[Phylobase-devl] phylobase in R comparative methods course
mbutler at hawaii.edu
Wed Jul 23 08:09:40 CEST 2008
I noticed that the pdfs didn't go through. I've posted them on my
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?
> 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
>> 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
>> 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:).
>> 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:
>> The Phylobase chapter:
>> 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
> 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
Marguerite A. Butler
Department of Zoology
University of Hawaii
2538 McCarthy Mall, Edmondson 259
Honolulu, HI 96822
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