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

[Sang Chul Choi]

Hi,

I cannot keep up with last few correspondences since I am learning  
phylobase package. This may be due to my lack of knowledge of "using  
R." Since it is okay for me to know how many mutation events  
"happened" on branches, I could use one more column to phylo4 class  
e.g., n.mutations. The following code would generate a genealogy with  
one mutation event for each branch.

 > c1 <- rcoal(10)
 > c2 <- as(c1, "phylo4")
 > c2d <- phylo4d(c2, node.data=data.frame(n.mutations=c(0,rep(1,8))))

Here is my question. Is it possible or legitimate to have a phylo4d  
object that has mutation events with their event time points? Then,  
each node has an array of mutation event time not a single value that  
is the case for number of mutations.

Thank you,

Sang Chul

On Apr 6, 2008, at 9:08 PM, Peter Cowan wrote:

> 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)
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