[R] list of complex objects?

Nick Matzke matzke at berkeley.edu
Thu May 27 02:23:12 CEST 2010

Erik Iverson wrote:
> Nick Matzke wrote:
>> Hi all,
>> If I would like to make a list of complex objects -- in my case, 
>> phylogenetic trees, but it could be e.g. statistical results from 
>> something like lm, or whatever -- how can I put them into a list?
>> When I try the obvious methods, e.g. cat, append, list, etc., I seem 
>> to get weird behaviors where R is trying to merge the subfields within 
>> the objects or something.
>> Any help much appreciated.  Cheers!!
>> Nick
> Perhaps you can give us a reproducible example that shows
> a) what you tried
> b) what happened
> c) what you expected to happen

Hi!  Sorry, I should have done that initially.  Here's my 

# example of the issue with lists of objects:


# Jukes-Cantor (starting tree from NJ)
fitJC1 <- pml(tree, Laurasiatherian)

# optimize edge length parameter
fitJC2 <- optim.pml(fitJC1)

# search for a better tree using NNI rearrangements
fitJC3 <- optim.pml(fitJC2, optNni=TRUE)

# Now, the function SH.test can allegedly take "objects of
# class 'pml' separated by commas, [or] a list containing
# such objects".  Since I'm going to have hundreds of these
# fits, I'd like to make submit a list of them to SH.test,
# something like this:

list_of_fits = c(fitJC1, fitJC2, fitJC3)
SH.test(list_of_fits, B=100)

# ...but "list of fits" is something weird, e.g.

#...does not return the same thing as:

Nicholas J. Matzke
Ph.D. Candidate, Graduate Student Researcher
Huelsenbeck Lab
Center for Theoretical Evolutionary Genomics
4151 VLSB (Valley Life Sciences Building)
Department of Integrative Biology
University of California, Berkeley

Graduate Student Instructor, IB200A
Principles of Phylogenetics: Systematics

Lab websites:
Dept. personal page: 
Lab personal page: 
Lab phone: 510-643-6299
Dept. fax: 510-643-6264
Cell phone: 510-301-0179
Email: matzke at berkeley.edu

Mailing address:
Department of Integrative Biology
3060 VLSB #3140
Berkeley, CA 94720-3140

"[W]hen people thought the earth was flat, they were wrong. 
When people thought the earth was spherical, they were 
wrong. But if you think that thinking the earth is spherical 
is just as wrong as thinking the earth is flat, then your 
view is wronger than both of them put together."

Isaac Asimov (1989). "The Relativity of Wrong." The 
Skeptical Inquirer, 14(1), 35-44. Fall 1989.

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