phylo_pieces {treesliceR}

Slices a phylogenetic tree into multiple temporal slices

Description

This function slices a phylogenetic tree into multiple slices, spaced equally either in million years or intervals of phylogenetic diversity (PD).

Usage

phylo_pieces(tree, n, criterion, method, timeSteps, dropNodes, returnTree)

Arguments

tree

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

n

numeric. A numeric value indicating either the number of temporal slices (method = 1) or the time interval in million years (or phylogenetic diversity) among the tree slices (method = 2). Default is 1.

criterion

character string. The method for slicing the tree. It can be either "my" (million years) or "PD" (accumulated phylogenetic diversity). Default is "my".

method

numerical. A numerical value indicating the method to make the multiple slices. Setting "method = 1" will slice the phylogeny based on an "n" number of slices. If method = 2, the slices will be created based on a temporal interval. Default is 1.

timeSteps

logical. A logical value indicating whether the vector containing the time-steps used for creating the multiple slices should be returned. If "timeSteps = TRUE", then it returns a list containing both the time vector and a list with the multiple tree slices. Default is FALSE.

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.

returnTree

logical. A logical value indicating whether the original input tree should be returned with its slices in a list. Default is FALSE.

Value

The function returns a list containing multiple slices of a phylogenetic tree. The slices list is ordered from roots to tips. Thus, the first object within the outputted list is the root-slice, whereas the last is the tips-slice.

Author(s)

Matheus Lima de Araujo [e-mail]

See Also

Other slicing methods: squeeze_root(), squeeze_tips(), squeeze_int(), prune_tips()

Examples

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

# Cuts a phylogeny into multiple temporal slices
tree <- phylo_pieces(tree, n = 3, criterion = "my", method = 1)

# Plotting the three slices of our phylogeny
plot(tree[[1]])
plot(tree[[2]])
plot(tree[[3]])