Label nodes with jackknife support values

Label nodes with jackknife support values

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.

See also

Jackknife(): Generate trees by jackknife resampling

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

Author

Martin R. Smith (martin.smith@durham.ac.uk)

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)

#>   11   12   13   14   15 
#> 0.13 0.08 0.14 1.00 1.00 

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