Package index

Cloud Storage (GCS)

functions for Google Cloud Storage operations

cc_stage_dir(): Local Staging Root for Bulk Data
cc_stage_path(): Path Within the Local Staging Root
check_release_complete(): Assert a frozen release is structurally complete
cleanup_gcs_obsolete(): Clean up obsolete GCS directories from dataset renames
copy_gcs_file(): Server-side copy between GCS paths
create_gcs_manifest(): Create a manifest of current GCS files
delete_gcs_prefix(): Delete all objects under a GCS prefix
gcs_object_md5() local_md5_base64(): The MD5 of a GCS object, as GCS reports it (base64), or NA when it does not exist
get_calcofi_file(): Get a CalCOFI file from the immutable archive
get_gcs_file(): Get a file from Google Cloud Storage
get_historical_file(): Get historical file from a specific date
get_manifest(): Get manifest for a specific date
list_calcofi_files(): List CalCOFI files from manifest
list_gcs_files(): List files in a GCS bucket/prefix
list_gcs_versions(): List versions of a file in GCS archive
promote_release(): Promote a release to latest.txt
put_gcs_file(): Upload a file to Google Cloud Storage
read_promoted_release(): Read the currently promoted release, authoritatively
sync_to_gcs(): Sync local files to GCS, skipping unchanged files

Parquet

functions for Apache Parquet file operations

add_parquet_metadata(): Add metadata to Parquet file
csv_to_parquet(): Convert CSV file to Parquet format
export_parquet(): Export a DuckDB Table or Query to Parquet
get_parquet_metadata(): Get Parquet file metadata
read_parquet_table(): Read a Parquet table
upload_parquet(): Upload Parquet file to GCS
write_parquet_table(): Write data to Parquet format

DuckDB

basic DuckDB database operations

close_duckdb(): Disconnect from DuckDB and shutdown
create_duckdb_from_parquet(): Create DuckDB from Parquet files
create_duckdb_views(): Create views from a manifest
duckdb_to_parquet(): Export DuckDB table to Parquet
get_duckdb_con(): Get a DuckDB connection
get_duckdb_tables(): Get table information from DuckDB
load_duckdb_extension(): Install and load DuckDB extension
save_duckdb_to_gcs(): Save DuckDB to GCS
set_duckdb_comments(): Set table and column comments in DuckDB

Working DuckLake

functions for the internal Working DuckLake with provenance tracking

add_provenance_columns(): Add provenance columns to a data frame
get_working_ducklake(): Get Working DuckLake connection
ingest_dataset(): Ingest Dataset into Working DuckLake
ingest_to_working(): Ingest data to Working DuckLake
list_working_tables(): List tables with provenance in Working DuckLake
load_prior_tables(): Load Tables from a Prior Ingest's Parquet Directory
query_at_time(): Query Working DuckLake at a point in time
save_working_ducklake(): Save Working DuckLake to GCS
strip_provenance_columns(): Strip provenance columns from data

Frozen Releases

functions for creating and managing frozen DuckLake releases

compare_releases(): Compare two frozen releases
freeze_release(): Freeze a release of the DuckLake
get_release_metadata(): Get metadata for a frozen release
list_frozen_releases(): List available frozen releases
upload_frozen_release(): Upload Frozen Release to GCS
validate_for_release(): Validate Working DuckLake for release

Read

functions reading data, particularly from CSV files in the Google Drive CalCOFI data folder

create_redefinition_files(): Create Redefinition Files for Tables and Fields
determine_field_types(): Determine Field Types for Database
read_csv_files(): Read CSV Files and Their Metadata
read_csv_metadata(): Read CSV Files and Extract Metadata

Transform

functions to transform data, after reading data and before ingesting into the database

detect_csv_changes(): Detect Changes in CSV Files
display_csv_changes(): Display CSV Changes in a Formatted Table
print_csv_change_stats(): Print CSV Change Statistics
transform_data(): Transform Data for Database Ingestion

Check

functions for data validation and integrity checking

check_cruise_coverage(): Cruises that carry samples but no observations — the silent-loss guard
check_data_integrity(): Check Data Integrity for Ingestion
check_dataset_taxon(): The ingest asserts its own taxon crosswalk (taxon plan D6)
check_multiple_datasets(): Check Multiple Datasets for Integrity
check_taxon_ids(): The taxa that no authority resolved, per dataset — reported, and gated
check_taxon_registries(): Every dataset a taxon registry names must be one some dataset supplies
check_ungridded_obs(): Observations that resolve no CalCOFI grid cell — reported, never dropped
render_integrity_message(): Render Data Integrity Check Message

