Root1 {shipunov} | R Documentation |
Roots phylogenetic trees even if outgroup is not monophyletic
Description
Root1
non-interactively reroots a phylogenetic tree with respect
to the specified outgroup even if it is not monophyletic.
Usage
Root1(phy, outgroup, select=1, ...)
Arguments
phy |
An object of class |
outgroup |
A vector of mode numeric or character specifying the new outgroup. |
select |
Which element of outgroup to select if it is not monophyletic. |
... |
Arguments passed to ape::root(). |
Details
This is a wrapper of ape::root() to use in non-interactive mode. If specified outgroup is not monophyletic, instead of error, it issues error _message_, and chooses the 'select' element as a new outgroup.
Value
An object of class "phylo"
Author(s)
Alexey Shipunov
See Also
ape::root
Examples
data(bird.orders, package="ape")
ape::root(bird.orders, 1:2)
## ape::root(bird.orders, 1:3) # gives error
Root1(bird.orders, 1:3) # only outputs error _message_
Root1(bird.orders, 1, resolve.root=TRUE)
[Package shipunov version 1.17.1 Index]