squeeze_tips: Slices a phylogenetic tree following a 'tipward' orientation

In treesliceR: To Slice Phylogenetic Trees and Infer Evolutionary Patterns Over Time

Slices a phylogenetic tree following a 'tipward' orientation

Description

This function slices a phylogenetic tree in a 'tipward' orientation, starting from the tips and moving towards the root of the tree.

Usage

squeeze_tips(tree, time, criterion = "my", dropNodes = FALSE)

Arguments

tree	phylo. An ultrametric phylogenetic tree in the "phylo" format.
time	numeric. A value that determines the time, or accumulated phylogenetic diversity (PD), at which the tree should be cut.
criterion	character string. The method for cutting the tree. It can be either "my" (million years) or "PD" (accumulated phylogenetic diversity). Default is "my".
dropNodes	logical. A logical value indicating whether the nodes that were sliced (void nodes, presenting no branch length) should be preserved in the node matrix. Default is FALSE.

Details

Slicing approach The treesliceR package uses a simple approach for cutting phylogenies, which reduces branch lengths in relation to an inputted temporal threshold.

Value

The function returns a time-slice of an inputted phylogenetic tree in the "phylo" format, following a 'tipward' orientation.

Author(s)

Matheus Lima de Araujo [e-mail]

References

See the tutorial on how to use this function on our website.

See Also

Other slicing methods: squeeze_root(), squeeze_int(), phylo_pieces(), prune_tips().

Examples

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

# Slice "tipwardly" the phylogeny at 0.1 million years
tree <- squeeze_tips(tree, time = 0.1)

# Plot it
plot(tree)

treesliceR documentation built on Sept. 11, 2024, 8:47 p.m.