phylobase 0.8.0

CHANGES IN phylobase VERSION 0.8.0

New features

• Initial basic support for converting RNeXML objects in phylo4 and phylo4d
  format.
• New methods: internalEdges(), terminalEdges()
• descendants() has now a "ALL" argument to include self in results
• New method: nodeHeight() provides a consistent and comprehensive way of
  calculating the distance between a node and either the root or the tips. (fix
  #3)
• The replacement methods for labels, tipLabels, nodeLabels, edgeLabels
  now accept NA or NULL to remove labels (fix #2)

Major changes

• readNexus and readNewick now internally use the package rncl to parse
  files. They also use a different approach to reconstruct the edge
  matrix. These changes make file parsing faster. Objects created with this new
  approach may not exactly be identical to those created in previous versions as
  node numbering might differ, they should however be fully compatible with each
  others.
• readNexus and readNewick can now parse tree files with trees containing a
  subset of the taxa listed in the TAXA Block.
• Source code for the package is hosted on GitHub at https://github.com/fmichonneau/phylobase

Minor changes

• All tests done with testthat
• rootNode returns the rootNode using the same format as getNode().
• All documentation is in Roxygen format
• hasPoly, hasRetic, hasSingle are now methods instead of functions.

Deprecated functions

• nodeDepth and depthTips are now deprecated and are replaced by nodeHeight

Bug fixes

• Fix bug: NA in labels were considered duplicated by checkPhylo4().
• Fix bug #605 (R-forge) -- treePlot subsets numeric data for plotting.
• Fix bug #4: descendants() behave like ancestors() when provided with a
  vector of nodes and is consistent across all arguments.