timeslice {phyloregion} | R Documentation |
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 darunabas@gmail.com
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)
[Package phyloregion version 1.0.8 Index]