Validate

functions for referential integrity validation and flagging invalid rows

bounds_datatable(): Render a bounds check as the standard notebook table
check_measurement_bounds(): Check measured values against the registry's declared bounds
delete_flagged_rows(): Delete Flagged Rows from Database
drop_out_of_bounds(): Delete values outside their declared bounds
flag_invalid_rows(): Flag and Export Invalid Rows
validate_dataset(): Run All Validations for a Dataset
validate_egg_stages(): Validate Egg Stage Values
validate_fk_references(): Validate Foreign Key References
validate_lookup_values(): Validate Lookup Values Exist

Ingest

functions for ingesting data into the database (PostgreSQL deprecated, use DuckLake)

changed_inputs(): Which inputs changed since a recorded fingerprint
ingest_csv_to_db() deprecated: Ingest CSV data to PostgreSQL database (DEPRECATED)
ingest_dataset_pg() deprecated: Ingest a Dataset to PostgreSQL (DEPRECATED)
input_fingerprint(): Fingerprint the inputs an ingest's outputs depend on
read_input_fingerprint(): Read a previously recorded input fingerprint
write_input_fingerprint(): Record an input fingerprint next to an ingest's outputs

Version

functions for schema and package versioning

get_schema_versions(): Get Schema Version History
init_schema_version_csv(): Initialize Schema Version CSV
record_schema_version(): Record Schema Version

Utilities

utility functions for database operations (PostgreSQL deprecated)

copy_schema(): Copy Database Schema
get_db_con() deprecated: Get a database connection to the CalCOFI PostgreSQL database (DEPRECATED)

Wrangle

functions for local DuckDB wrangling (keys, IDs, table consolidation)

apply_data_corrections(): Apply Data Corrections
assign_deterministic_uuids(): Assign deterministic UUIDs from composite key columns
assign_deterministic_uuids_md5(): Assign deterministic UUIDs using DuckDB-native md5
assign_sequential_ids(): Assign Sequential IDs with Deterministic Sort Order
build_metadata_json(): Build Metadata JSON for Parquet Outputs
build_relationships_json(): Build Relationships JSON from dm Object
collect_cruise_key_mismatches(): Collect Cruise Key Mismatches
collect_measurement_type_mismatches(): Collect Measurement Type Mismatches
collect_ship_mismatches(): Collect Ship Mismatches
consolidate_ichthyo_tables(): Consolidate Ichthyoplankton Tables into Tidy Format
convert_cruise_key_format(): Convert Old YYMMKK Cruise Key to YYYY-MM-NODC Format
create_cruise_key(): Create Cruise Key from Ship NODC Code and Date
create_lookup_table(): Create Lookup Table from Vocabulary Definitions
derive_measurement_type_datasets(): Derive measurement_type → contributing datasets from the data
enforce_column_types(): Enforce Column Types Before Export
ingest_yaml_to_dataset_df(): Build the dataset registry table from ingest YAML blocks
merge_metadata_json(): Merge Per-Ingest metadata.json into a Release-Level Sidecar
merge_relationships_json(): Merge Multiple Relationships JSON Files
propagate_natural_key(): Propagate Key from Parent to Child Table
read_calcofi_meta(): Read the calcofi YAML block from a single workflow file
read_ingest_yaml(): Read calcofi YAML blocks from ingest_*.qmd front matter
read_relationships_json(): Read Relationships JSON and Optionally Apply to dm
release_excluded_datasets(): Datasets held out of the release by calcofi.in_release: false
replace_uuid_with_id(): Replace UUIDs with Integer Foreign Keys
scan_metadata_gaps(): Scan a metadata sidecar for missing documentation
standardize_site_key(): Standardize Site Key from Line and Station Columns
write_parquet_outputs(): Write Tables to Parquet Files
write_spatial_manifest(): Write Spatial Manifest

Workflow

functions for orchestrating ingestion workflow steps

build_release_table_registry(): Build Release Table Registry from Ingest Manifests
build_targets_list(): Build Targets List from Quarto Frontmatter
finalize_ingest(): Finalize Ingest — Push Parquet Tables to Working DuckLake
integrate_to_working_ducklake(): Integrate Ingest Outputs into Working DuckLake
list_ingest_outputs(): List Available Ingest Outputs
parse_qmd_frontmatter(): Parse YAML Frontmatter from Quarto Notebooks
read_ingest_manifest(): Read Ingest Manifest from GCS
read_ingest_parquet(): Read Ingest Parquet Table from GCS
write_ingest_outputs(): Write Ingest Workflow Outputs to GCS

