avian_molecular_shifts

Release Notes for "Genome and life-history evolution link bird diversification to the end-Cretaceous mass extinction"

Version: 1.0.0
Release Date: 24 June 2024

Highlights

• Initial release of the repository containing comprehensive analysis scripts with extensive documentation.
• Implementation of logistic regression, phylogenetic signal estimation, codon usage analysis, and many others.

New Features

• Primary Analysis Script: constrained_species_tree.R containing code for key analyses, divided into 17 well-documented sections.
• Utility Scripts: Includes custom functions in Functions_consensus_genetrees.R and RandomForest analysis in RandomForest_var_imp.R.
• Simulation Tools: shift_model_sims.R for assessing the statistical performance of Janus on substitution model shifts.

Improvements

• Structured code with detailed comments for reproducibility purposes.
• Included RDS files for immediate data loading and analysis without re-processing.

Documentation

• Detailed READMEs across directories explaining file contents and their use.
• Supplementary material provided in various formats (Excel, RDS) for comprehensive data analysis.

Known Issues

• As this is the initial release, users are encouraged to report any discrepancies or issues found during the execution of scripts or data handling.

Dependencies

• Requires R and specific packages detailed in the system report section of the primary script. Ensure all dependencies are installed prior to running the scripts.

How to Install/Upgrade

1. Clone the repository from GitHub.
2. Install R and necessary R packages as listed in the script annotations.
3. Run the scripts sequentially as per the guidelines provided in the repository README.

Acknowledgments

Thanks to all authors involved in the manuscript and code preparation, especially Jacob S. Berv, who led the corresponding research and compilation of this repository.

For any support or additional information, contact Jacob S. Berv at jberv@umich.edu or jacob.berv@gmail.com.