[Phylobase-devl] phylo4: tabulate() requires nbins argument

[Ben Bolker]

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~  At the moment plot.phylo detects these "singleton nodes"
(as I call them) and asks the user to get rid of them ...
so I wouldn't feel bad about relaxing the rule now and
waiting for the plotting code to catch up.

~ if (any(tabulate(x$edge[, 1]) == 1))
~        stop("there are single (non-splitting) nodes in your tree; you
may need to use collapse.singles().")



Thibaut Jombart wrote:
| Hi people !
|>     ~  Now, I will admit that we do not currently prevent this; we should
|>     (1) decide whether we want to accept all of these rules for phylo4
|>     objects as well (I would like to eliminate rule b below, to
|>     allow "singleton" nodes); (2) add these rules to phylo4 object
|>     checking so that they can't happen.
|>
|>     ~  Thoughts, anyone?
|>
|>     ~  Ben
|>
| I agree we could relax rule b. I think we should get progressively
| independent from ape where it is useful. But maybe we should wait for
| the plot stuff to be recoded (I think this part includes most of the C
| code that phylobase calls from ape). We have seen how ugly it can get
| when we try to plot malformed phylo objects, and we cannot decently ask
| users not to plot there data until new methods are available.
|
| Cheers,
|
| Thibaut.
|>
|>     b· All nodes appear in the first column at least twice.
|>
|
|

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