[R] populating a large matrix

[Nick Matzke]

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
>>
>> 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
>>
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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: 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