treeman

treeman provides manipulation and analysis of phylogenetic trees in R by implementing a TreeMan list-based class and methods for tip operations, tree-growth model simulations, taxon pinning to supertrees, and detection of phylogenetic turnover for evolutionary studies.

Key Features:

• TreeMan class: A list-based R class named TreeMan encodes phylogenetic trees for direct manipulation.
• Tip addition and removal: Functions enable explicit addition and removal of tips from tree objects.
• Vectorized and parallelized methods: Implements vectorized and parallelized computations to reduce runtimes and handle large datasets.
• Tree-growth model simulations: Provides functionality to simulate evolutionary processes using tree-growth models.
• Pinning missing taxa to supertrees: Supports integrating incomplete or missing taxa into larger supertree frameworks.
• Detection of phylogenetic turnover: Includes methods to identify significant changes or turnover within phylogenetic trees.

Scientific Applications:

• Pinning Missing Taxa to a Supertree: Integration of incomplete or missing taxa into larger phylogenetic frameworks to improve supertree completeness.
• Simulating Evolution with Tree-Growth Models: Simulation of evolutionary processes via tree-growth models to explore diversification and evolutionary scenarios.
• Detecting Significant Phylogenetic Turnover: Identification of significant changes in phylogenetic composition or structure within or between datasets.

Methodology:

Implements a list-based TreeMan class in R and employs vectorized and parallelized methods to perform tree manipulations (adding/removing tips), simulate tree-growth models, pin missing taxa to supertrees, and detect phylogenetic turnover.