Display

helper functions for workflow display outputs (GitHub links, validation tables)

dt(): Create Interactive Data Table with CSV Export
github_file_link(): Create GitHub File Link
preview_tables(): Preview Tables with Head and Tail Rows
show_flagged_file(): Show Flagged File Result
show_validation_results(): Show Validation Results with GitHub Links

Version Sync

functions for synchronizing schema and package versions

commit_version_and_permalink(): Commit Version Changes and Get Permalink
complete_version_release(): Complete Version Release Workflow
get_package_version(): Get Current Package Version
suggest_next_version(): Suggest Next Version
update_package_version(): Synchronized Version Management for Package and Database

Visualize

functions visualizing diagnostic outputs, particularly color coded data tables

show_fields_redefine(): Show fields to redefine
show_source_files(): Show source files
show_tables_redefine(): Show tables to redefine

Other

check for other functions or datasets not captured by above categories

CC_DEPTH_MAX_M: Deepest plausible sample depth in the CalCOFI region, metres
CC_PARQUET_WRITER: Pinned parquet writer options for released tables
CC_RELEASE_PREFIX CC_TABLES_PREFIX: Release layout prefixes (bucket-relative)
OBS_VIEW_COLUMNS: The 18 columns of obs, in order
add_cruise_date_span(): Add the observed date span of each cruise to the cruise reference
add_point_geom(): Add Point Geometry Column to a DuckDB Table
add_release_citation(): Write the release citation into a catalog.json list
add_sample_seafloor(): Stamp seafloor_depth_m onto the sample table
append_dataset_taxon(): Stage a dataset's taxon vocabulary in dataset_taxon (taxon plan D1)
append_obs(): Append occurrence-headline rows into the core obs table
append_obs_attribute(): Append sub-occurrence attribute rows into the core obs_attribute table
append_sample(): Append event rows into the core sample dimension
append_sample_measurement(): Append event-level (effort) rows into the core sample_measurement table
apply_taxon_common(): Apply the common-name precedence to the merged taxon table
assemble_core(): Assemble the whole consolidated core from the ingest shards
assemble_core_table(): Assemble one core table from its per-dataset shards
assert_dataset_catalog(): Stop on any non-exempt error finding from check_dataset_catalog()
assert_dataset_citation(): Stop on any non-exempt error finding from check_dataset_citation()
assert_dwc(): Stop when a Darwin Core check found an error
assert_eml(): Stop on any non-exempt error finding from check_eml()
assert_sitemap(): Stop when check_sitemap() found an error
assert_stac(): Stop when check_stac() found an error
assign_grid_key(): Assign Grid Key via Spatial Join
build_climatology(): Build the release's climatology table
build_coverage(): The coverage cube behind the explorer's first paint
build_coverage_stations(): The per-station coverage card: n obs by dataset x year and by dataset x month, for one station
build_dataset_catalog(): Build the dataset catalog record — datasets.json
build_datasets_sitemap(): Build the rows of datasets/sitemap.xml from the record
build_eml(): Build one dataset's EML 2.2 document from the catalog record
build_eml_catalog(): Build an EML document for every dataset in the catalog record
build_grid_reference(): Build the shared grid reference table (deterministic, dataset-independent)
build_obs_slim(): The bio or env realm of obs, browser-shaped — and, since 3.31.0, its physical store
build_release_catalog(): Build the release catalog with per-table hashes and objects
build_sample_root(): Root sampling events with a dense integer id
build_sample_spatial(): Exact polygon membership of every root sample, one layer at a time
build_spatial_layers(): The explorer's boundary-layer sidecar: the registry joined with the release's spatial table
build_stac(): Build the static STAC catalog of a release
build_taxon_group(): Build the taxon_group grouping table (many taxa per group) from the registry
build_taxon_hierarchy(): Build Taxon Hierarchy from Local spp.duckdb via Recursive CTEs
build_taxon_reference(): Build the unified taxon reference table
build_taxon_table(): Build Taxonomic Hierarchy Table from WoRMS
build_versions_json(): Build the versions.json register of every release under a prefix
canonical_path(): Canonical (content-addressed) object path for a table or partition
catalog_findings(): The findings check_dataset_catalog() can report, with their level
cc_calcofi_to_lonlat(): Convert CalCOFI line/station to longitude/latitude
