Hi,
I'm working on a problem that involves calculating a very
large, sparse transition probability matrix, P. It takes
significant time to run through the whole matrix, check all
the transitions, and put in the appropriate probabilities,
based on multiplying parameter values j, d, e, etc.
Each time I update j, or d, or e, I would rather not go
re-process which cells of P get j, j*d, d*e, etc. It would
be better to just do this once, with j, d, and e each just
referring to a memory address. I could then update the
values at that memory address and re-use the matrix P
without re-building it again and again.
Currently, my script builds P via an Rcpp function, then
passes it to R, where it gets used (with the values
calculated) a few hundred times (via another Rcpp function);
then j, d, and e are updated and I have to re-calculate P.
So, my question is, is there a way to make P, currently a
vector of float vectors, into a vector of float pointers,
which can be passed to R and then back to Rcpp? Or is this
just ridiculous?
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
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