[Phylobase-devl] Conference call minutes

[Ben Bolker]

Hilmar Lapp wrote:
> 
> On Mar 23, 2008, at 6:07 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.
> 
> For reticulating "trees" that's actually not true (though phylo4 might 
> expressly prohibit reticulating trees; but even if it does, it may still 
> be better to be prepared for a future extension that doesn't).

   Hmm.  I would think that might be a way in the future ...
> 
>> There are (usually) multiple descendants,
>> so this shortcut doesn't work for descendants.
>>
>>   (1) we could leave it this way (too confusing?)
> 
> I think anything that wouldn't provide for a default that's consistent 
> between the two is going to result in a gotcha for users. I'm a fan of 
> the principle of least surprise, and inconsistent defaults I would think 
> will be a surprise for many.
> 
>>   (2) we could switch the default to "tips" (probably the second
>> most common request)
> 
> But that's also not consistent with the "all" default of ancestors().
> 
> Just my $0.02.
> 
>     -hilmar

   So what would you recommend ... ?

   Ben


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