Thanks! I tried that before but for some reason didn't
notice that it was working correctly.
PS: How would I append another element to the list? This
doesn't work:
x = append(list_of_fits, fitJC1)
# still works, from original list construction
x[3]
# but this doesn't work
x[4]
Cheers!
Nick
Peter Langfelder wrote:
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.
--
====================================================
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.
