[Phylobase-devl] Latest changes

[François Michonneau]

Hi all,

  I committed quite a few changes to phylobase in the last few days.
The main user-visible changes are:

- There are now global options for phylobase, that can be accessed by
phylobase.options(). They allow the modification of the constraints on
checkTree such as allowing polytomies or not. Before there were no
other way to change these options other than changing the source code.
The default values are the same as before (polytomies are ok,
reticulated trees, mutirooted trees, trees with singleton all produce
warnings).

- Non-unique labels are now allowed. I have started to write and adapt
unit tests for this. However, I haven't tried to use the replace
methods for tdata or addData to see how they were behaving. I'll try
to do this in the next few days. Because of this -- at least for now,
objects with duplicated labels return a warning.

- I created a new method, that I called nData() which returns the
number of datasets associated with the tree, in other words, it's just
a wrapper for ncol(x at data). If you have a better idea for the name of
this method, I'll take it.

  If you have any feedback or comment, please let me know!

  Cheers,
  -- François