parse_annotated: Parse an annotated phylogenetic tree

In phylotate: Phylogenies with Annotations

Description

This function takes the given text string, containing data in either NEXUS or Newick format, and returns annotated phylogenetic trees.

Usage

parse_annotated(str, format="nexus")

Arguments

str	a text string, containing tree data
format	a format specifier; either "nexus" or "newick"

Details

The given file text is parsed and a tree object is constructed which can be used with the functions in the ape package. Annotations of the kind produced by, for example, MrBayes, are parsed and preserved in the returned object.

In addition to edge, edge.length and tip.label, two additional vectors are added. These are node.comment and node.distance.comment. These contain annotations associated with nodes and their distance values. These arrays are indexed by node number, not by edge. The reason for this is that this ensures that the object will remain in a valid state after a call to reorder which might change the ordering of the edge arrays without being aware of annotations. If you need to obtain annotations in edge-order, subset by the second column of the edge array.

Value

an object of type "phylo" or "multiPhylo", augmented with node annotations.

Author(s)

Daniel Beer [e-mail]

References

Paradis, E. Definition of Formats for Coding Phylogenetic Trees in R. http://ape-package.ird.fr/misc/FormatTreeR_24Oct2012.pdf

See Also

print_annotated, read_annotated, write_annotated, finches

Examples

  # Parse the example data included with this package
  data(finches)
  t <- parse_annotated(finches, format="nexus")

  # Obtain annotations in edge-order, rather than node-order
  edge.comment <- t$node.comment[t$edge[,2]]

Example output

phylotate documentation built on June 30, 2019, 1:01 a.m.