[Phylobase-devl] accessor and replace method consistency

[Jim Regetz]

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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