transferBootstrap: Transfer Bootstrap

In KlausVigo/phangorn: Phylogenetic Reconstruction and Analysis

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 [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, drawSupportOnEdges

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")

KlausVigo/phangorn documentation built on Nov. 5, 2024, 11 a.m.