nodes_config {treesliceR}

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)

Arguments

tree

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

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.

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").

Author(s)

Matheus Lima de Araujo [e-mail]

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