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Changelog

Source: NEWS.md

obisindicators 0.5.0

  • Essential Ocean Variables (EOVs) — new R/eov.R maps the GOOS/IOOS biology & ecosystems EOVs onto the H3 store. The IOOS Marine Life Data Network defines each EOV as a handful of root WoRMS AphiaIDs (33 seeds across 7 EOVs: fish, hardCorals, mangroves, marineMammals, seabirds, seagrasses, seaTurtles), which is exactly a multi-seed version of the existing subtree walk.

    • obis_eov_seeds() / obis_eov_aphiaid() — the EOV definitions.
    • obis_eov_sql() — tile SQL for an EOV, routing to a precomputed layer when it can and to the live AphiaID-subtree path when it must (year filters, several EOVs at once, or a store without the layer baked).
    • obis_eov_bake() — adds eov (membership) and idx_h3_eov (precomputed indicators, res 1-7) to a store; now also a step in build_obis_h3_duckdb(), skipped with a note when taxon is absent.
    • New driver data-raw/migrate_add_eov.R.

  • WoRMS gap-fill — new R/taxon_gapfill.R closes a silent coverage hole. The bulk WoRMS taxon.txt download is not a complete cover of the AphiaIDs OBIS carries: on the 2026-07 global store 12,021 of 167,190 distinct occ_h3.aphiaid values (~7%, covering 8.3M of 121.9M records) were absent from taxon, so they were invisible to every aphiaid / EOV / SPUE query.

    • obis_taxon_orphans() — report the gap.
    • wm_aphia_records() — batched, parallel WoRMS REST lookups (AphiaRecordsByAphiaIDs, 50 ids/request), the per-id supplement to the bulk download.
    • obis_taxon_fill_gaps() — fills orphans and iterates to transitive closure, because inserting an orphan whose ancestors are still missing leaves it disconnected from any seed above it. Warns and reports closed = FALSE rather than implying a whole tree if max_rounds is hit.
    • New driver data-raw/migrate_fill_taxon_gaps.R.
    • Adds httr2 to Suggests.

  • Two taxon-group presets in the h3-db app returned zero records (fixed in MarineSensitivity/apps/h3-db, noted here because it motivated the EOV design): filtering the DwC class column cannot match when WoRMS files the name at another rank — class='Actinopterygii' (a Gigaclass; OBIS’s class is Teleostei, 44.2M records) and class='Anthozoa' (a Subphylum; OBIS uses Hexacorallia/Octocorallia) both matched nothing. AphiaID subtree walking is rank-agnostic and immune to this.

  • Parity: .h3t_idx_eov_sql() is a fifth copy of the calc_indicators() ES(n) term and is pinned cell-for-cell by the new tests/testthat/test-eov-parity.R.

obisindicators 0.4.2

  • Vignette H3 tile maps now actually render (the mapgl/MapLibre chunks that 0.4.1 still left as code-only):
    • vignette("h3t") renders the interactive ES50 hexagon map; vignette("taxon_children") renders the Cetacea-records map and the SPUE map. These are client-side MapLibre widgets — tiles are fetched from the deployed h3t service in the reader’s browser, so they need no store/S3 at build time.
    • New Remote dependency: the maps require the h3t-antimeridian fix in mapgl (renders H3 hexagons that cross the dateline), pinned via Remotes: mapgl=bbest/mapgl@fix/h3t-antimeridian (walkerke/mapgl#211). Switch to upstream mapgl once that PR merges.
    • Fixed a latent bug in the h3t map example — interpolate(values=) now has the same length as stops= (a 3-stop viridis ramp), which previously would have errored had the chunk been evaluated.
    • vignette("scaling") stays code-only: every chunk runs live benchmark queries against the deployed DuckDB store (no map widgets), which CI cannot reach.

obisindicators 0.4.1

  • Vignettes now render their evaluable R chunks on the pkgdown site instead of showing code-only:
    • vignette("h3") runs the full h3-grid → calc_indicators() → gmap_indicator() pipeline on shipped occ_1M and renders the ES(50) map (only the deckgl install/demo stays code-only).
    • vignette("taxon_children") now renders the generated WITH RECURSIVE tile SQL and tile URLs from obis_h3t_sql(aphiaid=) / obis_spue_sql() (pure builders, no store needed); only the DB-connection and mapgl widget chunks stay code-only.
    • vignette("h3t") suppresses package-load messages so the evaluated obis_h3t_sql() output is clean.
    • Chunks that genuinely require the deployed S3 / DuckDB store / h3t tile service (vignette("scaling"), the build/deploy/map chunks) remain illustrative code, as they cannot run in CI.

