[R] populating a large matrix

[Nick Matzke]

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: matzke at 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