[Phylobase-devl] Conference call minutes

Marguerite Butler mbutler at hawaii.edu
Mon Mar 24 21:40:26 CET 2008


On Mar 23, 2008, at 12:07 PM, Ben Bolker wrote:

> Hilmar Lapp wrote:
>> On Mar 22, 2008, at 2:56 PM, Peter Cowan wrote:
>>> ancestors(..., which = c("all", "parent")) # default to "all"  
>>> since ancestor() exists
>>>
>>> descendants(..., which = c("children", "tips", "all")) # first  
>>> option calls children()
>> Does that mean the default for descendants() is which="children",  
>> meaning only direct children? Isn't that inconsistent with the  
>> default of ancestors()?
>>     -hilmar
>
>   Yes, it is.
>   The problem is that I think people will frequently want to access  
> direct ancestors and descendants (parents/children).  "ancestor" is
> a nice short term for "only direct ancestors", because there is by
> definition only one of them.  There are (usually) multiple  
> descendants,
> so this shortcut doesn't work for descendants.
>
>   (1) we could leave it this way (too confusing?)
>   (2) we could switch the default to "tips" (probably the second
> most common request), and indicate that children() is available if
> one wants a shortcut for descendants(tree,which="children")
>
>   votes?
>

I vote for ancestor() = direct ancestor, and descendant() = direct  
descendant.
ancestors() = all ancestors by default, descendants() = all  
descendants by default.
descendants(some option for tips only) = tip descendants only.

I know that grammatically it is not corrrect to use the singular form  
when there could be more than one, but it could simply be explained  
in the help file that this is to make it logically consistent (which  
I think is more important).

I don't have any feeling for whether users will want tips only more  
often than all descendants. But if someone is sophisticated enough to  
be editing the trees in this fashion (or subsetting the data), then I  
think it's simple enough for them to learn to set an option.

Marguerite

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

Phone: 808-956-4713
Lab:  808-956-5867
FAX:   808-956-9812
Dept: 808-956-8617
http://www.hawaii.edu/zoology/faculty/butler.html
http://www2.hawaii.edu/~mbutler
http://www.hawaii.edu/zoology/


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