c concatenates all arguments. For example, c(c(0,1,2), c(3,4,5)) gives a vector 0,1,2,3,4,5. Another example:
> c(list(a=c(0,1), b = c(2,3)), list(c = c(4,5), d = c(5,6))) $a [1] 0 1 $b [1] 2 3 $c [1] 4 5 $d [1] 5 6 So instead of a list of two lists, you get a single list with 4 components. If you want to make a list of objects, use list_of_fits = list(fitJC1, fitJC2, fitJC3) HTH, Peter On Wed, May 26, 2010 at 5:23 PM, Nick Matzke <mat...@berkeley.edu> wrote: > > > 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 problem: > > #==================== > # example of the issue with lists of objects: > > library(ape) > library(phangorn) > example(NJ) > > # Jukes-Cantor (starting tree from NJ) > fitJC1 <- pml(tree, Laurasiatherian) > > # optimize edge length parameter > fitJC2 <- optim.pml(fitJC1) > fitJC2 > > # search for a better tree using NNI rearrangements > fitJC3 <- optim.pml(fitJC2, optNni=TRUE) > fitJC3 > > # 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. > (list_of_fits[1]) > > #...does not return the same thing as: > (fitJC1) > #==================== > > > > > > > -- > ==================================================== > 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 > http://ib.berkeley.edu/courses/ib200a/index.shtml > > Lab websites: > http://ib.berkeley.edu/people/lab_detail.php?lab=54 > http://fisher.berkeley.edu/cteg/hlab.html > Dept. personal page: > http://ib.berkeley.edu/people/students/person_detail.php?person=370 > Lab personal page: http://fisher.berkeley.edu/cteg/members/matzke.html > Lab phone: 510-643-6299 > Dept. fax: 510-643-6264 > Cell phone: 510-301-0179 > Email: mat...@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. > http://chem.tufts.edu/AnswersInScience/RelativityofWrong.htm > > ______________________________________________ > R-help@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. > ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
