STOPeData/_pkgdown.yml at main · NIVANorge/STOPeData · GitHub

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url: https://nivanorge.github.io/STOPeData/
template:
  bootstrap: 5
  bslib:
    font-size: "0.75rem"
  light-switch: true

reference:
  - title: "Summarise"
    desc: "Summarise session data into text strings for CREED quality assessment reporting."
    contents:
      - starts_with("summarise_")
      - calculate_coordinate_precision
      - manual_completion_message

  - title: "Validate"
    desc: "Validate data formats and structures."
    contents:
      - starts_with("validate_")

  - title: "Zenodo"
    desc: "Helpers for preparing and submitting datasets to Zenodo."
    contents:
      - starts_with("zenodo_")
      - generate_zenodo_readme

  - title: "Create"
    desc: "Create new data rows and structures."
    contents:
      - starts_with("create_")

  - title: "Data Export"
    desc: "Build and download session data as ZIP archives and metadata files."
    contents:
      - write_metadata_txt
      - write_metadata_yaml
      - format_duration
      - get_git_commit
      - get_export_metadata
      - get_dataset_display_name
      - object_to_text
      - build_session_zip
      - download_all_data
      - write_creed_report_txt

  - title: "Data Import"
    desc: "Import session data from exported ZIP archives."
    contents:
      - read_zip_metadata
      - import_session_from_zip
      - import_module_table
      - detect_dataset_type
      - get_reactiveValues_key
      - read_metadata_txt

  - title: "Reference Management"
    desc: "Parse BibTeX, look up DOIs and PMIDs, and manage bibliographic references."
    contents:
      - bib_string2df_alt
      - map_bibtex_to_reference_fields
      - map_crossref_to_reference_fields
      - clean_bibtex_text
      - extract_clean_doi
      - extract_clean_pmid
      - pmid_to_doi
      - lookup_crossref_doi
      - validate_and_lookup_identifier
      - reference_character_limits

  - title: "Data Setup"
    desc: "Look up and generate IDs for parameters, samples, and protocols."
    contents:
      - get_parameters_of_types
      - get_parameters_filtered

  - title: "CREED Utilities"
    desc: "Configuration and helper functions for CREED quality assessment criteria."
    contents:
      - collect_CREED_data
      - CREED_reliability_criteria_config
      - CREED_relevance_criteria_config
      - copper_CREED_purpose_statement

  - title: "Testing"
    desc: "Generate dummy data for development and testing."
    contents:
      - populate_session_with_dummy_data
      - creed_tibble_to_mock_input

  - title: "Utilities"
    desc: "General-purpose helpers for the Shiny app."
    contents:
      - printreactiveValues
      - info_accordion
      - get_session_data_safe

  - title: "LLM Extraction"
    desc: "Run structured data extraction from PDFs using an LLM."
    contents:
      - extract_pdf_with_llm

  - title: "App"
    desc: "Run the STOPeData Shiny application."
    contents:
      - run_app

deploy:
  install_metadata: true # permits linking between local websites