[Phylobase-devl] File reorgnization

[Thibaut Jombart]

Peter Cowan wrote:

>Hi all,
>
>I've move a bunch of code around and attempted to pretty up the code  
>as well.  The most obvious changes should be fairly self explanatory.
>
>phylo4, phylo4d have their own file for class definition and  
>constructors.  I put both multiphylo definitions in the same file as  
>they are small, the same goes for the oldClass definitions.
>
>All setAs() functions are condensed into one file.
>
>I moved all the methods for the classes, into Method-"class" files.
>
>While I did this I removed a couple of methods that have been long  
>commented out.  If this is problem, it's easy enough to get them back  
>(yea, svn).
>
>I also attempted to clean up much of the code, given that I was doing  
>large code moving already.
>
>Mostly I did the process described here:
><http://cran.r-project.org/doc/manuals/R-exts.html#Tidying-R-code>
>
>And, put comments back by hand.  In other cases, especially the class  
>definitions, this didn't make the code clearer, so I added spaces to  
>either side of operators (e.g. foo(bar = baz) instead of foo(bar=baz))  
>and a space after every comma.
>
>There appear to be two functions for printing phylo4 objects,  
>printphylo() and printphylo4() with the latter seemingly the default,  
>can we, should we delete one?
>
>I still find the Methods-phylo4 file a bit much.  And, I didn't move  
>methods that were in separate files, such as subset and plot.  Maybe  
>the longer methods should be moved to individual file like subset and  
>plot already are?
>
>The package passes R CMD check on my computer, and hopefully I haven't  
>messed anything up.  It'd be great if others could clean up the last  
>of what is left in phylo4.R, including perhaps renaming it to  
>"generics-phylo4.R".
>
>Happy hacking,
>
>Peter
>  
>
Great ! It passes the check for me.

Thanks Peter.

Thibaut.

-- 
######################################
Thibaut JOMBART
CNRS UMR 5558 - Laboratoire de Biométrie et Biologie Evolutive
Universite Lyon 1
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Tél. : 04.72.43.29.35
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jombart at biomserv.univ-lyon1.fr
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