Hi all,
I am thinking to remove the option 'original.data' in write.nexus(). The
reasons are:
1. It doesn't seem useful because most NEXUS files read by this function
store only trees (at least those reported to me). I believe most users
keep their data (seqs, morpho, ...) and trees in separate files.
2. If some tips are deleted/removed from the tree, keeping track with
the original file might be tricky (currently nothing is done to check this).
3. phylobase has better support for NEXUS files, so trying to fix the
above in ape will be redundant.
4. Removing this option will make write.tree() slightly more efficient.
Any advice/comment welcome.
Cheers,
Emmanuel
--
Emmanuel Paradis
IRD, Jakarta, Indonesia
http://ape.mpl.ird.fr/
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