treesliceR (version 1.0.3)

squeeze_root: Slices a phylogenetic tree following a 'rootward' orientation

Description

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

Usage

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

Value

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

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.

Author

Matheus Lima de Araujo

Details

Slicing approach

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

References

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

See Also

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

Examples

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

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

# Plot it
plot(tree)