The hardware and bandwidth for this mirror is donated by dogado GmbH, the Webhosting and Full Service-Cloud Provider. Check out our Wordpress Tutorial.
If you wish to report a bug, or if you are interested in having us mirror your free-software or open-source project, please feel free to contact us at mirror[@]dogado.de.

ShiVa: Detection of Evolutionary Shifts in both Optimal Value and Variance

Version: 1.0.2
Authors:
- Wensha Zhang wn209685@dal.ca
- Lam Si Tung Ho Lam.Ho@dal.ca
- Toby Kenney tb432381@dal.ca

Overview

ShiVa is an R package for detecting evolutionary shifts in both optimal trait values (mean) and diffusion variance across phylogenetic trees, based on the Ornstein-Uhlenbeck (OU) model. While many existing methods detect shifts in optimal values only, ShiVa simultaneously identifies both types of shifts using a penalized likelihood framework with L1 regularization.

The method is designed for researchers in evolutionary biology and comparative methods, particularly those interested in identifying abrupt regime changes along a phylogeny.

See our preprint for methodological details: arXiv:2312.17480

Features

• Automatively estimates shifts in both mean (θ) and variance (σ²) under the OU model
• Supports model selection using BIC, mBIC, or pBIC
• Includes backward correction for improved parsimony
• Can optionally account for measurement error
• Fast optimization using coordinate descent and soft-thresholding

Installation

To install the package from GitHub:

# install.packages("devtools") # if not already installed
devtools::install_github("WenshaZ/ShiVa")

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
Health stats visible at Monitor.