edaphos 0.8.0 — Pillar 1 at literature scale

Summary

Promotes Pillar 1 (Causal AI) from a ten-abstract demo to a
literature-scale extractor. The LLM + Knowledge-Graph pipeline now
handles tens of thousands of abstracts end-to-end.

New features

• Paginated corpus clients. causal_corpus_openalex() cursor-pages
  through the OpenAlex Works API transparently past the 200-per-page
  cap. causal_corpus_deduplicate() collapses DOI + title overlap
  between SciELO and OpenAlex.

• Resumable cached ingestion. causal_llm_ingest_corpus() gains
  cache_dir + max_retries. Per-abstract tools::md5sum() keys each
  JSON cache entry; cache hits short-circuit the LLM call so
  interrupted runs resume exactly where they stopped. Malformed
  responses trigger exponential backoff; exhausted rows land in
  attr(kg, "failed"). A txtProgressBar tracks runs of ≥ 5 rows.

• Live AGROVOC SPARQL alignment. causal_ontology_agrovoc_align()
  and causal_kg_alignment(vocab = "agrovoc") resolve KG labels
  against FAO's live AGROVOC endpoint, picking the
  Levenshtein-nearest skos:prefLabel and caching resolutions to disk.

Bundled live corpus

• inst/extdata/cerrado_claims_real_corpus.jsonl — 210 causal claims
  extracted by Ollama + Gemma-4 from 100 deduplicated OpenAlex
  abstracts across three Cerrado queries, aligned against AGROVOC.
  Reproduced end-to-end by data-raw/run_large_corpus.R.

Documentation

• Vignette pilar1-causal gains §10 "Scaling to tens of thousands of
  abstracts" deriving the pagination, cache, and AGROVOC alignment
  primitives from first principles.
• README + roadmap + package doc updated to reflect the upgrade.

Quality

• 105 / 105 causal tests pass (17 new scale tests covering pagination,
  cache hits, retry on malformed responses, AGROVOC Levenshtein
  selection, and kg_alignment(vocab = "agrovoc") plumbing).
• R CMD check --as-cran clean: 0 errors / 0 warnings / 1 harmless
  "unable to verify current time" NOTE.

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