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

In 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 = TRUE)

Arguments

tree	tree 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(s)

Klaus Schliep

See Also

node.depth.edgelength, consensus, maxCladeCred

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)

phangorn documentation built on Jan. 23, 2023, 5:37 p.m.