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Changelog

Source: NEWS.md

BioticExplorerServer 0.8.0

2026-06-19

  • Added incremental update refinements to updateDatabase(). Progress reporting is now concise by default, interactive sessions use a progress bar, and verbose = TRUE still exposes delivery-level logging. Metadata scans stop after the first changed delivery in a year while still tracking post-download baselines so later additions, removals, and changes are detected reliably.
  • Updated updateDatabase() to refresh the cruise-series, gear, taxa, and coded-field reference tables on every run. Reference tables are replaced together only after all downloads succeed, and fresh cruise-series and gear mappings are used immediately for changed annual data.
  • Improved resilience for incremental updates. Missing deliveries that return HTTP 404 during metadata lookup are skipped with one aggregate warning, while other HTTP failures remain fatal, and incremental writes from data.table inputs now target the actual database columns correctly.
  • Added start time, successful finish time, and elapsed minutes to the log output from compileDatabase() and updateDatabase().
  • Added the missing dbplyr runtime dependency required by indexDatabase() on fresh R installations.
  • Added regression tests covering concise and verbose update progress output, unavailable deliveries, data.table writes, and operation timing helpers.

BioticExplorerServer 0.7.0

2026-06-18

  • Added updateDatabase(), which uses delivery-level API metadata to download and atomically replace only years whose data changed, were added, or were removed.

  • Added database schema and package-version metadata. An incompatible schema now triggers a full sibling rebuild through compileDatabase() and a validated swap.

  • Fixed overwrite = TRUE so existing annual data are replaced instead of duplicated.

  • Added a delivery manifest containing metadata-only change signals from the Biotic API.

  • Added prepareReferenceCodes(), which pulls the simple coded KeyType fields (sex, maturationstage, missiontype, nation, …) from the NMD Reference API and writes them to the DuckDB database as the long-format codeindex table via compileDatabase(). This lets agents and the Shiny app decode these fields offline with a join instead of a per-code API call. Editor-identity columns (updatedBy/insertedBy/timestamps) are stripped on build so no staff usernames enter the database. Composite taxa/sex-keyed tables (specialstage, eggstage, …) are left to the API.

BioticExplorerServer 0.6.0

2026-06-15

  • Added taxa reference export to DuckDB as the taxaindex table through downloadDatabase().
  • Updated database examples and agent guidance for the taxa index.
  • Removed generated documentation output that exposed local machine-specific database paths.

BioticExplorerServer 0.5.0

2026-05-19

Bug fixes

  • Fixed a critical crash caused by self-referential default arguments (icesAreas = icesAreas, cruiseSeries = cruiseSeries, gearCodes = gearCodes) in bioticToDatabase(), downloadDatabase(), and downloadDatabaseToFiles(). These now default to NULL and load the bundled package data in the function body.
  • stndat merge changed from right join (all.y = TRUE) to full outer join (all = TRUE), so empty fishing stations (tows with no catch) are now correctly preserved in $stnall with commonname = NA instead of being silently dropped.
  • Individual records that cannot be matched to a catch sample entry now emit a warning and are excluded from $indall before age merges, rather than stopping execution with an error.
  • Added a guard for empty age data (nrow(age) == 0) before computing $ageall to prevent crashes on surveys with no age readings.
  • Fixed progress bar maximum in bioticToDatabase() (10 → 11 steps) and indexDatabase() (6 → 7 steps).
  • Fixed outdated API URL in downloadDatabaseToFiles() (old tomcat7.imr.no:8080 → biotic-api.hi.no).
  • Fixed typo “Gead codes” → “Gear codes” in compileDatabase().

Other changes

  • Added pkgdown website.
  • Added comprehensive @return documentation for all exported functions.
  • Added NEWS.md.

BioticExplorerServer 0.4.4

2025-02-25

  • Updated Biotic API URL to https://biotic-api.hi.no.
  • Rewrote prepareTaxaList() to handle missing names in the taxa reference list.
  • Updated reference API URL.

BioticExplorerServer 0.4.3

2025-01-22

  • Completed conversion from MonetDB to DuckDB.
  • Fixed dbPath handling on Windows.
  • Added read_only connection mode documentation to README.

BioticExplorerServer 0.4.x

2022–2024

BioticExplorerServer 0.3.x

2021

  • Replaced sp and rgdal dependencies with sf for spatial operations.
  • Fixed CRS transform issue on Linux (sf#1419).
  • Fixed ICES area CRS assignment.
  • Fixed a critical issue with NA commonname values crashing database compilation.
  • Stopped converting station dates with as.Date to preserve time-zone information.

BioticExplorerServer 0.2.x

2020–2021

  • Transitioned from MonetDBLite to DuckDB as the embedded database engine.
  • Added ICES area calculation using bundled simplified polygons.
  • Added cruise series information and index (csindex table).
  • Added age reading data ($ageall / ageall table).
  • Added gear category classification.
  • Added downloadDatabaseToFiles() for saving XML and RDS outputs.
  • Improved performance of indexDatabase().

BioticExplorerServer 0.1.0

2020-05-14