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

[Sang Chul Choi]

I think that that is enough information for me. Thank you so much. I  
am going home now.

Thank you,

Sang Chul

On Apr 6, 2008, at 11:35 PM, Ben Bolker wrote:

>
>  If you're willing to set a maximum number of mutations, and
> live with some inefficiencies, you can do this by setting up
> a matrix with times, with NAs filling in beyond the number of
> mutations -- so if there were 0, 1, 2, 0 mutations (say) along
> 4 edges the mutation-time matrix would be
>
> NA,  NA, NA, NA
> t11, NA, NA, NA
> t21, t22, NA, NA
> NA, NA, NA, NA
>
>  I can't send you code for how to do this at this moment ...
>
>  Ben Bolker
>
>
>
>
>
> Sang Chul Choi wrote:
>> 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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