[Phylobase-devl] several proposed additions

Hilmar Lapp hlapp at duke.edu
Wed Jun 24 15:04:09 CEST 2009

Hi Jim -

this sounds great! I can't speak on behalf of the phylobase leads, but  
can you commit all your changes to a branch? That would make it  
easiest for people to check out and play with your code. The unit  
tests sound cool - haven't been aware of this, but if it is what the  
name suggests it will be highly useful.


On Jun 24, 2009, at 3:45 AM, Jim Regetz wrote:

> Hi all,
> I'd love to get feedback on any/all of the following. Below, when I  
> talk
> about things I've done, I mean in my local sources -- I haven't  
> actually
> committed any of the following. But it is all more or less ready to  
> go,
> albeit with a couple of minor rough edges that we can discuss  
> further if
> folks want to move ahead on any of these:
> * NAMESPACE: I've created one. Seems to work fine. I'm basically
> exporting all functions and methods now. I figure it's easier to start
> with a liberal approach, and later remove whatever items folks agree  
> are
> only required internally.
> * Unit tests: I've created a handful of RUnit tests, and added the
> necessary "run tests" machinery as documented here:
> http://wiki.r-project.org/rwiki/doku.php?id=developers:runit
> The tests are not even remotely comprehensive, but they do test  
> against
> the bug fixes I've implemented in the last week or so. I find unit  
> tests
> to be hugely helpful in making sure that fixed bugs stay fixed, and  
> that
> code changes in one area don't unexpectedly break things somewhere  
> else.
> And I find RUnit testing to provide better structure and test
> expressivity than you get with unstructured test scripts in the pkg/ 
> test
> directory.
> I'm not 100% certain that R-forge would do the right thing with these
> tests without some additional tweaking, but they are successfully  
> run by
> R CMD CHECK on my local machine (at least as long as phylobase is
> already installed).
> * phylo4 generic: Any reason why there has been a generic for phylo4d,
> but not phylo4? I've now created a phylo4 generic, along with two
> methods: one with signature x="matrix" (replacing the original phylo4
> constructor function), and one with signature x="phylo" (imports phylo
> to phylo4). I updated the associated doc pages to match, plus fixed a
> few places in the examples and sources where phylo(edge=...) was  
> called
> explicitly (the first argument is now the more generic 'x', not  
> 'edge').
> * Dealing with messy node labels: My motivation for creating the  
> phylo4
> generic was to expose an option allowing node labels to be dropped  
> (or,
> in the case of phylo4d, added to the tree data) during phylo import.
> This is basically just a modified implementation of what François  
> did to
> deal with MrBayes sorts of trees, except now focused specifically on
> phylo import (it could be added elsewhere too), and now with user- 
> level
> control of the behavior. I'm glossing over the details, but for those
> not paying attention to the bug tracker, see more discussion here:
> https://r-forge.r-project.org/tracker/index.php?func=detail&aid=466&group_id=111&atid=488
> FYI, R CMD CHECK passes on all the above changes (well, aside from a
> latex documentation issue that I think has been around for some time).
> I'll be traveling much of the next month, but would be happy to  
> discuss
> any of this further. And of course, I can push some/all of this up to
> the repository at any time, or send relevant code to the list if  
> requested.
> Thanks,
> Jim
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: Hilmar Lapp  -:-  Durham, NC  -:- hlapp at duke dot edu :

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