Changelog

Source: NEWS.md

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• Fixed outdated API URL in downloadDatabaseToFiles() (old tomcat7.imr.no:8080 → biotic-api.hi.no).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.

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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.

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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.

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BioticExplorerServer 0.4.x

2022–2024

• Increased download timeout limit.
• Fixed a bug in the age element of bioticToDatabase().
• Fixed a bug in calculation of numberofreads in $ageall.
• Removed debugging messages from prepareCruiseSeriesList().
• Added all age readings to $ageall. Fixed a warning in prepareCruiseSeriesList().
• Turned off s2 for ICES area determination to improve spatial join compatibility.
• Fixed crash in compileDatabase() → indexDatabase().
• Fixed default path for the index file.

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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.

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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().

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BioticExplorerServer 0.1.0

2020-05-14

• Initial release.
• compileDatabase(), downloadDatabase(), bioticToDatabase(), and indexDatabase() functions.
• DuckDB backend for storing NMD Biotic data parsed from annual XML files.
• ICES area and gear category added to station data.
• Cruise series index stored in the database.