README.md

In franciscorichter/emphasis: Evolutionary Modeling on Phylogenetic Applications with Simulations and Importance Sampling

EMPHASIS is an advanced R package designed to perform statistical inference on phylogenetic trees using evolutionary models. By integrating simulations and importance sampling techniques, EMPHASIS offers a powerful toolkit for researchers in evolutionary biology, genetics, and related fields.

Key Features

• Simulations: Generate and manipulate phylogenetic trees under various evolutionary models.
• Inference: Perform statistical inference on phylogenetic trees using state-of-the-art methods.
• Analysis and Prediction: Analyze the structure and dynamics of phylogenetic trees, forecast evolutionary outcomes and assess the uncertainty of phylogenetic inferences.

Installation

To install the latest version of EMPHASIS from GitHub, use the following command in R:

devtools::install_github("franciscorichter/emphasis")

References

For further reading and a deeper understanding of the methodologies and theories behind EMPHASIS, we recommend the following papers:

1. Richter, F., Baegeman, B., Etienne, R. S., & Wit, E. C. (2020). Introducing a general class of species diversification models for phylogenetic trees. Statistica Neerlandica, 74(3), 261-274. Read the paper

2. Richter, F., Janzen, T., Hildenbrandt, H., Wit, E. C., & Etienne, R. S. (2021). Detecting phylodiversity-dependent diversification with a general phylogenetic inference framework. bioRxiv. Read the preprint

franciscorichter/emphasis documentation built on Aug. 27, 2024, 8:20 p.m.