Rhobots 0.1.10

CRAN policy fixes

• DESCRIPTION rewritten to spell out all acronyms in full (Uniform Manifold Approximation and Projection, Hierarchical Density-Based Spatial Clustering of Applications with Noise, term frequency-inverse document frequency, part-of-speech) and remove author-name citations, eliminating all spell-checker NOTEs in the automated CRAN incoming feasibility check.
• nanoflann.hpp moved from inst/include/ to src/ (internal use only); removes the ‘cc not on path’ NOTE on Windows by taking it out of the public header path that R’s compiled-code checker inspects.

Rhobots 0.1.9

CRAN policy fixes

• All \dontrun{} example blocks replaced with \donttest{} (examples require a model download and cannot run in < 5 s; \dontrun{} retained only for rhobots_install() which installs the torch backend).
• Software and package names in DESCRIPTION now consistently wrapped in single quotes per CRAN policy.

Rhobots 0.1.8

Bug fixes

• load_specter2() now correctly injects adapter weights into all transformer layers. The previous code used a nested replacement chain (enc$model$encoder$layer[[i]]$adapter <- adp) which R desugars into a [[<- write-back that can reinitialise the submodule; weights from earlier layers were silently overwritten by each successive iteration. Fixed by pre-fetching direct layer references (lapply(seq_len(n_layers), \(i) ...)). SPECTER2 embeddings now match the Python reference (cosine similarity > 0.9999).

• load_hf_bert() / load_specter2() now correctly read safetensors files named pytorch_model.safetensors in addition to model.safetensors.

• weight_loading.R now detects ZIP-archive .bin files (PyTorch 1.6+ format, magic bytes PK) and emits a clear error message with conversion instructions, in addition to the pre-existing guard for legacy pickle format (0x80).

• torch::torch_load() call updated from deprecated map_location argument to device (renamed in torch 0.16.3).

• Default repositories for load_specter2() updated to NetworkIsLife/specter2_base and NetworkIsLife/specter2, which host safetensors versions of the original allenai/specter2_base and allenai/specter2 (the AllenAI repos only provide .bin files that R torch cannot read directly).

Rhobots 0.1.7

New features

• hdbscan_clustering() gains allow_single_cluster (default FALSE, matching Python hdbscan’s default). When FALSE, EOM never returns a single root cluster when sub-structure is present in the condensed tree. This fixes cases where diffuse embedding spaces (continuous sentiment data, overlapping topics) collapsed to 1 cluster. On the validation suite, datasets that previously returned 1 cluster (Emotion, Yelp Reviews, IMDB, Rotten Tomatoes) now match Python’s cluster counts within ±1.

• topic_quality() gains a space argument ("original" / "reduced"). When "reduced", cohesion, separation, and silhouette are measured in the UMAP-reduced space rather than the full encoder embedding. This makes quality metrics much more sensitive to different UMAP/HDBSCAN parameter choices and is the recommended setting when using sweep_topics().

• sweep_topics() gains a corresponding quality_space argument that is forwarded to topic_quality() (default "reduced").

Rhobots 0.1.6

New features

• hdbscan_clustering() gains a knn argument that selects the tree data structure used during Borůvka MST construction:
  • "balltree" (default) — dual-tree Borůvka with a Ball-tree index (bounding hyperspheres; effective pruning in ≥3-D).
  • "kdtree" — dual-tree Borůvka with a KD-tree index (axis-aligned bounding boxes; faster to build, pruning degrades above three dimensions).
  • "adaptive" — pre-computed kNN graph via dbscan::kNN(), growing k until the MST is fully connected (guaranteed connectivity, no cap).
  • "fixed" — same as "adaptive" but caps k at 200 (faster).
  The "balltree" default replaces the previous fixed-kNN approach and matches the algorithm used by the Python hdbscan package’s boruvka_balltree mode. Validation on two scientific-abstract corpora (n = 3,328 and n = 9,035) confirms Adjusted Rand Index > 0.97 and Normalised Mutual Information > 0.98 against the Python reference.

Rhobots 0.1.5

• Initial CRAN submission release.
• Auto-install of gutenbergr and plotly in rhobots_demo().
• Fixed useDynLib being overwritten by roxygen2 regeneration.
• Fixed CUDA error handling and demo topic quality.
• Added rhobots_demo() — Gutenberg pipeline walkthrough.