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

In KlausVigo/phangorn: Phylogenetic Reconstruction and Analysis

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)))

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.

Value

The tree with newly assigned edge length.

Author(s)

Klaus Schliep

See Also

node.depth.edgelength, 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)

KlausVigo/phangorn documentation built on June 23, 2024, 10:49 p.m.