[Phylobase-devl] Splitting up the source files

Peter Cowan pdc at berkeley.edu
Thu Feb 28 00:29:06 CET 2008

To follow up on my own suggestion, I looked at several S4 packages.   
Most packages break up the class definitions and the methods into  
separate files.

I have two possible suggestions, once we decide I'm willing to  
implement it.  The only downside to implementing this is that we are  
going to lose file histories in SVN, but we'd have the opportunity to  
settle on some coding standards such as those of bioconductor <http://wiki.fhcrc.org/bioc/Coding_Standards 

1. One file with all the class descriptions and one with all the  
generics, with methods in files named for the generic, e.g show- 
methods.R.  This the approach of bioconductor and lme4, which has a  
similar number of classes but fewer methods.

2. One file for each class (e.g. a phylo4 file, phylo4d file,  
multiphylo file ...) and a corresponding generics/methods file for  
each.  This is the approach of the sp package, which is similar in  
number of classes and methods.


On Feb 26, 2008, at 1:24 PM, Peter Cowan wrote:

> Would it be possible to divide up the source files a bit more.  Right
> now phylo4.R is a bit difficult for me to navigate.  Could one of the
> developers more familiar with it, pick natural divisions?
> Peter
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