[Phylobase-devl] phylobase in R comparative methods course

[Marguerite Butler]

Ooops sorry!  One more question.

One thing that I couldn't figure out was given a tree, how get the rep 
() function to make a list of duplicate trees. I just wanted to make  
a list of 10 trees, for example, and then try to modify them. Maybe  
there's a better way?

Thanks,
Marguerite

On Jul 22, 2008, at 4:20 PM, Marguerite Butler wrote:

> Hi Folks,
>
> I will be teaching the R comparative methods workshop at NESCENT  
> very soon. I know you are probably very busy trying to get  
> everything done before summer ends, but if you have the time and  
> inclination to look this over, please do so. Any comments at all  
> would be greatly appreciated.
>
> I tried to show off some of the major features of phylobase,  
> working from the vignette mostly. I know that there have been new  
> developments, so if you'd like them featured, please send me code  
> snippets.
>
> In general, I think the appeal to end users would be much greater  
> if there were packages that use the phylo4d structure (or at least  
> and equivalent). I don't know much, so maybe it's already out  
> there? But as far as I understand, there's no tree+data object in  
> ape, for example, so the best users can do is to take their phylo4d  
> object, and export the phylo tree plus the data frame. Of course  
> it's in the proper order and with appropriate labels, but being  
> able to use it more directly would be better.
>
> The subsetting function with the [ was a little confusing at first.  
> I had it stuck in my mind that you could use it to access tree  
> elements (replacing the value of a branch length, for example). But  
> I got it ... it returns a subtree only.
>
> Also, I consistently get this warning when I generate the Sweave  
> document:
>
> Warning messages:
> 1: In findGeneric(nm, envir = as.environment(w)) :
>   'subset' is a formal generic function; S3 methods will not likely  
> be found
>
> It would be nice if we could run the code without warnings. I'm  
> trying to impress upon the students that they should write code  
> that is error-free:).
>
> Thanks!
> Marguerite
>
> This is a very rough draft for the first part of the class which is  
> for the "users".  I am still wondering if I should cut out some of  
> the S3 S4 content.
>
> The S3 vs. S4 classes chapter:
>
>
> <Untitled.pdf>
>
>
> The Phylobase chapter:
>
> <Untitled.pdf>
> ____________________________________________
> Marguerite A. Butler
> Department of Zoology
> University of Hawaii
> 2538 McCarthy Mall, Edmondson 259
> Honolulu, HI  96822
>
> Phone: 808-956-4713
> FAX:   808-956-9812
> Dept: 808-956-8617
> http://www2.hawaii.edu/~mbutler
> http://www.hawaii.edu/zoology/

____________________________________________
Marguerite A. Butler
Department of Zoology
University of Hawaii
2538 McCarthy Mall, Edmondson 259
Honolulu, HI  96822

Phone: 808-956-4713
FAX:   808-956-9812
Dept: 808-956-8617
http://www2.hawaii.edu/~mbutler
http://www.hawaii.edu/zoology/

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