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

[Peter Cowan]

Ben,

I think we could take that approach, but it *could* require changes to  
the plotting commands, and a variety of other commands.

To meet it seems a bit overboard to update the tree structure when  
mapping data onto a tree.  For example, if I want to generate a null  
model of a character then I have to store a 1000 copies of a tree,  
instead of some lists that correspond to a tree. Also, adding data to  
a list is going to be far less expensive than rewriting the whole edge  
matrix every time the state changes (does that example make sense?).

Are you thinking that we want to support singleton nodes anyway, and  
then we can use them to store edge data?  That would potentially make  
plotting them easier.

I don't recall if there was a consensus view before, which is probably  
why nothing has happened.

Peter

On Apr 6, 2008, at 6:50 PM, Ben Bolker wrote:
>  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)
>>>>> _______________________________________________
>>>>> Phylobase-devl mailing list
>>>>> Phylobase-devl at lists.r-forge.r-project.org
>>>>> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/phylobase-devl
>>> _______________________________________________
>>> Phylobase-devl mailing list
>>> Phylobase-devl at lists.r-forge.r-project.org
>>> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/phylobase-devl
>> _______________________________________________
>> Phylobase-devl mailing list
>> Phylobase-devl at lists.r-forge.r-project.org
>> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/phylobase-devl
>
>