Changelog

bitriad 0.4.0

Code (re)generation

OpenCode was used for the following tasks, which were manually reviewed and minimally revised, with summaries copied below.

Update C++ and R code, especially {igraph} syntax, per changes to languages and packages since the last revision.

All tests pass, examples run, and vignette knits successfully. Here's a summary of all bugs found and fixed:
C++ Compilation Errors
src/censuses.cpp — 14 errors, ~50 warnings:
- Ambiguous std::vector<int> assignment from Rcpp NameProxy: The code assigned p_ego["d1"] (a NameProxy) to std::vector<int> variables. With C++17/libc++, this is ambiguous because there are multiple valid conversion paths. Fixed by changing the receiving variables to IntegerVector (Rcpp's own type).
- Ambiguous std::back_inserter/std::inserter on IntegerVector: IntegerVector variables used as output targets of std::set_intersection/std::set_difference via back_inserter/inserter fail with current libc++. Fixed by changing these variables to std::vector<int>.
- Bitwise operators on booleans: | and & used instead of || and && throughout. Fixed ~50 instances.
- Unused variables: 6 int tot = 0 variables declared but never read. Removed.
src/combinatorial-bijections.h — 4 warnings:
- Same bitwise-on-bool pattern (| → ||). Fixed.
R-Level Bugs
- R/utils.r: wedgeReturn() had no default for add.names, but three call sites omitted it (would crash at runtime). Added default add.names = NULL.
- R/utils.r: census_scheme() had duplicate conditions — both "binary" and "simple" branches checked c(4, 1), making "simple" unreachable. Fixed "binary" to check c(4, 2).
- R/triad.R: degree(graph, V(graph)$type == TRUE) passed a logical vector instead of vertex IDs, checking only vertex 1. Fixed to degree(graph, V(graph)[V(graph)$type == TRUE]).
Deprecated igraph API
- neighborhood() → ego() + as_ids(): 26 occurrences across 8 files. Replaced all.
- layout.fruchterman.reingold() → layout_with_fr(): 3 occurrences in vignette/doc files.
- as.directed() → as_directed(): 1 occurrence in R/triad-census.R.
- as.undirected() → as_undirected(): 1 occurrence in R/an.R.
- are.connected() → are_adjacent(): 2 occurrences in R/dynamic-triad-closure.R.
Test Incompatibilities
- tests/testthat/test-empty-graphs.r: expect_false(a, b) and expect_true(a, b) patterns — expect_* only takes one argument in testthat 3.x. Split into separate calls.
- tests/testthat/test-empty-graphs.r: Multi-argument expect_equal(a, b, c, d, e, NaN) — invalid in testthat 3.x. Replaced with individual expect_true(is.nan(...)) calls.
- tests/testthat/test-censuses.r: Multi-argument expect_equal(a, b, c) and expect_equal(a, b, c, d) — invalid in testthat 3.x. Split into separate expect_equal pairs.
Other
- R/triadic-internal.R: Contained a hardcoded .Random.seed assignment that would clobber R's RNG state on package load. Cleared the file.

Convert {roxygen2} documentation to Markdown syntax.

All done. Here's the summary:
- Converted all 20 R files and 2 template files from LaTeX-style roxygen markup to markdown
- Added Config/roxygen2/markdown: TRUE to DESCRIPTION
- Regenerated all .Rd files via roxygen2::roxygenize()
- Verified: All 32 tests pass, 0 failures/warnings/skips
Key conversions:
- \code{x} →  `x`
- \link[package]{target} → [target]
- \link{target} → [target]
- \strong{x} → **x**
- \emph{x} → *x*
- \pkg{x} → **x**
- \eqn{}/\deqn{} preserved as-is (native roxygen2 support)
- Nested \code{\link{...}} → [...]
- Removed empty @details tags from template files

Other changes

Bugs were patched in as_an(), as_dynamic_an(), and schedule().

Helpers actor_attr() and event_attr() built on vertex_attr() were added.

Documentation was expanded where needed, including examples “Value” sections where absent.

The vignette was rebuilt after some restyling of the code.

Package description was revised and hyperlinks were updated per checks.

‘NEWS.md’ was initiated.