GrENE-net: Global Evolutionary Network Experiment

Overview

GrENE-net (Global Evolutionary Network Experiment) is a collaborative research project studying plant evolution on a global scale. This R package contains the complete toolkit for managing and analyzing data from the GrENE-net experiment, including sample metadata, environmental data, and genomic analysis tools.

For more information, visit grene-net.org.

Features

• Sample metadata management
• Environmental data processing
• Climate and geographical data integration

Installation

Prerequisites

• R (>= 3.5.0)
• devtools package

Installing from GitHub

# Install devtools if you haven't already
if (!require("devtools")) install.packages("devtools")

# Install GrENE-net package
devtools::install_github("moiexpositoalonsolab/grene")

Alternatively, you can install locally:

1. Clone the repository
2. Run ./build.R
3. Execute ./install

Package Structure

Core Directories

• R/: Core R functions for data analysis and manipulation
• data/: Processed datasets (accessible via data("dataset_name")), including:
  • Climate data: bioclimvars_ecotypes_era5.csv, worldclim_sitesdata.csv, weatherstation_data.rda
  • Sample data: samples_data.csv, sbsamples_data.csv, seedbank_samples.csv
  • Experimental data: siliques_data.csv, census_data.csv, ecotypes_data.csv
  • Location data: locations_data.csv, sites.clim.csv
  • Environmental data: soilsamples_data.csv, temphum_ib_data.csv
  • Sequencing data: fastq_info.csv
• data-raw/: Raw data files and processing scripts, containing:
  • Original experimental data: SURVIVAL_total_flowers_collected.csv, samples_records.csv
  • Location information: locations_dataraw.csv
  • Census data: census_samples.xlsx
  • Ecotype information: ecotypes_seedmix.csv, accessions_1001g.csv
  • Python scripts for data processing in python_scripts/
• man/: Package documentation and function references

Additional Components

• CPP/: C++ source code for performance-critical operations
• gsod/: Global Surface Summary of Day weather data processing
• srtm/: Shuttle Radar Topography Mission data utilities
• wc2-0.5/: Climate data processing tools

Usage

# Load the package
library(grene)

# Access documentation
?grene

# Load included datasets
data("dataset_name")

We welcome contributions! Please:

1. Fork the repository
2. Create a feature branch
3. Submit a pull request

Support

For questions, bug reports, or feature requests:

• Open an issue on GitHub

License

This project is licensed under LICENSE.md

Citation

If you use GrENE-net in your research, please cite:

[Citation information to be added]

Acknowledgments

Thanks to all contributors and participants in the GrENE-net experiment worldwide.

Example

#library(grene)