse_names(): optional, standalone utility that reorders author names to "First Last" and parses each into first/last/particle/suffix components (attached as the "parts" attribute). Handles three conventions: "Last, First" (comma), the Scopus / bibnets "SURNAME Initials" label form ("WANG Y", "AYALA-ROMERO JA"), and "First Last". The surname_first argument ("auto"/"yes"/"no", default "auto") controls comma-less interpretation, with auto-detection biased toward the bibnets/Scopus convention so native bibnets labels parse without extra arguments. Case-insensitive (recognises particles in bibnets' uppercased labels). format argument selects output style: "first_last" (default), "last_initials" ("Saqr M."), or "last" ("Saqr"). Detects group/corporate authors and leaves them, NA, and empty strings unchanged. Not called by any reader or network builder — entity labels are still matched verbatim unless you apply this yourself. Base R only; no new dependencies. Documented in detail in ?parse_names and the new vignette vignette("parsing-author-names").

Bug fixes

• Positional counting ("harmonic", "first", etc.) on a plain character author column now splits correctly. Previously a delimited string was treated as a single author, silently producing a wrong network.
• author_network(type = "co_citation", self_loops = TRUE) now honors self_loops (previously ignored).
• author_network(type = "equivalence") now forwards deduplicate (previously ignored).
• A wrong separator (split yields no multi-entry rows, yet most values contain a structural delimiter ";", "|", or tab) now emits a warning instead of silently building a degenerate network. The heuristic deliberately ignores commas and " and ", which occur inside valid single labels ("Last, First" names, reference strings, "Smith and Sons"), so correct data is never warned about.
• read_biblio(format = "generic") now warns, listing the available columns, when an actors column is not found (previously skipped silently).

Deprecations

• keyword_network(field = ) is deprecated in favor of keyword_network(keywords = ). The old argument still works (with a warning) and stays in its original second position, so keyword_network(d, "author_keywords") is unchanged.

bibnets 0.4.4

CRAN pre-test fix

• The four test-equiv-*.R equivalence suites (vs bibliometrix and biblionetwork) have been moved out of the package into a local-only local_testing_and_equivalence/ directory. These developer checks pulled in data.table/biblionetwork, whose OpenMP parallelism caused the "CPU time 4 times elapsed time" NOTE on the Debian r-devel pre-test. They remain runnable locally but are no longer part of R CMD check.
• bibliometrix, biblionetwork, and data.table removed from Suggests — they were used only by the relocated equivalence tests.
• tests/testthat.R keeps a 2-thread BLAS/OpenMP cap as defence for crossprod() / tcrossprod() in multiply_bipartite().
• No user-facing code changes.

bibnets 0.4.3

CRAN reviewer requests

• All no-run wrappers in reader examples replaced with runnable examples, per CRAN reviewer guidance. File-based readers (read_scopus, read_wos, read_dimensions, read_lens) now use small bundled fixtures under inst/extdata/, reached via system.file(). API-wrapper readers (read_openalex, read_crossref) use an inline data frame matching the upstream column shape so the conversion path runs without a network call. read_biblio examples now demonstrate multi-file, directory, and generic-CSV modes against the bundled fixtures.
• New fixtures: inst/extdata/scopus_sample.csv, wos_sample.txt, dimensions_sample.csv, lens_sample.csv (2 records each).

bibnets 0.4.2

Documentation

• Title renamed to "Importing, Constructing, and Exporting Bibliometric Networks" to reflect the full lifecycle scope.
• Description rewritten to lead with attention-weighted networks (lead, last, proximity, circular) and other differentiators (position-aware counting, similarity/dissimilarity normalisations, temporal windows, disparity-filter backbone, historiograph, local citation scoring), dropping the enumeration of standard co-network types.
• README intro re-leads with capabilities; numerical method counts removed.
• Internal-comment author attributions stripped throughout.

bibnets 0.4.1

Bug fixes

• read_lens() no longer inflates output to n^2 rows when neither Lens ID nor ID columns are present.
• read_openalex() no longer inflates output to n^2 rows when the id column is absent.
• read_scopus() now normalises empty-string DOIs to NA, so is.na(doi) deduplication checks behave as expected.
• read_wos() empty-file return now includes the keywords_plus list-column to match the non-empty schema.
• read_crossref() no longer crashes with "row names contain missing values" when the issued column has NA entries.

Documentation

• Converter examples (to_igraph(), to_tbl_graph(), to_cograph()) now use @examplesIf requireNamespace(...) so they execute when the suggested package is installed instead of being silently skipped.
• read_biblio(), read_bibtex(), and read_ris() now ship runnable examples backed by either the bundled extdata/openalex_works.csv fixture or a tempfile()-based minimal record.
• Reference list streamlined across DESCRIPTION, README, vignette, and Rd files.

Testing

• Added eight new test files covering read_scopus(), read_wos(), read_ris(), read_lens(), read_dimensions(), read_crossref(), read_biblio(), read_openalex(), plus dedicated coverage for R/edgelist.R and build_bipartite_long().
• Suite size: 1268 tests (was 499). Package line coverage: 92.5% (was 61.8%).

bibnets 0.3.0

New functions

• temporal_network() — builds time-windowed networks with fixed, sliding, or cumulative strategies. Results include a window column for easy stacking.
• historiograph() — Garfield-style chronological citation network among the most locally cited documents.
• local_citations() — counts within-dataset citations (Local Citation Score).
• backbone() — disparity filter for extracting statistically significant edges from dense weighted networks.
• prune() — threshold and top-n edge pruning.
• read_biblio() — universal reader with auto-format detection (Scopus, WoS, BibTeX, RIS, Dimensions, Lens.org).
• read_dimensions() — Dimensions CSV export reader.
• read_crossref() — converter for rcrossref::cr_works() output.
• to_gephi() — exports node and edge tables in Gephi CSV format; writes nodes.csv + edges.csv when a directory path is supplied.
• to_graphml() — pure base-R GraphML writer; no XML package required.
• to_cograph() — converts edge list to a cograph_network object with optional node metadata for direct use with cograph::splot().

Improvements

• All edge list functions now sort output by weight descending and reset row names.
• local_citations() canonical column order: id, lcs, gcs, year, title, journal, doi.
• historiograph() empty-result schema matches non-empty schema.
• All readers share a standard column order: id, title, year, journal, doi, cited_by_count, abstract, type, authors, references, keywords, then source-specific extras.
• backbone() and prune() use single-pass O(m) node statistics via tapply() / split() — faster on large networks.
• temporal_network() converted from for loop to lapply.
• read_dimensions() / read_crossref() now apply standardize_authors() and standardize_refs() for consistency with other readers.

bibnets 0.2.0

Breaking changes

• Argument count renamed to counting; measure renamed to similarity across all network functions.
• co_network() renamed to conetwork().

New functions

• read_openalex() — reads OpenAlex JSON export.
• filter_top() — keeps only the top-n most connected nodes.
• normalize() — post-hoc normalisation of any edge list.

bibnets 0.1.0

Initial release.

• 8 network builders: author_network(), document_network(), reference_network(), keyword_network(), institution_network(), country_network(), source_network(), conetwork().
• 13 counting methods including harmonic, geometric, golden ratio, adaptive geometric.
• 6 similarity normalisations: association strength, cosine, Jaccard, inclusion, equivalence.
• 6 readers: Scopus, Web of Science, OpenAlex, BibTeX, RIS, Lens.org.
• Converters: to_igraph(), to_tbl_graph(), to_matrix().
• Numerically validated against bibliometrix and biblionetwork.

bibnets documentation built on June 19, 2026, 1:06 a.m.