[Phylobase-devl] Conference call minutes

[Marguerite Butler]

Hi Folks,

Here are two responses to some of the issues in the conference call  
minutes. It was started off-list, so I am copying them here.

Marguerite
-----
Begin forwarded message:

> Hi All,
>
> On Mar 22, 2008, at 11:29 AM, Steve Kembel wrote:
> Hi all,
>
>>> The unique label restriction should be lifted
>>
>>
>>  I don't think it exists, except in the documentation ?
>
>
> The problem with non-unique node labels happens when you try to  
> create a phylo4d object, this will be fixed when we switch to using  
> a vector/list of labels to identify nodes in place of the current  
> use of the row.names of the data frame for node ID and data  
> attachment:
>
> small <- read.tree(text="(((A,B)C,D),E);")
> small4 <- as(small,"phylo4")
> small4d <- phylo4d(small4,node.data=rnorm(3))
>
> Error in `row.names<-.data.frame`(`*tmp*`, value = c("", "", "C")) :
>   duplicate 'row.names' are not allowed
> In addition: Warning message:
> non-unique value when setting 'row.names': ‘’
>

Yes, I realize this. That is why I was insisting earlier that  
matching shouldn't be done on labels. Either they are labels for  
convenience or they are not. We can't have it both ways. If users  
want to match their data, then they should make sure that the data  
are assigned to the proper node by providing the "node index" that  
they match to. It would be a simple thing, so long as they can print  
the node index and enter them into a spreadsheet with the data. It is  
a lot easier, for example, than making sure that each species name is  
spelled correctly in each dataset.

Sometimes this is a big pain because you get one set of species names  
from PAUP or whatever, but you have a different abbreviation in your  
phenotypic data. Then all species must be renamed in one dataset or  
the other.  It's a lot easier just to make sure that a number matches.

Marguerite

>
>>> There was also a proposal to relax the restriction on node  
>>> numbers being 1:length(nodes).
>
> I feel like we're mixing up what I am going to call node indexing  
> and node labelling. Node indexing is purely for internal/ 
> development purposes - currently nodes are indexed as 1:NNodes, all  
> functions and methods can safely assume that they can iterate over  
> nodes in this way, end users never need to think about these  
> numbers unless they want to. Node labelling encompasses any other  
> sort of data or identifier that you want to associate with a node,  
> i.e. for end-users who want to be able to identify nodes that are  
> the 'same node' across multiple trees, which could be implemented  
> as actual node labels accessed via labels() or could be included as  
> node data in a phylo4d object, since both labels and data persist  
> across subset operations.
>
>>> Pros:
>>> Easier diffing of trees. For example, if I have a large tree of  
>>> birds, but only have beak trait data for a subset and tarsus  
>>> length for a different subset, comparing the two subsets is  
>>> easier if the nodes are NOT renumbered.
>
>
> If I understand the example, it sounds like what you want is a set  
> of unique node labels on the large tree of birds that would allow  
> an end-user to match nodes between subsequent subsets of the large  
> tree:
> intersect(labels(subTree1),labels(subTree2))
>
> I think this is a problem that is best solved by adding node labels  
> to the large tree, not by changing the way nodes are indexed by all  
> functions and methods in phylobase. It sounds like we do need a  
> method to create unique node labels, either as labels() or phylo4d  
> data, when users need them? I may just be missing the point of  
> changing the way nodes are indexed, I think about this stuff as  
> someone who writes functions that iterate over the nodes on a tree,  
> which would be more complicated if nodes had arbitrary index numbers.
>
> Cheers,
> Steve

____________________________________________
Marguerite A. Butler
Department of Zoology
University of Hawaii
2538 McCarthy Mall, Edmondson 259
Honolulu, HI  96822

Phone: 808-956-4713
FAX:   808-956-9812
Dept: 808-956-8617
http://www2.hawaii.edu/~mbutler
http://www.hawaii.edu/zoology/

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