transferBootstrap: Transfer Bootstrap
In phangorn: Phylogenetic Reconstruction and Analysis

transferBootstrap

R Documentation

Transfer Bootstrap

Description

transferBootstrap assigns transfer bootstrap (Lemoine et al. 2018) values to the (internal) edges.

Usage

transferBootstrap(tree, trees, phylo = TRUE, scale = TRUE)

Arguments

`tree`	The tree on which edges the bootstrap values are plotted.
`trees`	a list of trees (object of class "multiPhylo").
`phylo`	Logical, return a phylogentic tree with support value or a vector of bootstrap values.
`scale`	scale the values.

Value

a phylogentic tree (a phylo object) with bootstrap values assigned to the node labels.

Author(s)

Klaus Schliep klaus.schliep@gmail.com

References

Lemoine, F., Entfellner, J. B. D., Wilkinson, E., Correia, D., Felipe, M. D., De Oliveira, T., & Gascuel, O. (2018). Renewing Felsenstein’s phylogenetic bootstrap in the era of big data. Nature, 556(7702), 452–456.

Examples

fdir <- system.file("extdata/trees", package = "phangorn")
# RAxML best-known tree with bipartition support (from previous analysis)
raxml.tree <- read.tree(file.path(fdir,"RAxML_bipartitions.woodmouse"))
# RAxML bootstrap trees (from previous analysis)
raxml.bootstrap <- read.tree(file.path(fdir,"RAxML_bootstrap.woodmouse"))

tree_tbe <- transferBootstrap(raxml.tree,  raxml.bootstrap)
par(mfrow=c(1,2))
plotBS(tree_tbe)
# same as
plotBS(raxml.tree,  raxml.bootstrap, "p", "TBE")

phangorn documentation built on Sept. 17, 2024, 5:08 p.m.