CalCOFI integrated database release v2026.08.07

Release date: 2026-08-07

The Wilkinson CTD archive and three data stages

JRW's Shared-Drive _CTDFinalDB archives are ingested alongside calcofi.org's, adding 45 gap cruises; data_stage splits into final, preliminary_with_bottle and preliminary_without_bottle (the sensor-only tier reaches the release with no salinity or oxygen corrections). obs_ctd_full 212.4 M → 274.9 M rows; obs +6.2 M.

Taxon authorities are cross-referenced and lineages completed

Birds key itis: because WoRMS bird taxonomy lags, but nothing populated worms_id for them, so a consumer joining on worms_id matched zero rows for every seabird and marine mammal (92 % of the Farallon census). ensure_taxon_xref() crosswalks TSN ↔ AphiaID by exact id; taxonomic_status is fetched with status_checked instead of stamped "accepted"; ancestors are first-class taxa with rank order from one vocabulary. Four new release gates cover it.

Coverage is measured, never asserted

coverage_temporal/coverage_spatial were hand-written in each ingest and seven of fifteen were wrong at v2026.08.06; observed_coverage() now measures both from the assembled core and the measurement surfaces coordinate bugs the prose hid. Bulk parquet moved outside the repo to $CALCOFI_STAGE_DIR; the JSON sidecars stay tracked in git.

Packages: calcofi4db 3.5.0–3.9.3; calcofi4r 1.5.0–1.5.4 (shared transect/climatology/anomaly functions, summer-anomaly vignette).

Contents (generated)

18 tables, 323,733,662 rows, 2.12 GB.

Datasets (15): calcofi_bottle, calcofi_ctd-cast, calcofi_dic, calcofi_mets, calcofi_phyllosoma, calcofi_phytoplankton, cce-lter_euphausiids, cce-lter_picoplankton-bacteria, cce-lter_zoodb, cce-lter_zooscan, farallon_bird-mammal, sio_mesopelagic-fish, sio_pic-zooplankton, swfsc_cufes, swfsc_ichthyo

Validation: 28 pass / 0 fail / 4 skip (consumer-contract suite, 2026-08-07T13:41:56Z).

How to cite

CalCOFI (2026). CalCOFI Integrated Database, release v2026.08.07 [Data set]. Scripps Institution of Oceanography, NOAA Fisheries, and California Department of Fish and Wildlife. https://calcofi.io/db-schema/?v=v2026.08.07

Cite the source datasets you use alongside the release:

• calcofi_bottle — CalCOFI. (2023). CalCOFI Bottle Database 194903-202105. CalCOFI.org. · license pending
• calcofi_ctd-cast — CalCOFI. (2023). CalCOFI CTD Cast Files. CalCOFI.org. · license pending
• calcofi_dic — Keeling, C.D.; Lueker, T.J.; Emanuele, G.; Dickson, A.G.; Martz, T.R.; Wolfe, W.H.; Mau, A. (2025). Discrete profile dissolved inorganic carbon, total alkalinity, water temperature and salinity measurements for CalCOFI (NCEI Accession 0301029). NOAA NCEI. https://doi.org/10.25921/3w9f-jd72 · CC BY 4.0
• calcofi_mets — CalCOFI. Underway (METS) TSG/Meteorology Data. CalCOFI.org. · license pending
• calcofi_phyllosoma — citation pending · license pending
• calcofi_phytoplankton — citation pending · license pending
• cce-lter_euphausiids — citation pending · license pending
• cce-lter_picoplankton-bacteria — Landry, M. (2004-2023). Picoplankton and Bacteria Abundance (CalCOFI Cruise). CCE LTER. · license pending
• cce-lter_zoodb — citation pending · license pending
• cce-lter_zooscan — citation pending · license pending
• farallon_bird-mammal — citation pending · license pending
• sio_mesopelagic-fish — Koslow, J. Anthony (2016). CalCOFI Trawl Data. In California Cooperative Oceanic Fisheries Investigations (CalCOFI): Acoustic and Trawl Data. UC San Diego Library Digital Collections. https://doi.org/10.6075/J0BZ64DH · CC BY 4.0
• sio_pic-zooplankton — citation pending · license pending
• swfsc_cufes — citation pending · license pending
• swfsc_ichthyo — NOAA Fisheries SWFSC. CalCOFI Ichthyoplankton Database. · license pending

Access

con <- calcofi4r::cc_get_db(version = "v2026.08.07")

con = calcofi4py.cc_get_db("v2026.08.07")

Parquet: https://storage.googleapis.com/calcofi-db/ducklake/releases/v2026.08.07/parquet/{table}.parquet; full history: RELEASES.md.