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

Sang Chul Choi Choi at Biology.Rutgers.Edu
Mon Apr 7 02:35:44 CEST 2008


Hi,

I am reading phylo4d class, which has node.data as one of its  
parameter. I think that I could use phylo4d class to put mutation  
events on branches.

Thank you,

Sang Chul

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

On Apr 6, 2008, at 9:20 PM, Ben Bolker wrote:

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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