[Phylobase-devl] I am on hopefully the right track in manipulating "trees" using R.

[Sang Chul Choi]

Hi,

I think that mutation events on branch may be tree information  
additional to branch length. I am wondering whether adding mutation  
events directly to phylo4 class or indirectly subclassing phylo4 class  
is better. Since I have been skimming through phylobase code for a  
day, I am not sure which way is good one for me. I will appreciate any  
input.

Thank you,

Sang Chul

On Apr 6, 2008, at 7:30 PM, Sang Chul Choi wrote:

> Hi,
>
> I think that I might have to change or extend phylo4 class if I want
> to have mutation events on branches. Otherwise, I may have to have
> other variables out side the phylo4 class, which does not seem to be a
> good idea.
>
> Thank you,
>
> Sang Chul
>
> On Apr 6, 2008, at 7:04 PM, Sang Chul Choi wrote:
>
>> Hi,
>>
>> After asking a few people, I think that I am on the right place to do
>> manipulation of "trees" using R.
>>
>> I am trying to do a simple coalescent simulation: 1. generates a
>> genealogy, and 2. puts mutations on each branch. I am wondering if I
>> could use phylobase package to do the second one.
>>
>> Thank you,
>>
>> Sang Chul
>>
>> P.S. The vignette (0.3r104) has typos at page 5.
>>> NodeLabels(g1)   ---> > nodeLabels(g1)
>>> EdgeLabels(g1)   ---> > edgeLabels(g1)
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>