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
On Tue, Jun 19, 2012 at 8:10 PM, Nick Matzke <mat...@berkeley.edu> wrote:
> Hi all,
>
> This question is slightly weird. I am trying to populate a matrix with
> equations. The matrix represents transition probabilities between states.
> A simple example is:
>
> state1 state2 state3
> state1 s d d*d
> state2 e s d*e
> state3 e*e e*d s
>
> The parameters s, d, and e need to be optimized with an iterative algorithm.
> This means I have to modify, say, d, and then recalculate the transition
> probabilities for each cell.
>
> Currently, I do this by making a matrix with the equations in character
> format, setting s, e, and d to values, and then running each cell through
> parse(eval(text=celltxt)). As follows:
>
> #################################
> # Test code:
> # Make the text matrix
> txtmat = matrix(c("s", "d", "d*d", "e", "s", "d*e", "e*e", "e*d", "e*d"),
> nrow=3, byrow=TRUE)
>
> s=0.7
> d=0.2
> e=0.1
>
> doit <- function(celltxt)
> {
> cellval = eval(parse(text=celltxt))
> return(cellval)
> }
>
> # Calculate the matrix with numerical values
> matrix_vals = sapply(X=txtmat, FUN=doit)
> valmat = matrix(matrix_vals, nrow=3, byrow=TRUE)
> valmat
> # End test code
> #################################
>
>
> ...however, this seems to get slow for large matrices. Since I have to
> optimize all the parameters I need something that updates the matrix quickly
> when s, d, or e is changed. Perhaps this is a job for pointers in C++ or
> something, but I figure there must be a better way in R.
>
> Can anyone think of something more sophisticated than my current method?
>
> Thanks in advance for any and all help!!
>
> Cheers,
> Nick
>
>
>
>
> --
> ====================================================
> 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
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--
Joshua Wiley
Ph.D. Student, Health Psychology
Programmer Analyst II, Statistical Consulting Group
University of California, Los Angeles
https://joshuawiley.com/
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