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Changelog

Source: NEWS.md

algaware 0.1.0

First release.

Shiny application

  • Interactive Shiny app (launch_app()) for end-to-end IFCB cruise reporting.
  • Sidebar workflow: Settings → Data → Validate → Report.
  • Loading overlay with smooth fade-in on first render.

Data loading

  • Downloads IFCB samples from an IFCB Dashboard instance for a selected cruise or date range.
  • Automatic spatial matching of IFCB samples to AlgAware monitoring stations using a configurable bin radius.
  • Merges FerryBox chlorophyll fluorescence from a locally configured data folder.
  • Processes HDF5 classification files together with feature files into biovolumes and carbon estimates using iRfcb.
  • SQLite annotation database (ClassiPyR-compatible schema) for exporting validated image annotations as training data.

Validation

  • Gallery tab for browsing IFCB images organised by class.
  • Per-image and per-class relabelling (reassign to any class in the global class list or a custom class) and invalidation.
  • Custom class creation with full scientific name, AphiaID, HAB flag, and italic formatting metadata.
  • Corrections log importable in future sessions to replay relabellings automatically.

Samples tab

  • Table view of all samples with exclusion/re-inclusion controls.
  • Excluded samples are removed from all summaries, maps, mosaics, and the report.

Images (mosaic designer)

  • Interactive mosaic builder for Baltic Sea and West Coast images.
  • Binary-search layout algorithm to maximise image size within canvas bounds (rectpacker).
  • Per-taxon image re-rolling and configurable image count per mosaic.

Maps and plots

  • Station maps: image count, phytoplankton group composition pie chart (Diatoms, Dinoflagellates, Cyanobacteria, Cryptophytes, Mesodinium spp., Silicoflagellates, Other), and chlorophyll maps.
  • Cyanobacteria pie slice colour: teal-cyan (#14B8A6).
  • Image count map legend: “Images (counts/L)”; width matched to chlorophyll map so y-axes align in the Word report.
  • Chlorophyll source selector: FerryBox, CTD fluorescence, LIMS bottle (0–20 m), or LIMS hose-integrated (0–10 m).
  • Regional heatmaps and stacked bar charts for Baltic Sea and West Coast.
  • Summary DT table with per-station taxa and biovolume data.

CTD panel

  • Fluorescence depth profiles per station from CNV files (oce).
  • Regional Chl-a time-series with 1991–2020 climatological mean ± SD ribbon.
  • Automatic station name synonym resolution via station_mapper.txt.

Word report generation

  • Generates a Word .docx report from an officer template with:
    • Front page with logo, diarienummer, phytoplankton group composition pie map, and report number.
    • Swedish summary (Sammanfattning) and English summary (Abstract).
    • Cruise metadata table.
    • Image mosaic overview with numbered captions and italic species formatting.
    • Image count map, chlorophyll map, heatmaps, and stacked bar charts.
    • Per-station sections with image mosaics.
    • CTD fluorescence profiles and Chl-a time-series.
  • Species names are italicised in Word output; HAB taxa are marked with a red bold asterisk.

LLM text generation

  • Optional AI-generated report text via OpenAI (OPENAI_API_KEY) or Google Gemini (GEMINI_API_KEY).
  • Generates Swedish summary, English summary, and individual station descriptions guided by a configurable writing guide (inst/extdata/report_writing_guide.md).
  • HAB taxa are deterministically marked with * regardless of LLM output.
  • Default OpenAI model: gpt-5.1. Override via OPENAI_MODEL environment variable.
  • Retry on HTTP 429 (rate-limited) and 503 (service overload) with exponential back-off up to 120 s.
  • Bloom alert instructions appended to prompts when conditions are met: spring bloom (West Coast, Jan–Feb, diatoms > 50 % biovolume at any station, chl > 3 µg/L) and cyanobacterial bloom (Baltic, Jun–Aug, cyanobacteria > 50 % biovolume at any station, chl > 3 µg/L).

Taxa lookup and warning levels

  • Bundled taxa_lookup.csv maps classifier class names to WoRMS scientific names, AphiaID, HAB flag, italic formatting, warning level abundance, and sflag qualifiers.
  • Custom classes can be added interactively in the app and are merged into the taxa lookup at report time.

Configuration

  • inst/extdata/standard_stations.yaml — standard CTD stations and regional groupings.
  • inst/extdata/station_mapper.txt — raw station name synonyms for CNV/LIMS matching.
  • inst/extdata/annual_1991-2020_statistics_chl20m.txt — Chl-a climatology for CTD time-series ribbon.
  • inst/extdata/report_writing_guide.md — LLM system prompt / style guide.
  • inst/config/phyto_groups.yaml — phytoplankton group definitions (class, phylum, genus mappings for WoRMS lookup). Edit to add or rename groups without touching R code. Read via the exported assign_phyto_groups().