obisindicators 0.4.0

  • Automatic per-tile spatial pruning via hex_prune (supersedes 0.3.0’s client-side {{bbox}} placeholder). The tile bbox is fully determined by the z/x/y tile address, so the client no longer states it — the h3t server derives each tile’s covering coarse H3 cells from z/x/y and injects the prune itself:
    • build_obis_h3_duckdb() now materializes a coarse H3-parent column hex_prune = h3_cell_to_parent(cell_id, LEAST(res, H3T_PRUNE_RES)) (res 3) on occ_h3 and idx_h3 and clusters both by (res, hex_prune, cell_id). This replaces the interim lat/lng clustering — pruning on the H3 index is 2D (tighter than a latitude band), needs no extra float columns, and the covering ids are canonical H3 (they match across the R build and the server with no version drift). Store schema change — rebuild, or migrate with data-raw/migrate_add_spatial_cluster.R (drops lat/lng, adds hex_prune).
    • obis_h3t_sql() / obis_spue_sql() now emit plain per-resolution SELECTs — the bbox_placeholder argument is removed. The server (MarineSensitivity/server/h3t, CalCOFI/api-h3t-py) rewrites the query to add hex_prune IN (<covering cells>) to any scan of a table carrying that column; stores without it are untouched.
    • The math is unchanged and still pinned to calc_indicators() / calc_spue(); test-h3t-prune.R asserts the prune is result-preserving (a hex_prune-pruned scan + the server’s outer centroid filter returns exactly the same cells and values as the unpruned scan).

obisindicators 0.3.0

  • Spatial (bbox) tile pruning (interim — the {{bbox}} placeholder and lat/lng clustering here were replaced by the hex_prune approach in 0.4.0; kept for history). Live occ_h3 / idx_h3 tile maps were pruned per tile instead of aggregating the whole globe for every tile:

obisindicators 0.2.0

  • Added WoRMS taxonomy children resolution and an effort proxy (SPUE) so OBIS can be filtered by any WoRMS AphiaID at any rank from the local snapshot (see vignette("taxon_children"), vignette("scaling")):
    • obis_taxon_children() / obis_taxon_subtree_sql() recursively walk a taxon table (baked into the store; data-raw/build_taxon_parquet.R + data-raw/migrate_add_taxon.R) to return every descendant taxon.
    • obis_h3t_sql(aphiaid=) serves arbitrary-rank children maps by filtering occ_h3.aphiaid to the resolved subtree via a WITH RECURSIVE CTE.
    • calc_spue() (R reference) + obis_spue_sql() compute the presence-only effort proxy records(target subtree) / records(effort subtree) per cell, pinned by test-spue-parity.R.
  • Added an H3 tiling (h3t) workflow to serve indicators as on-demand H3 hexagon map tiles (see vignette("h3t")):
    • build_obis_h3_duckdb() builds an authoritative DuckDB store from OBIS open-data parquet — a precomputed all-taxa indicator layer (idx_h3, res 1–7) plus a species-level store (occ_h3, tiers 3/5/7) for on-the-fly taxon/year-filtered queries. The ES50/Shannon/Simpson/richness math is the SQL translation of calc_indicators(), pinned by a new parity test.
    • obis_h3t_sql() / obis_h3t_url() compose the validated read-only SELECT and the base64-encoded tile URL for the h3t service (MarineSensitivity/server/h3t) and mapgl::add_h3t_source().
    • canonical SQL in inst/sql/; server build driver in data-raw/build_obis_h3_duckdb.R.

obisindicators 0.0.2

  • Renamed functions for consistency:
  • Fixed gmap_indicator() to use default Robinson projection.
  • Updated vignettes with name changes and use of “indicators” over “metrics”.
  • Supplemented documentation for calc_indicators() with expected input and output columns to data frame.
  • Added documentation for occ_fk and occ_1960s to occ_2010s
  • Made generation of occ_* datasets more reproducible with set.seed() and sampled versions of dataset to minimize file size on Github in data-raw/occ.R.

obisindicators 0.0.1

  • Added a NEWS.md file to track changes to the package.