fmristore

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An R package for efficient storage and retrieval of neuroimaging data using HDF5 format with specialized data structures for fMRI analysis.

Features

Efficient Storage: HDF5-based storage for large neuroimaging datasets
Memory-Optimized: Latent vector representations for reduced memory footprint
High Performance: Optimized data access patterns for fMRI analysis workflows
Rich Data Structures: Support for clustered, dense, and sparse neuroimaging vectors
Comprehensive Testing: Extensive test suite ensuring reliability and correctness

Installation

From GitHub

# Install development version from GitHub
# install.packages("devtools")
# devtools::install_github("bbuchsbaum/fmristore")
install.packages("fmristore", repos = c('https://bbuchsbaum.r-universe.dev', 'https://cloud.r-project.org'))

Dependencies

The package requires HDF5 system libraries. Installation instructions by platform:

Ubuntu/Debian

sudo apt-get install libhdf5-dev

macOS

# Using Homebrew
brew install hdf5

# Using MacPorts
sudo port install hdf5

Windows

HDF5 libraries are automatically handled during R package installation.

Quick Start

library(fmristore)

# Load neuroimaging data
# Example workflow here...

Documentation

Development

Running Tests

# Install test dependencies
devtools::install_dev_deps()

# Run tests
devtools::test()

# Check test coverage
covr::package_coverage()

Code Style

This package strictly follows the tidyverse style guide. Style compliance is enforced through automated checks:

Automated Style Enforcement:

GitHub Actions automatically check style on every push/PR
Pre-commit hooks available for local development
Configured with strict tidyverse linting rules

Checking and Fixing Style Issues:

# Check for style violations
lintr::lint_package()

# Automatically fix style issues
styler::style_pkg()

# Check what styler would change without modifying files
styler::style_pkg(dry = "on")

Setting Up Pre-commit Hooks (Recommended for Contributors):

# Install pre-commit (requires Python)
pip install pre-commit

# Install the git hook scripts
pre-commit install

# (Optional) Run against all files
pre-commit run --all-files

The pre-commit hooks will automatically:

Format code with styler according to tidyverse style
Run lintr to catch style violations
Check roxygen documentation
Ensure DESCRIPTION file follows tidy format

Contributing

Fork the repository
Create a feature branch (git checkout -b feature/amazing-feature)
(Recommended) Set up pre-commit hooks: pre-commit install
Make your changes
Ensure tests pass (devtools::test())

Ensure code follows tidyverse style:

styler::style_pkg()      # Auto-fix style issues
lintr::lint_package()    # Check for remaining violations

Commit your changes (git commit -m 'Add amazing feature')
Push to the branch (git push origin feature/amazing-feature)
Open a Pull Request

Style Requirements:

All code must pass lintr::lint_package() with no violations
Code should be formatted with styler::style_pkg() using tidyverse style
Pre-commit hooks will help ensure compliance automatically

License

This project is licensed under the [license specified in DESCRIPTION file].

Citation

To cite this package in publications, use:

citation("fmristore")

Getting Help

Issue tracker for bug reports and feature requests
Discussions for questions and community support

Albers theme

This package uses the albersdown theme. Vignettes are styled with vignettes/albers.css and a local vignettes/albers.js; the palette family is provided via params$family (default 'red'). The pkgdown site uses template: { package: albersdown }.