Second CRAN release: rncl 0.4.0

rncl 0.4.0

New features

• rncl now allows the parsing of tree files that contain some missing edge
  lengths, using the missing_edge_length argument in the read_newick_phylo
  and read_nexus_phylo. By default, if a tree has at least one missing edge
  length, all edge lengths are dropped. Alternatively, the user can provide a
  numeric value that will be used to replace all missing edge lengths. (#33 from
  rotl)
• If read_newick_phylo and read_nexus_phylo return a list of trees, the
  elements of the list are named according to the names found in the tree file.

Major changes

• Parsing tree files is now quiet, the default output of NCL is
  silenced. Because of the implementation of this output, it's difficult to give
  control to the user over this, but it's probably best to keep it quiet rather
  than having unneeded messages pollute the screen.
• The documentation of the function rncl is improved.
• The function make_phylo is now deprecated and will be removed in the next
  version. Use read_newick_phylo or read_nexus_phylo instead.

Minor changes

• The option spacesAsUnderscore now also applies to the slot taxaNames and not
  only to the elements of the slot taxonLabelVector.
• If the file parsed contains trees that only include a subset of the taxa
  listed in the NEXUS taxa block, the function fails more explicitly.

Bug fixes

• The slot treeNames had duplicated values for each tree name.
• Labels could have been assigned to the incorrect tips in some NEXUS files