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 locally
devtools::install("path/to/icesdata")

Usage

Loading Data

library(icesdata)

# Load ICES stock data
stock_data <- loadIcesStockData("path/to/stock_data.csv")

# Load ICES RData files
loadIcesRdata("data/icesdata.RData")

# Process ICES data
processed_data <- processIcesData("data/data.RData", "data/info.RData")

Analysis

# Calculate benchmark reference points
benchmarks <- calculateBenchmarks(processed_data)

# Calculate time series
ts_data <- calculateTimeseries(processed_data, benchmarks)

# Calculate management plan statistics
mp_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.