transferBootstrap: Transfer Bootstrap

In phangorn: Phylogenetic Reconstruction and Analysis

Transfer Bootstrap

Description

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

Usage

transferBootstrap(tree, BStrees)

Arguments

tree	The tree on which edges the bootstrap values are plotted.
BStrees	a list of trees (object of class "multiPhylo").

Value

plotBS returns silently a tree, i.e. an object of class phylo with the bootstrap values as node labels. The argument BSTrees is optional and if not supplied the labels supplied in the node.label slot will be used.

Author(s)

Klaus Schliep [e-mail]

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.

See Also

plotBS, maxCladeCred

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 Jan. 23, 2023, 5:37 p.m.