[Phylobase-devl] accessor and replace method consistency

[Ben Bolker]

  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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-- 
Ben Bolker
Associate professor, Biology Dep't, Univ. of Florida
bolker at ufl.edu / www.zoology.ufl.edu/bolker
GPG key: www.zoology.ufl.edu/bolker/benbolker-publickey.asc

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