- Le 27 Juin 20, à 16:53, Yan Wong y...@pixie.org.uk a écrit :
> This is extremely helpful, thanks Emmanuel. I think it might be useful to note
> this in the documentation for multi2di (or give a pointer to the description),
> as it wasn’t obvious to me how to find out this information from
Thanks very much Martin. I’m glad that I brought this up (I think the
documentation should probably make this clearer). Your extra functions,
together with the corrected Dendropy code and Emmanuel’s hints, should all be
useful for me to check I’m doing it right for larger trees.
Cheers
Yan
>
This is extremely helpful, thanks Emmanuel. I think it might be useful to note
this in the documentation for multi2di (or give a pointer to the description),
as it wasn’t obvious to me how to find out this information from within R. Even
better would be an option that allowed equiprobable
Hi Yan,
multi2di() calls rtree() if random = TRUE. As you rightly guessed, the
algorithm used by this latter function is (described in APER2, p. 313):
1. Draw randomly an integer a on the interval [1, n − 1]. Set b = n − a.
2. If a > 1, apply (recursively) step 1 after substituting n by a.
3.
5.864.5860
==
From: R-sig-phylo on behalf of Yan Wong
Sent: Friday, June 26, 2020 4:46 PM
To: r-sig-phylo@r-project.org
Subject: [R-sig-phylo] Breaking polytomies such that all topologies are
equiprobable
I�m trying to figure out how t
I’m trying to figure out how to randomly resolve polytomies such that there is
an equal probability of any topology being generated. I thought that the ape
function “multi2di” did this, but when I have tried it repeatedly with a
4-tomy, multi2di seems to produce the 3 balanced trees
