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CalCOFI integrated database release v2026.10.13

RELEASE_NOTES.md on gs://calcofi-db/ducklake/releases/v2026.10.13

Release date: 2026-10-13 · promoted (latest.txt)

CalCOFI 2607 (2026-07-3322): the corrected preliminary CTD files

The CTD team re-published 20-2607SH_CTDPrelim.zip on calcofi.org on 2026-10-12 (Ben Gire). The Shared Drive copy the pipeline reads was replaced with it the next day. The bins and columns are the same as before. Diffed per measurement type against the shards v2026.10.08 was cut from, nothing outside 2607 changed (0 of 4,931 obs and 0 of 6,093 obs_ctd_full cruise × type cells). In 2607:

  • A new CTD quality code, 4: a corrected chlorophyll-a or nitrate estimate that came out negative is now 0 instead of blank. It is registered in metadata/measurement_qual.csv as set_to_zero, and qual_ok keeps it: the zero is a real value and counts in averages, integrated chlorophyll and anomalies. This fills about 1,000–2,900 bins per estimate (est_chlorophyll_a_*, est_nitrate_*).
  • The nitrate and chlorophyll estimates were recalibrated by the provider: nitrate by up to 1.0 µM (est_nitrate_sta_corr), chlorophyll by up to 0.003 µg/L.
  • Sensor-2 oxygen (oxygen_umol_kg_2_*) was recalibrated (up to 1.06 µmol/kg), and 2,213 of its values were blanked and flagged 9 on the early casts. The averaged oxygen and temperature are unchanged: the pipeline already used sensor 1 alone on casts 1–6 (flag_overrides.csv, from the provider's cruise note that the secondary temperature sensor was faulty; question Q37), and rebuilds every pair with combine_sensor_pair_sql().
  • btl_temperature is new for 2607 (2,396 bins: the provider filled the file's BTL_Temp column). Two bottles' nutrients moved out of their 1 m bins.
  • Derived products: chl_integrated changed on 72 casts (mean +0.01 mg/m², at most +0.75), and chl_integrated_depth deepened on 54 casts (mean +5 m, at most +132 m), because the zeros now count as good bins instead of ending the integral. The mixed-layer depths, chl_max_depth, spiciness0 and sigma_theta_ave are unchanged.

Anomalies for the derived CTD products, and a seasonal baseline

Rasmus Swalethorp asked for both (2026-10-06, 2026-10-07). The climatology table (calcofi4db 4.24.0) now carries:

  • Per-cast baselines for the derived products in sample_measurement: the three mixed-layer depths (mld_sigma_theta_002, mld_sigma_theta_0125, mld_temperature_02), chl_max_depth, chl_max and chl_integrated. They use the same rules (station, cruise month, 1993–2013, at least 5 cruises). Such a value has no depth, so its row's depth_bin is NULL. relationships.json declares that column as nullable_key_columns.
  • A seasonal baseline beside the monthly one: new columns quarter, season_mean, season_sd, season_n, season_n_cruises, by the quarter of the cruise's month (Q1 Jan–Mar … Q4 Oct–Dec). They are set on every month of a quarter that has at least 5 cruises. Where only the season passes (mostly the northern lines 60–73.3), the row has a seasonal mean and a NULL clim_mean.

obs_env / obs_bio year and quarter are the cruise's, not the cast's calendar date. 2607's inshore 93.3 casts were worked on 30 June and now fall in Q3 with the rest of the July cruise, the same season their baseline is filed under.

Consumers: a row that exists is no longer always a monthly baseline. Test clim_mean IS NOT NULL before subtracting. A per-bin join on depth_bin = <n> never matches a per-cast cell. Columns were appended, never renamed.

The US EEZ, territorial sea and contiguous zone are areas you can filter by

sample_spatial had no memberships for the three US maritime zones, because the NOAA limits they were drawn from are lines (workflows#169). They are now polygons of the Pacific coast from the Marine Regions Maritime Boundaries Geodatabase (Flanders Marine Institute; EEZ v12, 12 NM and 24 NM v4; CC BY 4.0), so the Explorer's Area filter and Regions lens can use them. The layer ids and names are unchanged: 200NM EEZ (0–200 NM), 12NM Territorial Sea (0–12 NM) and 24NM Contiguous Zone, the band from 12 to 24 NM. All three are named Pacific Coast.

BOEM's 2023 Wind Planning Areas, which BOEM rescinded on 30 July 2025, are no longer an area layer: spatial and sample_spatial drop BOEM Wind Planning Areas (in v2026.10.08, 793 samples in 3 areas). The Explorer draws BOEM's current wind leases, the rescinded planning areas and three other BOEM layers from the Ocean Metrics gazetteer instead; those are map layers only, not areas you can filter samples by.

Seabird and marine mammal surveys of July 2021 and August 2022 now have their cruise

farallon_bird-mammal matches each survey to the CalCOFI cruise its observers rode by the stations occupied the same day. The track was the ichthyoplankton tows alone, so the two surveys on cruises without a tow, CAC2021_7 (2021-07-33P4) and CAC2022_8 (2022-08-39C2), had a NULL cruise_key (workflows#74). The track now includes the CTD casts. Fronts_0711, a CCE-LTER process cruise with no CalCOFI cruise, stays NULL. CAC2021_7's 466 transects carry no observations in the source (question Q11, also open for January 2021 and October 2022), so 2021-07-33P4 is a third farallon cruise with effort and no sightings.

Contents (generated)

table rows
climatology 1,828,215 partitioned
cruise 845
dataset 19
dataset_taxon 1,940
fish 10,796
grid 225
grid_crosswalk 673
lookup 26
measurement_type 231
obs 33,326,406 deprecated → obs_bio, obs_env (objects removed in next)
obs_attribute 455,300
obs_bio 1,586,795
obs_env 31,739,611 partitioned
region 4
sample 1,467,016
sample_measurement 658,009
sample_spatial 1,387,517
ship 49
spatial 3,122
spatial_attribute 36,261
taxon 2,606
taxon_group 438
obs_ctd_full 281,888,334 supplemental
obs_mets_full 19,926,523 supplemental
sample_root 419,050 supplemental

25 tables, 374,740,011 rows, 2.74 GB.

Datasets (19): calcofi_2022-edna, calcofi_bottle, calcofi_ctd-cast, calcofi_ctd-derived, calcofi_dic, calcofi_mets, calcofi_phyllosoma, calcofi_phytoplankton, cce-lter_euphausiids, cce-lter_iron, cce-lter_picoplankton-bacteria, cce-lter_zoodb, cce-lter_zooscan, cdfw_dungeness-crab, farallon_bird-mammal, sio_mesopelagic-fish, sio_pic-zooplankton, swfsc_cufes, swfsc_ichthyo

Validation: 97 pass / 0 fail / 4 skip (consumer-contract suite, 2026-10-14T00:08:13Z).

Software: calcofi4db 4.24.0, calcofi4r 1.28.0.

How to cite

CalCOFI (2026). CalCOFI Integrated Database, release v2026.10.13 [Data set]. Scripps Institution of Oceanography, NOAA Fisheries, and California Department of Fish and Wildlife. https://doi.org/10.5281/zenodo.23354090

Cite the source datasets you use alongside the release:

Access

con <- calcofi4r::cc_get_db(version = "v2026.10.13")

con = calcofi4py.cc_get_db("v2026.10.13")

Parquet: https://storage.googleapis.com/calcofi-db/ducklake/releases/v2026.10.13/parquet/{table}.parquet; full history: RELEASES.md.