timeslice: Slice phylogenetic tree at various time depths

In phyloregion: Biogeographic Regionalization and Macroecology

Slice phylogenetic tree at various time depths

Description

This function slices a dated phylogenetic tree at successive time depths back in time by collapsing younger phylogenetic branches into older ones to infer the origins of species assemblages.

Usage

timeslice(phy, n = 0.2, collapse = FALSE, ...)

Arguments

phy	A dated phylogenetic tree as an object of class “phylo”.
n	Time depth to slice the phylogenetic tree (often in millions of years for dated trees).
collapse	Logical, collapse internal edges with zero edge length.
...	arguments passed among methods.

Value

A tree with the phylogenetic structure removed at the specified time depth

Author(s)

Barnabas H. Daru [e-mail]

References

Daru, B.H., van der Bank, M. & Davies, T.J. (2018) Unravelling the evolutionary origins of biogeographic assemblages. Diversity and Distributions 24: 313–324.

Examples

library(ape)

set.seed(1)
tree <- rcoal(50)
x <- timeslice(tree, .5)

old.par <- par(no.readonly = TRUE)
par(mfrow = c(1, 2))
plot(tree)
axisPhylo()
plot(x)
axisPhylo()
par(old.par)

phyloregion documentation built on Aug. 15, 2023, 9:07 a.m.