[Phylobase-devl] Issues with NCL and/or NCL interface

[François Michonneau]

> Obviously, this feature doesn't play nice with polymorphic characters.
>
> Why not? Is there a difference between '{0, 1}' and '{nocturnal, diurnal}'?
> The latter would only be an issue if some state names had commas in them,
> but that's such an infrequent use case that we could just have a warning if
> a comma in a state name is detected and there is a polymorphic character.

It's just because of the way the labels are encoded. It would (in
theory) be possible to come up with {nocturnal, diurnal} coding for
the levels but it would require some good amount of coding I think.

The code I committed today brings a few bug fixes, and it's now
possible to import several matrices from the same nexus file: for
instance discrete (e.g. datatype=Standard) and continuous (e.g.
datatype=Continuous). I however finished this part last, and the unit
tests still need to be written for this. Another area of investigation
would be sequence data... Otherwise, I think we have a pretty robust
readNexus function now...

  Cheers,
  -- François

  Cheers,
  -- François