treesliceR (version 1.0.3)

nodes_config: Capture general branching information for an inputted phylogenetic tree

Description

This function captures general tree information, including branching, node positions, and depths. It serves as a core function underlying all algorithms for slicing phylogenies.

Usage

nodes_config(tree)

Value

The function returns a phylogenetic tree in the "phylo" format containing three novel pieces of information (stored within "config", "node_matrix", and "tree_depth").

Arguments

tree

phylo. An ultrametric phylogenetic tree in the "phylo" format.

Author

Matheus Lima de Araujo

Details

This function captures node and edge information from an ultrametric phylogenetic tree. The function provides a data frame containing detailed branching information (within the internal "config" object), a node matrix (within "node_matrix"), and the tree age (within "tree_depth").

More specifically, the "config" object returns the following information: NodeBegin: the node at which a given branch begins. NodeEnd: the node at which a given branch ends. NodeLength: the branch length of that nodes interval. YearBegin: the year at which a given node begins. YearEnd: the year at which a given node ends.

See Also

Phylogenetic slicing methods: squeeze_tips(),squeeze_root(),squeeze_int().

Examples

# Generate a random tree
tree <- ape::rcoal(20)

# Capture tree information
tree <- nodes_config(tree)

# Accessing these informations
tree$config # Nodes configurations
tree$node_matrix # Node matrix
tree$tree_depth # Tree age