icesdata: ICES Age-Structured Stock Assessment Data and Utilities

A comprehensive R package for ICES age-structured stock assessment data, including utility functions for data processing, analysis, and visualization. This package consolidates functionality from multiple ICES-related packages into a single, maintainable codebase.

Features

• Data Loading: Functions to load and process ICES stock assessment data from various formats
• Analysis Tools: Utilities for calculating benchmarks, time series, and management plan statistics
• Visualization: Plotting functions for stock status, fishing mortality, and reference points
• Core Utilities: FLR-compatible functions for stock assessment workflows

Installation

# Install from GitHub (if available)devtools::install_github("your-username/icesdata")
# Or install locallydevtools::install("path/to/icesdata")

Usage

Loading Data

library(icesdata)
# Load ICES stock datastock_data<- loadIcesStockData("path/to/stock_data.csv")
# Load ICES RData files
loadIcesRdata("data/icesdata.RData")
# Process ICES dataprocessed_data<- processIcesData("data/data.RData", "data/info.RData")

Analysis

# Calculate benchmark reference pointsbenchmarks<- calculateBenchmarks(processed_data)
# Calculate time seriests_data<- calculateTimeseries(processed_data, benchmarks)
# Calculate management plan statisticsmp_stats<- calculateMpStats(ts_data)

Visualization

# Plot stock status over time
plotStockStatus(stock_data)
# Plot fishing mortality
plotFishingMortality(stock_data)
# Plot management plan statistics
plotManagementPlanStats(mp_stats)
# Plot benchmark reference points
plotBenchmarks(benchmarks)

Package Structure

icesdata/
├── R/ # R source code
│ ├── data-loading.R # Data loading functions
│ ├── analysis-functions.R # Analysis utilities
│ ├── plotting-functions.R # Visualization functions
│ └── icesdata-utils.R # Core utility functions
├── data/ # Package datasets
├── vignettes/ # Package vignettes
├── tests/ # Unit tests
└── man/ # Documentation

Dependencies

Required

• R (>= 4.0.0)
• methods
• stats
• utils

Suggested

• testthat (>= 3.0.0)
• knitr
• rmarkdown
• ggplot2
• dplyr
• tidyr
• plyr

Dataset Storage

Note: The datasets in this package are too large for GitHub. They are stored externally and can be accessed through:

1. Zenodo: [DOI: TBD] - Long-term storage for research data
2. ICES Data Portal: Official ICES data repository
3. Local Network: For internal institutional use
4. Cloud Storage: AWS S3, Google Cloud, or Azure Blob Storage

To use the package with datasets, download them from the external source and place them in the data/ directory.

Contributing

1. Fork the repository
2. Create a feature branch
3. Make your changes
4. Add tests for new functionality
5. Submit a pull request

License

This package is licensed under the MIT License. See the LICENSE file for details.

Citation

If you use this package in your research, please cite:

ICES Working Group. (2024). icesdata: ICES Age-Structured Stock Assessment Data and Utilities. R package version 0.1.0.

Contact

For questions or issues, please contact:

• Maintainer: ICES Working Group ices@ices.dk
• Issues: GitHub Issues

Acknowledgments

This package consolidates functionality from:

• bimResilience package
• BRebuildUtils package
• Original icesdata utilities

Special thanks to the ICES community for providing the underlying data and methodologies.