NEWS.md

In rncl: An Interface to the Nexus Class Library

rncl 0.8.7

• Maintenance release that fixes warnings on CRAN checks related to the deprecation of sprintf.

rncl 0.8.6

• Maintenance release that fixes warnings on CRAN checks related to the deprecation of the binary_function in gcc 12/clang 14.

rncl 0.8.4

• Maintenance release that fixes warnings on CRAN checks.

rncl 0.8.3

• Maintenance release that fixes notes and warnings from CRAN checks.

rncl 0.8.2

New features

• The re-numbering of the edge matrix to deal with singleton is now performed in C++, leading to improved speed (about 3x for a 1700 tip tree) (#11).

• A progress bar is displayed when removing the singleton, which is useful when the tree is very large.

Major changes

• the components of the edge matrix are storred as integer (they were storred as double. (#17, reported by @KlausVigo)

rncl 0.6.0

New features

• rncl now allows the parsing of tree files where the trees contain a subset of the taxa listed in the TAXA block.

Major changes

• Missing edge lengths are now represented by -999 instead of -1 in the object returned by the rncl function.

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

rncl 0.2.2

• change roles in authors to have a single creator ('cre')
• fix typo in documentation

rncl 0.2.0

• initial release on CRAN

rncl documentation built on Jan. 9, 2023, 1:28 a.m.