| midpoint_root {phytools} | R Documentation |
Midpoint root a phylogeny
Description
These functions midpoint root a rooted or unrooted tree (Farris 1972).
Usage
midpoint_root(tree)
## S3 method for class 'root'
midpoint(tree, node.labels="support", ...)
Arguments
tree |
an object of class |
node.labels |
argument to be passed to |
... |
optional arguments to be passed to |
Details
Midpoint rooting involves locating the midpoint of the longest path between any two tips and putting the root in that location.
The function midpoint_root performs the same operation as midpoint in the phangorn package, but uses no phangorn (Schliep, 2011) code internally.
The function midpoint.root is a pseudo S3 method for the object class "root" that exists because when midpoint was created in phangorn it was not defined as a generic method. This function merely points to midpoint and is being deprecated out.
Value
An object of class "phylo" containing a rooted phylogenetic tree.
Author(s)
Liam Revell liam.revell@umb.edu
References
Farris, J. (1972) Estimating phylogenetic trees from distance matrices. American Naturalist, 106, 645-667.
Paradis, E., J. Claude, and K. Strimmer (2004) APE: Analyses of phylogenetics and evolution in R language. Bioinformatics, 20, 289-290.
Revell, L. J. (2024) phytools 2.0: an updated R ecosystem for phylogenetic comparative methods (and other things). PeerJ, 12, e16505.
Schliep K. P. (2011) phangorn: phylogenetic analysis in R. Bioinformatics, 27, 592-593.