plotBeta cannot handle phylogenies where the tip names contain parentheses about hmsc

[jarioksa]

Confirmed, but I don't know yet how to fix this, or should we leave this for users to fix. This is indeed documented behaviour in ape:::write.tree():

The tip labels (and the node labels if present) are checked before
being printed: the leading and trailing spaces, and the leading
left and trailing right parentheses are deleted; the other spaces
are replaced by underscores; the commas, colons, semicolons, and
the other parentheses are replaced with dashes.

The tip labels are sanitized, because parentheses and some other characters have special meaning in Newick trees that we handle later in the code. The taxon names are sanitized in the Newick tree, but not in the other data (Traits, Y data) and this gives the mismatch where taxa in Y are not found in the tree.

If you have an idea how to fix this, please feel free to submit a fix.