cc_lonlat_to_calcofi(): Convert longitude/latitude to CalCOFI line/station
cc_station_regions(): Region polygons from a station-membership list
check_core_pk_unique(): Fail unless every core table is unique on its primary key
check_cruise_key_integrity(): Fail (or ratchet) the release on a cruise_key that does not hold up
check_dataset_catalog(): Check every record of the dataset catalog
check_dataset_citation(): Check every dataset's citation, license and DOI, structurally and against its authority
check_dataset_meta_split(): Assert that no notebook still carries a descriptive dataset_meta key
check_depth_bounds(): Check depth coordinates against an absolute range
check_depth_vs_seafloor(): Find samples deeper than the seafloor at their position
check_eml(): Check one dataset's EML document
check_eml_catalog(): Check every dataset's EML document
check_obs_pair_parity(): Assert that obs_bio + obs_env hold exactly the rows of obs
check_registry_na_strings(): Reject sentinel strings that should have been empty cells
check_release_relationships(): Measure every declared primary and foreign key on the frozen tables
check_seafloor_nulls(): Classify the samples whose seafloor_depth_m is NULL, by cause
check_sitemap(): Check a generated sitemap
check_stac(): Validate a written STAC catalog
citation_findings() citation_error_findings(): The findings check_dataset_citation() can report, with their level
classify_portal(): Which portal family a URL belongs to
clean_taxon_name(): Normalize a source taxon name for an authority lookup
compat_event_sql(): Rebuild a per-dataset event table as a VIEW over the core sample
compat_measurement_sql(): Rebuild a per-dataset measurement table as a VIEW over obs
complete_cruise_reference(): Complete the cruise reference with cruises no SWFSC site row names
core_output_tables(): Core tables an ingest writes to parquet
core_relationships(): PK/FK spec for the consolidated core tables
core_shard_paths(): Find the per-dataset parquet shards for a core table
ctd_map_columns(): Map an uploaded file's columns onto measurement types
ctd_upload_to_core(): Project an uploaded file into the core obs / sample shape
dataset_distributions(): Every endpoint of one dataset, measured and curated
dataset_meta_descriptive_keys() dataset_meta_structural_keys(): The dataset_meta keys that live in the descriptive sidecar, not the notebook
dataset_since_versions(): The first release each dataset appeared in
declare_measurement_bounds(): Declare valid_min / valid_max on measurement types that already exist
declare_measurement_fields(): Declare category / variable / derivation / is_canonical / NERC ids on measurement types that already exist
derive_cruise_key_on_casts(): Derive Cruise Key on Bottle Casts via Ship Matching
derive_registration_id(): The identifier a portal knows a dataset by, read off its own URL
discover_sample_levels(): Discover a dataset's sampling hierarchy from the core sample table
distribution_changes(): What changed since the last observation
distribution_kinds() distribution_portals() distribution_statuses() registration_statuses() holding_statuses() visibility_values(): The controlled vocabularies of the dataset catalog registries
distribution_targets(): Every external endpoint worth observing: the registry plus the holdings' links
dwc_absence_rule(): Which occurrenceStatus rule a dataset falls under
dwc_archive(): Write a Darwin Core Archive and its manifest
dwc_check(): Check an archive's three tables before it is written
dwc_datasets(): The biological datasets a Darwin Core Archive can be built for
dwc_emof(): Build the ExtendedMeasurementOrFact extension for one dataset
dwc_event(): Build the Darwin Core Event core for one dataset
dwc_findings(): The findings dwc_check() can report, with their level
dwc_manifest_status(): Read a Darwin Core Archive manifest and say whether the OBIS copy is current
dwc_meta_xml(): Generate meta.xml for an Event-core archive
dwc_occurrence(): Build the Darwin Core Occurrence extension for one dataset
dwc_registries(): Read the three registries a Darwin Core Archive needs
dwc_term_map(): The Darwin Core term URI for every column the archive can carry
eml_contact_address(): The CalCOFI role address used as the EML contact of last resort
eml_findings(): The findings check_eml() can report, with their level
ensure_interim_ships(): Ensure Interim Ship Entries for Unmatched Ships
ensure_measurement_taxon(): Stage the _measurement_taxon crosswalk in a connection
ensure_taxon_common(): Fetch and cache vernacular (common) names from WoRMS
ensure_taxon_lineage(): Materialize the WoRMS/ITIS lineage build_taxon_reference() reads
