Changelog

Source: NEWS.md

calcofi4r 1.3.0

Dataset-driven ERD coloring (stroke-based)

• cc_erd() stroke-only coloring Entity classDefs now color the table outline (stroke) instead of the fill, so multi-row entities read cleanly. The colors argument is unchanged.
• cc_erd_color_map() New exported helper that builds the colors list for cc_erd() from authoritative table → dataset metadata: single-owner tables take their dataset color, shared/multi-dataset tables take a neutral color, and per-table overrides win. Drives the dataset-source coloring on the schema site (calcofi.io/schema).

calcofi4r 1.1.10

Local data download and table filtering in cc_get_db()

• local_data parameter cc_get_db(local_data = TRUE) now downloads parquet files to a local cache directory and creates TABLEs instead of remote VIEWs. Files are only downloaded if missing or if refresh = TRUE, making repeated calls idempotent.
• tables parameter cc_get_db(tables = c("species", "ichthyo", ...)) filters which tables to load from the catalog. Useful for excluding large tables like CTD data when building app-specific databases.

calcofi4r 1.1.9

Native GEOMETRY storage in cc_get_db()

• storage_compatibility_version = 'latest' cc_get_db() now uses a named DuckDB driver with autoload_known_extensions and latest storage format, matching calcofi4db’s get_duckdb_con() pattern. Ensures native GEOMETRY type is used for spatial queries.

calcofi4r 1.1.8

Require DuckDB >= 1.5.1 for native GEOMETRY

• Requires duckdb >= 1.5.1 Added minimum version constraint to ensure the native built-in GEOMETRY type is available for spatial queries.

calcofi4r 1.1.7

ERD diagrams render as PNG in Quarto via mermaid-cli

• knit_print.cc_erd() now renders Mermaid diagrams to PNG via mmdc (mermaid-cli) at 2x scale with transparent background, saving to knitr::fig_path() for proper Quarto HTML output. Lightbox applies automatically via _quarto.yml settings.
• Fallback chain: mmdc → DiagrammeR::mermaid() htmlwidget → raw mermaid code block.

calcofi4r 1.1.6

New cc_tbl() unified table accessor

• cc_tbl() New function providing unified access to any CalCOFI database table. Returns lazy dplyr::tbl() for non-spatial tables, sf object for spatial tables (via DuckDB EXCLUDE + ST_AsWKB), and pivoted-wide sf for _spatial table (requires layer argument). Optional geom_col selects alternate geometry columns (e.g., geom_ctr for grid centroids).

calcofi4r 1.1.5

• cc_erd() gains a rels parameter to accept pre-parsed relationship lists inline (as alternative to rels_path), matching the calcofi4db build_relationships_json() list format.
• knit_print.cc_erd() now outputs raw mermaid code blocks for Quarto native rendering (respects mermaid-format: png and lightbox settings in _quarto.yml) instead of rendering via DiagrammeR widget.

calcofi4r 1.1.4

• Enable reading of partitioned parquet files, eg table ctd_measurement (15 GB) partitioned by cruise_key, in online DuckDB for improved performance and scalability.

calcofi4r 1.1.3

• Fixed database functions: cc_get_db(), cc_list_versions()
• Updated vignette “Get started” to using the online DuckDB and latest functions.
• Added deprecation warnings to old functions that made API calls to Postgres database in favor of new direct data querying abilities with the online DuckDB.

calcofi4r 1.1.2

• Added database functions to make views, starting with casts_extra: cc_make_view(), cc_list_view_templates()

calcofi4r 1.1.1

• Added cc_read_sf() to read spatial tables in DuckDB connection as sf objects.

calcofi4r 1.1.0

• Highlights DuckDB as the primary data access method
  
• Quick Start Section - Shows cc_get_db() as the main entry point
• Convenience Functions - Documents the new read functions:
  • cc_read_larvae()
    
  • cc_read_bottle()
  • cc_read_cast()
  • With filter examples using dplyr syntax
• Version Control Section - Shows how to:
  • List versions with cc_list_versions()
  • Connect to specific versions
  • View release info and notes
• Custom Queries Section - Documents cc_query() and cc_describe_table()
• API Functions - Kept the existing API functions as a secondary option

calcofi4r 0.9.0

• Migrated functions.R from CalCOFI Integrated Assessment Shiny App that utilizes a local or remote duckdb of CalCOFI data (rather than an API).

