Phyto-MAP data viewer

Shiny web application for exploring the Phyto-MAP database of marine phytoplankton abundance records.

Status: in development, not yet deployed.

The application provides a sampling coverage map, a filterable data catalogue, a metadata dictionary, and panels for inspecting selected locations and records.

Planned deployment: Posit Connect Cloud.

Installation

Clone the repository and download the database from Zenodo (see below). Required R packages:

install.packages(c("shiny", "DBI", "RSQLite", "leaflet", "htmltools", "DiagrammeR", "DT"))

The application does not install packages automatically. At startup it reports any missing package and stops.

Database

The database is not included in this repository. Download it from Zenodo:

• Record: https://zenodo.org/records/23885976
• DOI: https://doi.org/10.5281/zenodo.23885976

Create the data/ directory if it does not exist, then place the downloaded SQLite file at data/phytomap.sqlite3.

The database is required to run the application and is not downloaded automatically.

Usage

From the project root:

shiny::runApp()

Features

• Home: database overview counts and notes on interpreting the records.
• Map explorer: sampling coverage by location, filtered by source and subsource, with rectangle selection, point details (events, samples, abundance records, taxonomy, sampling protocol) and PNG export.
• Data catalogue: browse and export joined database views to CSV, with filters.
• Metadata dictionary: table and field descriptions.
• Selected records: bounded table of records chosen on the map, with CSV export.

Project structure

app.R                 # UI definition and entry point
R/
  connection.R        # Read-only database connection
  queries.R           # SQL queries and bounded data retrieval
  server.R            # Session setup and module registration
  server_home.R       # Home overview
  server_map.R        # Map explorer
  server_catalog.R    # Data catalogue and metadata dictionary
www/                  # Custom JavaScript for filters and interactions
data/                 # Local database (not versioned)

Citation

If you use this viewer or the data, please cite the database:

Rayón-Viña, F., Finkel, Z. V., & Irwin, A. J. (2026). Phyto-MAP, a curated database of marine phytoplankton abundance records (Version 2.1.1) [Data set]. Zenodo. https://doi.org/10.5281/zenodo.23885976

License

MIT, © Fernando Rayón Viña. See LICENSE. The database has its own license on Zenodo.