ensure_taxon_xref(): Materialize the authority cross-reference .taxon_norm_sources() reads
erddap_globals(): The ERDDAP global attributes of one dataset, from the same record
erddap_grain_description(): What one ERDDAP grain means, in a sentence
export_release_parquet(): Deterministic parquet export of one released table
fetch_erddap_datasets() parse_erddap_all_datasets(): What ERDDAP serves now: allDatasets as a table
fetch_netcdf_manifests(): The netCDF manifests.json of every dataset published by publish_to-netcdf.qmd
fetch_ship_ices(): Fetch Ship Codes from ICES Reference Codes API
fetch_taxon_lineage(): Fetch (and cache) the WoRMS/ITIS lineage for a set of taxon ids
fetch_taxon_xref(): Fetch (and cache) the WoRMS <-> ITIS cross-reference for a set of taxa
format_bbox(): Format a Bounding Box as a Human-Readable Extent
freeze_plan(): Decide, per object, whether to upload or reuse
h3_parent_sql(): H3 parent of a cell as plain SQL (no extension)
holdings_from_sidecars() write_holdings_csv(): The holdings.csv index, generated from the holding sidecars
license_statuses(): The allowed status values of metadata/license.csv
load_gcs_parquet_to_duckdb(): Load a GCS Parquet File into DuckDB
mark_taxon_common_manual(): Tag the hand-picked rows of the registry as source = "manual"
match_by_site_datetime(): Match Records to a Reference Table by Key + Datetime Window
match_cruise_by_track(): Match Records to a Cruise by Space-Time Proximity to an Occupied-Station Track
match_nearest_by_depth(): Match Records to the Nearest Reference Row Along a Continuous Axis
match_ships(): Match Ship Codes Across Datasets Using Multi-Source References
match_station_occupation(): Stamp sample.station_uuid: the SWFSC station occupation an event belongs to
measurement_var_meta(): CF variable metadata from the measurement_type registry
merge_dataset_meta(): Merge a notebook's structural dataset_meta with its descriptive sidecar
merge_taxon_shards(): Merge the per-dataset taxon shards into one authoritative reference
nc_global_atts(): Build the CF/ACDD global attributes for a published dataset
nc_level_put(): Write the data and attributes for one level defined by nc_level_vars()
nc_level_vars(): Build the variable definitions for one level of a nested dataset
nc_profile_atts(): Write the CF Discrete-Sampling-Geometry attributes
nc_profile_def(): Define a CF Discrete-Sampling-Geometry file (profile or trajectory)
nc_profile_write(): Write one chunk of a CF profile file
normalize_citation(): Normalize a citation string for comparison
ns_key(): Namespaced sample_key expression: dataset_key:sample_type:id
obs_view_sql(): obs as a view over obs_bio + obs_env
obs_wide_sql(): SQL that widens long obs rows into one column per measurement type
observation_statuses(): The statuses an observation can report
observe_distributions(): Ask every portal what it says about our external copies
observe_methods(): The observation methods portal.csv may declare
observed_coverage(): Measure Observed Temporal and Spatial Coverage per Dataset
parse_edi_cite() parse_erddap_das() parse_ncei_landing() parse_datacite() parse_doi_bibliography(): Parse a resolver's response into the fields the citation cache carries
parse_registration(): Parse one publish_* cell of dataset_status.csv
plan_dataset_netcdf(): Plan the netCDF shape for a dataset
promote_unreleased(): Turn # Unreleased into the section for a version being cut
prune_taxon_shard(): Prune the taxa references to one dataset's shard
publish_release_notes(): Render and (re)publish RELEASE_NOTES.md for a version
qc_cast_base(): Strip the direction suffix from a CTD cast sample_key
qc_cast_direction(): Direction of a CTD cast sample_key
qc_cast_profile(): Fetch one physical cast's profile, both directions
qc_parse_params(): Parse a rule's params cell into a named list
qc_present_types(): Which measurement types actually exist for a dataset
qc_read_rules(): Read the rule registry, attaching SQL text and parsed params
qc_render_sql(): Substitute {{param}} placeholders into a rule's SQL
qc_run_all(): Run every rule in a registry, one at a time
qc_run_rule(): Execute one rule, returning its findings
qc_stage_reference(): Stage the QC reference tables a rule registry expects
qc_summarize(): Collapse rule results into one row per rule
qc_upload_con(): A connection an uploaded cast can be QC'd on
question_statuses() question_priorities(): The controlled vocabulary of the question registry
questions_datatable(): Render a question registry as the standard notebook table
read_catalog_registries(): Read every registry the dataset catalog joins
