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

[Ben Bolker]

   OK, now I'm confused.  Why can't we extend the branches
with singleton nodes?  Or is it that this is feasible but
would require to much hacking around (i.e., if we write
good tools we can still do it this way)?

   After deciding to throw out the edge data structure, I'd like to
see a good reason to put it back in ...

   but maybe I'm just confused about what's needed.

   cheers
     Ben


Peter Cowan wrote:
> Hi Sang Chul,
> 
> Thanks for taking a look at phylobase!  As you can see we are still  
> early on in the development (version 0.3) and greatly appreciate any  
> feedback we can get from users, so please keep the questions and bug  
> reports coming.
> 
> As I'm sure you've seen by now there are two basic data classes for  
> single trees, the phylo4 class and the phylo4d class.  This later one  
> is the probably interested in using.
> 
> As of now there is no good mechanism for adding variable length (such  
> as stochastic mutations) data to edges.  This was discussed on the  
> list a couple of weeks ago, but nothing is implemented yet.
> 
> One way to do this would to extend the phylo4d class and include a  
> slot for edge data that takes a list.  This approached was used with  
> ape style trees in the evolve.trait() function in the picante package  
> [^1](also alpha stage).
> 
> Peter
> 
> [1] <http://r-forge.r-project.org/projects/picante/>
> 
> 
> On Apr 6, 2008, at 5:16 PM, Sang Chul Choi wrote:
>> 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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