• TODO: add @concept to functions (to move out of Other heading in Reference) and build vignette (like Get started) demonstrating use of these new functions.

calcofi4r 0.8.1

• Added cc_db_catalog() to list tables and columns in the database with descriptions (possibly formatted in markdown) by reading from new CalCOFI API endpoints: api.calcofi.io/db_tables, api.calcofi.io/db_columns.

calcofi4r 0.8.0

• Removed non-ASCII characters to allow install of package on Windows.

• Used stars::st_as_stars() to use terra::rast() SpatRaster with mapview::mapView() (vs retired raster::raster()).

calcofi4r 0.7.0

• Added interpolation functions pts_to_rast_idw() and rast_to_contours(). Renamed map_contours() to pts_to_contours_gam() and moved concept from “visualize” to “analyze”.

• Added to cc_places:

  • “NOAA Aquaculture Opportunity Areas”
  • “BOEM Wind Planning Areas”
  • “National Marine Sanctuaries”: “Chumash Proposed Action”

calcofi4r 0.6.0

• Added database connection functions cc_db_connect() and create_index().

calcofi4r 0.5.5

• Fixed nearshore cc_grid to include sta_pos == 60. Renamed cc_grid_areas to cc_grid_zones with new categories for sta_shore (“nearshore” OR “offshore”) and sta_pattern (“standard”, “extended”, “historical”) per #4. Updated cc_places to have the 6 combinations of cc_grid_zones.

calcofi4r 0.5.4

• Added cc_places with three categories for places: 1) CalCOFI (Core, Extended, Nearshore, Offshore); 2) Integrated Ecosystem Assessment (California Current); and 3) National Marine Sanctuary (Cordell Bank, Channel Islands, Greater Farallones, Monterey Bay, Olympic Coast). Augmented cc_grid* with missing cells to reduce slivers when intersecting.

calcofi4r 0.5.3

• cc_grid_area -> cc_grid_areas data for showing study areas with combinations of sta_dpos nearshore (5), offshore (10) and outside (20); where area_dpos can be one of: "5", "10", "20", "5,10", "10,20" or "5,10,20"

calcofi4r 0.5.2

• Added cc_grid, cc_grid_ctrs showing the CalCOFI station sampling at varying seperation distances of station positions (sta_pos) in the CalCOFI coordinate system from nearshore (5), to offshore (10) to outside the 113 station extended repeated area (20), per Station Positions – CalCOFI}

calcofi4r 0.5.1

• handle defaults with plot_depth(), streamline headings in article and descriptions in functions

calcofi4r 0.5.0

• Added plot_depth() and example data bottle_temp_depth
• stations_t_degc -> bottle_temp_lonlat

calcofi4r 0.4.1

• rename tbl_to_contour_ply() to map_contours()

calcofi4r 0.4.0

• Added tbl_to_contour_ply() and example data area_calcofi_extended stations_t_degc

calcofi4r 0.3.0

• Added get_cruises() and get_raster() for reading from the CalCOFI API.
• Added map_raster() and plot_timeseries() for visualizing.
• Added “Get started” vignette and README.Rmd -> README.md with example usage

calcofi4r 0.2.0

• Added get_variables(), get_timeseries() for reading from the API at https://api.calcofi.io

calcofi4r 0.1.2

• ∆ order of stations columns

calcofi4r 0.1.1

• Added authors

calcofi4r 0.1.0

• Bumped version. Have functions for Analyze (get_oceano_var_aoi()) and Visualize (plot_timeseries()), plus Data (bottle, dic, stations).

calcofi4r 0.0.0.9000

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