phangorn (version 2.12.1)

add_edge_length: Assign and compute edge lengths from a sample of trees

Description

This command can infer some average edge lengths and assign them from a (bootstrap/MCMC) sample.

Usage

add_edge_length(tree, trees, fun = function(x) median(na.omit(x)),
  rooted = all(is.rooted(trees)))

Value

The tree with newly assigned edge length.

Arguments

tree

a phylogenetic tree or splitnetwork where edge lengths are assigned to.

trees

an object of class multiPhylo, where the average for the edges is computed from.

fun

a function to compute the average (default is median).

rooted

rooted logical, if FALSE edge lengths is a function of the observed splits, if TRUE edge lengths are estimated from height for the observed clades.

Author

Klaus Schliep

See Also

node.depth, consensus, maxCladeCred, add_boxplot

Examples

data("Laurasiatherian")
set.seed(123)
bs <- bootstrap.phyDat(Laurasiatherian,
                FUN=function(x)upgma(dist.ml(x)), bs=100)
tree_compat <- allCompat(bs, rooted=TRUE) |>
              add_edge_length(bs)
plot(tree_compat)
add_boxplot(tree_compat, bs, boxwex=.7)