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.
rncl now allows the parsing of tree files where the trees contain a subset of the taxa listed in the TAXA block.rncl function.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.
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.
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.
treeNames had duplicated values for each tree name.'cre')