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Convert legacy LTER-MareChiara zooplankton data to Darwin Core format

Source: R/processing.R
format_to_dc.Rd

This function converts preprocessed legacy zooplankton datasets from the LTER-MareChiara station into Darwin Core-compliant format for EMODnet Biology publication and Digital Twin Ocean integration. The function processes standardized parquet files containing taxonomically validated data with WoRMS LSIDs (Life Science Identifiers).

Usage

format_to_dc(verbose = TRUE)

Arguments

verbose

Logical. Whether to print processing messages. Default is TRUE.

Value

The Darwin Core data as a list (event, occurrence, emof tables plus raw data, processing info, and metadata).

Details

Input Data Format:

The function expects preprocessed legacy data in parquet format with the following structure:

  • eventID: Unique sampling event identifier (e.g., "mc_1", "mc_2")

  • eventDate: Sampling date in Date format (YYYY-MM-DD)

  • scientificName: Full scientific name with WoRMS validation

  • lsid: WoRMS Life Science Identifier URN (e.g., "urn:lsid:marinespecies.org:taxname:104251")

  • Abundance: Abundance measurement (ind/m³)

  • lifeStage: Life stage code ("f" = female, "m" = male, "j" = juvenile, "fm" = both sexes, "fmj" = all stages)

Current Implementation:

Merges legacy data (1984-2020 from hot storage) with ongoing survey landings (2021-present from the automation bucket) and converts the combined dataset to Darwin Core format. Output is uploaded as a versioned RDS to SharePoint.

Darwin Core Conversion:

The function creates three Darwin Core extension tables following OBIS (Ocean Biodiversity Information System) standards:

  • Event Extension: Core table with sampling event metadata including temporal (eventDate) and spatial information (decimalLatitude, decimalLongitude, locality, waterBody, depth ranges, samplingProtocol)

  • Occurrence Extension: Links to Event via eventID, contains species occurrences with scientificName, scientificNameID (WoRMS LSID), and occurrenceStatus (present/absent based on Abundance > 0)

  • eMoF Extension: Extended Measurement or Fact table linked via occurrenceID, containing quantitative measurements with standardized vocabulary terms from BODC NERC Vocabulary Server (NVS):

    • Individual counts with NERC P06 units (ind/m³)

    • Sex information (P01/ENTSEX01) with S10 controlled vocabulary

    • Life stage information (P01/LSTAGE01) with S11 controlled vocabulary

Geographic Information:

LTER-MareChiara station coordinates are automatically assigned to all events:

  • Latitude: 40.81°N

  • Longitude: 14.25°E

  • Locality: LTER-MareChiara station

  • Water Body: Mediterranean Sea (Gulf of Naples, Tyrrhenian Sea)

  • Depth range: 0-50 meters (vertical tow)

  • Country: Italy (Campania region)

Data Standards:

  • Taxonomic identifiers: WoRMS LSIDs

  • Measurement vocabulary: BODC NERC Vocabulary Server (NVS)

  • Format: Darwin Core Archive structure

  • Compliance: OBIS schema and EMODnet Biology requirements

See also

Examples

if (FALSE) { # \dontrun{
# Process legacy data and upload Darwin Core output to SharePoint
format_to_dc()

# Silent processing (no console messages)
format_to_dc(verbose = FALSE)
} # }