[Phylobase-devl] phylobase in R comparative methods course

[Marguerite Butler]

Hi Everyone,

I noticed that the pdfs didn't go through. I've posted them on my  
website:

http://www2.hawaii.edu/~mbutler/PDFs/Ch10.Phylobase.pdf
http://www2.hawaii.edu/~mbutler/PDFs/Ch9.S3vsS4.pdf

Thanks,
Marguerite

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

> 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/
>

____________________________________________
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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