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Label nodes with jackknife support values

Source: R/Jackknife.R
JackLabels.Rd

JackLabels() produces a list of node labels denoting split support from a set of resampled trees, optionally printing them on a tree.

Usage

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

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().

showFraction

Logical specifying whether to also annotate nodes with the fraction of replicates that were decisive for the split.

format

Character specifying return format. "character" returns a character string suitable to add to the node.labels attribute of a tree; "numeric" returns numeric values suitable for further analysis.

Value

A named vector specifying the proportion of jackknife iterations consistent with each node in tree, as plotted. If format = "character", blank entries are included corresponding to nodes that do not require labels, such that the return value is in the format required by phylo$node.label. If multiple trees are specified per iteration, the return value has an attribute decisive listing, for each entry in the return value, how many iterations were decisive for that split.

Details

If an element of jackTrees contains multiple trees, then the iteration is counted as supporting a split if all trees contain the split, and as contradicting the split if no trees contain it. If a split is only present in a subset of trees, that iteration is considered not to be decisive, and is ignored when calculating the support for that split.

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(), MostContradictedFreq(), PresCont(), 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() or Resample(),
# but for simplicity:
jackTrees <- as.phylo(1:100, 8)

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

#> [1] ""     ""     "0.13" "0.08" "0.14" "1"    "1"   

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

# Write the labelled tree to screen
ape::write.tree(tree)
#> [1] "(t1,((((((t2,t8)1,t7)1,t6)0.14,t5)0.08,t4)0.13,t3));"

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