[Phylobase-devl] Conference call minutes

[Thibaut Jombart]

Ben Bolker wrote:
> Thibaut Jombart wrote:
>> Hi all,
>>
>> sorry for not being there on friday's talk.Here are some comments 
>> about your resolutions.
>>>
>>>       Node index and labels
>>>
>>> There was an extensive discussion regarding node labeling and 
>>> indexing. It was determined that:
>>>
>>>    1. There should be /no/ default labels
>>>    2. The unique label restriction should be lifted.
>>>
>> While I understand that we can do without default labels, I can think 
>> of a case were multiple identical labels would be useful. Even for 
>> missing labels, I guess that their values should be NA rather than "".
>
>    ?? I think we are saying it *is OK* to have multiple labels.
> NA is an interesting possibility: what happens when it gets printed?
> (Appears to work OK in plot.phylo ...)
>
Sorry for the typo here; I meant: 'I can *not* think of a case were 
multiple identical labels would be useful.' I do not think NAs in labels 
could be a problem for plotting, since we can replace them internally by 
"" before plotting.
>>>    *
>>>
>>>       Different from the |ape| implementation
>>>
>> This would not be such a problem if we knew how all the code calling 
>> ape functions will be affected... do we? Anyway, I think we'll 
>> diverge from ape soon or later, so this time may be as good as any.
>
>   We should really really really try to get a series of "unit tests"
> compiled, for the expected results of various phylogenetic 
> manipulations -- does everyone know that if you save the output from a 
> test file to
> the /tests directory, checking the package will compare the output of
> the test file to the reference output?
I didn't. This sounds interesting.

Thibaut.