TreeSearch (version 1.6.1)

JackLabels: 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,
  ...
)

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.

Arguments

tree

A tree of class phylo.

jackTrees

A list or multiPhylo object containing trees generated by Resample() or 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().

Author

Martin R. Smith ()

See Also

Generate trees by jackknife resampling using Resample() for standard parsimony searches, or Jackknife() for custom search criteria.

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

Examples

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

# jackTrees will usually be generated with Jackknife() or Resample(),
# 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)