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

[Ben Bolker]

Sang Chul Choi wrote:
> Hi,
> 
> So am I since I could hear after three my own postings.
> 
> That is helpful. I do not know what OUCH means, but I will look for it. 
> What I want to do is to help me understand coalescent theory. Mutation 
> events on branches may be of non-negative numbers. Do you think that I 
> could use phylo4 class to add some information on each node without 
> changing phylobase code?
> 
> It would be nice to plot mutations events on branches, but it is not my 
> priority.
> 
> Thank you,
> 
> Sang Chul

   OUCH (perhaps better lowercase? I don't know) is Butler and
King's package for estimating the parameters of Ornstein-Uhlenbeck
processes.

   I just saw your other message, and yes, that's what I meant -- using
phylo4d to assign node information (meaning really branch information).

   One thing to keep in mind is that the "phylobase-devl" community
is still pretty small -- there are only 5 or 6 active developers.
So we'll try to answer your questions as promptly as possible,
but it might take a day or two sometimes ...

   cheers
     Ben Bolker



> 
> On Apr 6, 2008, at 9:20 PM, Ben Bolker wrote:
> 
>>    We had envisioned people adding branch information by coding
>> it as "node" information, with the understanding that the information
>> would apply to the branch/edge directly ancestral to a given node
>> (since this is unique).  (We originally had a separate data section
>> for edge information, but got rid of it since it can be coded
>> equivalently as node information.)
>>
>>  If you need to have more than one event on a branch, you can
>> subdivide the branch by adding "singleton" nodes (this is the
>> way OUCH works), but you won't be able (yet) to plot those
>> trees ...
>>
>>  does that help?
>>
>>  it's very exciting that someone is using phylobase!
>>
>>  Ben Bolker
>>
>> 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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>>>>>
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>>
>>


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