add_edge_length {phangorn} | R Documentation |
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)
[Package phangorn version 2.11.1 Index]