[Phylobase-devl] accessor and replace method consistency

[Jim Regetz]

Hi all,

We went ahead and conversed on IRC this morning, and doled out some 
duties regarding testing/fixing functions that might rely on the old 
accessor behavior.

I then committed changes, as proposed, to labels, edgeLength, 
edgeLabels, and nodeId, and added a new edgeId method analogous to nodeId.

During this processes, we (or just I, if you need someone to blame :) 
made a few changes to especially the 'type' defaults. I'm short on time 
right now, but will try to summarize to the group more fully this 
evening. I'll also summarize the related TODOs that I've jotted down. 
It's definitely a very manageable list. More later...

Cheers,
Jim

Ben Bolker wrote:
>   Oops.  I was completely spacing out and thought (believe it or not)
> that Peter said 11 PM PDT (two mistakes, and not very plausible either).
> 
>   I am in agreement about the accessor changes; if you want to assign me
> tasks I will try to give them a shot.
> 
>   Ben
> 
> 
> Jim Regetz wrote:
>> Great idea. I will aim to be on IRC at 11am eastern tomorrow. I think 
>> the main tasks are:
>>
>> * Briefly discuss then commit accessor changes (if we're in agreement). 
>> I have the changes mostly ready to go as proposed, but there are 
>> definitely a couple of minor things I'd love to chat about quickly on 
>> IRC before proceeding. The big exception is tdata -- I haven't touched 
>> it at all, so the work still needs to be done.
>>
>> * Split up duties for inspecting and, if needed, fixing functions that 
>> use one or more of these accessors. I've already cataloged them (see 
>> below), so we can just decide who wants to deal with which ones. Some 
>> clearly aren't affected by the changes, but others are. None of the 
>> fixes should be hard.
>>
>> * Revise the replace methods as needed. I haven't really looked at them yet.
>>
>> I can subsequently create a few simple unit tests of the revised 
>> accessors and setters.
>>
>> Thanks,
>> Jim
>>
>> Existing functions/methods that use one or more slot accessor method:
>>
>>        function/method              file
>>      checkPhylo4Data()       checkdata.R
>>            checkTree()       checkdata.R
>>          .phylo4Data()   class-phylo4d.R
>>           formatData()      formatData.R
>>   `labels<-`("phylo4")  methods-phylo4.R
>>     isRooted("phylo4")  methods-phylo4.R
>>       nodeId("phylo4")  methods-phylo4.R
>>     nodeType("phylo4")  methods-phylo4.R
>>     rootNode("phylo4")  methods-phylo4.R
>>      summary("phylo4")  methods-phylo4.R
>>     summary("phylo4d") methods-phylo4d.R
>>       tdata("phylo4d") methods-phylo4d.R
>>       prune("phylo4d")           prune.R
>>   .phylo4ToDataFrame()   setAs-Methods.R
>>          phylo4->phylo   setAs-Methods.R
>>          `[`("phylo4")          subset.R
>>         `[`("phylo4d")          subset.R
>>         phylobubbles()        treePlot.R
>>          plotOneTree()        treePlot.R
>>        tip.data.plot()        treePlot.R
>>              hasPoly()       treestruc.R
>>             hasRetic()       treestruc.R
>>            hasSingle()       treestruc.R
>>             ancestor()        treewalk.R
>>             children()        treewalk.R
>>      getNode("phylo4")        treewalk.R
>>
>>
>>
>> Peter Cowan wrote:
>>> On Sep 5, 2009, at 2:09 PM, François Michonneau wrote:
>>>
>>>> On Fri, 2009-09-04 at 17:37 -0700, Jim Regetz wrote:
>>>>
>>>> I agree.
>>>>
>>>> I can help with the changes (mostly in the evening). Maybe we can
>>>> organize an IRC meeting to distribute the tasks? Tuesday, 11am EST?
>>> Good idea.  Tuesday works for me.  In fact, I'm usually logged into  
>>> IRC and so is Jim, which is handy when I have a quick phylobase  
>>> question.  I'll try to be around IRC more this week.
>>>
>>> Peter
>>>
>>>> Cheers,
>>>> -- François
>>>>
>>>>> Thoughts?
>>>>>
>>>>> Jim
>>>>>
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