transferBootstrap
assigns transfer bootstrap (Lemoine et al. 2018)
values to the (internal) edges.
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.
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
Author
Klaus Schliep klaus.schliep@gmail.com
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")