phyloregion (version 1.0.8)

timeslice: 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, ...)

Value

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

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.

Author

Barnabas H. Daru

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)