read_ctd_upload(): Read any supported CTD upload
read_dataset_sidecar(): Read one descriptive sidecar, metadata/{provider}/{dataset}/dataset_meta.yml
read_dataset_sidecars(): Read every descriptive sidecar under a metadata/ root
read_dataset_status(): Read metadata/dataset_status.csv, the pipeline-stage tracker
read_distribution_observed(): Read metadata/distribution_observed.json
read_distribution_registry(): Read metadata/distribution.csv, the curated endpoints per dataset
read_gear_registry() dataset_gear(): Read metadata/gear.csv, the net-gear registry
read_license_registry(): Read metadata/license.csv, the registry of dataset licenses
read_life_stage_registry(): Read metadata/life_stage.csv, the life-stage registry
read_measurement_type(): Read metadata/measurement_type.csv, refusing a corrupted registry
read_portal_registry(): Read metadata/portal.csv, the portal capability registry
read_questions(): Read a dataset's questions.csv, validated and ranked
read_sbe_asc(): Read a Sea-Bird .asc ASCII export
read_sbe_btl(): Read a Sea-Bird .btl bottle summary
read_sbe_cnv(): Read a Sea-Bird .cnv converted data file
read_sbe_header(): Parse a Sea-Bird * / ** header block
read_taxon_common(): Read the vernacular-name registry
read_taxon_group_rules(): Read the taxon_group rule registry (metadata/taxon_group.csv)
register_measurement_types(): Append new measurement types to the shared registry, safely
release_citation(): The citation for a release of the integrated database
release_notes_section(): The RELEASES.md section that documents a version
release_notes_sections(): Split RELEASES.md into its top-level sections
release_objects(): Describe the objects an exported table consists of
release_sort_keys(): Sort keys (and partition column) for every released table
release_view_tables() substitute_view_tables(): The tables a catalog view reads, and the SQL with them resolved
release_views(): Views a release carries beside its tables
render_release_notes(): Render a version's RELEASE_NOTES.md: narrative + generated appendix
report_ship_matches(): Report Ship Matching Status for a Dataset
report_taxon_overrides(): What each taxon_override.csv row matched, applied to and skipped
resolve_cruise_key(): Resolve cruise_key on an event table by span, designation, then month
resolve_dataset_taxon() build_dataset_taxon(): Fill taxon_key on the dataset_taxon crosswalk (per-dataset vocabulary -> taxon)
resolve_source_accessed(): Resolve each dataset's source_accessed: the ingest's own stamp, else git
sample_arm_self(): Build a sample arm for a single self-contained event table
sample_seafloor(): Seafloor depth at each sample position from a GEBCO GeoTIFF
sbe_split_header(): Recover the column names from a fixed-width Sea-Bird ASCII header
sitemap_findings(): The findings check_sitemap() can report
source_accessed_from_git(): When was a dataset's source last read? Measured from git
stac_collection(): A STAC Collection for one dataset record
stac_findings(): The findings check_stac() can report
stac_item(): A STAC Item for one dataset at one release
stamp_source_access() sources_block(): Record when an ingest read its sources
standardize_species(): Standardize Species Identifiers Using WoRMS/ITIS/GBIF APIs
standardize_species_local(): Standardize Species Using Local spp.duckdb Lookups
summarise_netcdf_plan(): Summarise a netCDF plan as one row
supplemental_core_tables(): Supplemental full-resolution tables declared by the ingests
taxa_rank_reference(): The canonical taxonomic rank ordering (taxa_rank)
taxon_key_of(): Encode an authority-prefixed taxon_key
thin_plan(): Archive-thinning plan: which versions lose their parquet
unescape_unicode(): Decode \\uXXXX escapes in a character vector (what ERDDAP's CSV emits for non-ASCII)
upload_release_objects(): Execute a freeze plan against GCS
upsert_measurement_types(): Replace a measurement type's definition while keeping its curated columns
validate_dataset_catalog(): Validate a datasets.json against the package's JSON schema
write_dataset_catalog(): Write datasets.json and one datasets/{key}.json per dataset
write_distribution_observed(): Write metadata/distribution_observed.json
write_eml_files(): Write eml/{dataset_key}.xml for every built document
write_sitemap_xml(): Write a sitemap XML file (sitemaps.org 0.9)
write_taxon_common(): Write the vernacular-name registry
zenodo_doi_for_tag() zenodo_record_for_tag(): Find the Zenodo record (and DOI) minted for a release tag
zenodo_metadata() citation_cff() write_citation_files(): Metadata for .zenodo.json and CITATION.cff at the workflows repo root