JackLabels: Label nodes with jackknife support values

In TreeSearch: Phylogenetic Analysis with Discrete Character Data

Label nodes with jackknife support values

Description

Label nodes with jackknife support values

Usage

JackLabels(
  tree,
  jackTrees,
  plot = TRUE,
  add = FALSE,
  adj = 0,
  col = NULL,
  frame = "none",
  pos = 2L,
  ...
)

Arguments

tree	A tree of class phylo.
jackTrees	A list or multiPhylo object containing trees generated by Jackknife().
plot	Logical specifying whether to plot results; if FALSE, returns blank labels for nodes near the root that do not correspond to a unique split.
add	Logical specifying whether to add the labels to an existing plot.
adj, col, frame, pos, ...	Parameters to pass to nodelabels().

Value

A named vector specifying the proportion of jackknife trees consistent with each node in tree, as plotted. If plot = FALSE, blank entries are included corresponding to nodes that do not require labelling; the return value is in the value required by phylo$node.label.

Author(s)

Martin R. Smith ([e-mail])

See Also

Jackknife(): Generate trees by jackknife resampling

Other split support functions: Jackknife(), MaximizeParsimony(), SiteConcordance

Examples

library("TreeTools", quietly = TRUE) # for as.phylo

# jackTrees will usually be generated with Jackknife(), but for simplicity:
jackTrees <- as.phylo(1:100, 8)

tree <- as.phylo(0, 8)
JackLabels(tree, jackTrees)

tree$node.label <- JackLabels(tree, jackTrees, plot = FALSE)

# Write the labelled tree to screen
ape::write.tree(tree)

# Write labelled trees to a nexus file:
# write.nexus(tree, file = filename)

TreeSearch documentation built on April 11, 2025, 5:49 p.m.