[Phylobase-devl] improving getNode handling of NA_character_ and missing node IDs

Jim Regetz regetz at nceas.ucsb.edu
Thu Jun 18 00:54:27 CEST 2009

Hi all,

This is a followup to my recent r-forge bug report [#458]. See there for 
details. Sorry to split between these two modes of communication; my 
impression is that this list is the way to go for proposing/discussing 
changes, yet I'm definitely inclined to use the bug tracker for, well, 
tracking bugs. I'm certainly happy to do things differently in the 
future if its preferable.

The attached treewalk.R patch represents my proposed changes to getNode. 
In this revision, the result vector returns NA values with <NA> names 
both for nonexistent integer node IDs (i.e., those not occurring in the 
tree) and for NA characters, and the missingness check works in both cases.

I've also eliminated what seemed to be superfluous code that struck me 
as a holdover from when the function relied on a version of labels() 
that only matched tips. The updated version checks out well in my 
testing. However, it would be great if someone (Ben, as original 
author?) could do a sanity check.

Side question: are folks generally fine with communicating proposed 
changes in the form of attached patch (unified diff), as I've done here?


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