checkAndFixUltrametric {evolved} | R Documentation |
Find and fix small rounding errors in ultrametric trees
Description
checkAndFixUltrametric
finds and correct small numerical errors that
might appear in ultrametric trees that where created through simulations.
This function should never be used as a formal statistical method to make a
tree ultrametric, as it was designed just to correct small rounding errors.
Usage
checkAndFixUltrametric(phy)
Arguments
phy |
A |
Value
A check and fixed phylo
object.
Author(s)
Daniel Rabosky, Matheus Januario, Jennifer Auler
References
Paradis, E. (2012). Analysis of Phylogenetics and Evolution with R (Vol. 2). New York: Springer.
Popescu, A. A., Huber, K. T., & Paradis, E. (2012). ape 3.0: New tools for distance-based phylogenetics and evolutionary analysis in R. Bioinformatics, 28(11), 1536-1537.
Examples
S <- 1
E <- 0
set.seed(1)
phy <- simulateTree(pars = c(S, E), max.taxa = 6, max.t = 5)
phy$edge.length[1] <- phy$edge.length[1]+0.1
ape::is.ultrametric(phy)
phy <- checkAndFixUltrametric(phy)
ape::is.ultrametric(phy)
[Package evolved version 1.0.0 Index]