Hi! Thanks for the replies, comments below:
On 6/20/12 3:26 AM, Oliver Ruebenacker wrote:
Hello,
For an optimization strategy, we need to know more: do you have many
variables? do you have many different formulae? do you re-calculate
after changing only one variable?
Take care
Oliver
The probability of each transition (each cell in the matrix)
will be a function of 1-5 variables, depending on the
complexity of the model. And actually I am going to use a
Bayesian MCMC approach, changing variables one at a time and
accepting/rejecting the move using Metropolis-Hastings.
(However, I am interested in complementing this with an ML
approach, if you have any advice.)
I've got some libraries working for exponentiating large
matrices, so the main issue is just re-calculating the
relative rates for each cell when a variable changes.
This might work as a function that is called once instead of
for every cell, I will explore this:
On 6/19/12 8:32 PM, Joshua Wiley wrote:
> Hi Nick,
>
> Off the cuff:
>
> doit2<- function(s, d, e) {
> matrix(c(s, d, d*d, e, s, d*e, e*e, e*d, s), 3,
byrow=FALSE)
> }
>
> doit2(s, d, e)
>
> seems like it should offer a substantial speed up.
Unless the matrix
> can be populated with arbitrary formulae, I do not see
why it should
> be a text matrix and then evaluated. If you have not
already, I would
> also encourage you to check out OpenMx. It is a rather
flexible
> matrix optimizer, and you may be able to get it to do
what you want.
>
>
http://openmx.psyc.virginia.edu/docs/OpenMx/latest/Likelihood_Matrix.html
>
> Cheers,
>
> Josh
--
====================================================
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
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-----------------------------------------------------
"[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
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--
====================================================
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, IB200B
Principles of Phylogenetics: Ecology and Evolution
http://ib.berkeley.edu/courses/ib200b/
http://phylo.wikidot.com/
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
1005 Valley Life Sciences Building #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.
