Re: [R] How to fix error in the package 'rgenoud'
I could solve this problem by setting the boundary options as follows.
par1Bnd-c(0.001,0.999)
par2Bnd-c(-10,10)
DomainMat-matrix(c(par1Bnd,par2Bnd), nrow = 2, ncol=2, byrow=TRUE)
result-genoud(Qmin, nvars=2, starting.values=c(0.5,0),
Domains=DomainMat, control=list(ndeps=c(1e-7,1e-2)), boundary.enforcement=2)
To understand how to set up each option, you can refer to the links:
http://sekhon.berkeley.edu/rgenoud/genoud.html
http://sekhon.berkeley.edu/rgenoud/
In the above setting, Domains decides the boundary, and starting.values
indicates the initial values of parameters. control is the list of control
parameters in optim (For details, refer to
http://sekhon.berkeley.edu/stats/html/optim.html). boundary.enforcement
prevents the algorithm from going away from the boundary.
On 13 October 2010 15:01, Wonsang You [via R]
ml-node+2993619-1186574920-137...@n4.nabble.comml-node%2b2993619-1186574920-137...@n4.nabble.com
wrote:
I have to make correction in my error message which I introduced in my
original message. Sorry for my mistake.
Finally, I had the following error message after running the function
'genoud'.
Error in optim(foo.vals, fn = fn1, gr = gr1, method = optim.method, control
= control) :
non-finite finite-difference value [1]
When I execute 'traceback()' to trace where the error occured, I got the
following results. Unfortunately, I could not figure out what was the
problem from the above information.
6: optim(foo.vals, fn = fn1, gr = gr1, method = optim.method, control =
control)
5: function (foo.vals)
{
ret - optim(foo.vals, fn = fn1, gr = gr1, method = optim.method,
control = control)
return(c(ret$value, ret$par))
}(c(0.220878697173384, -13.3643173824871))
4: .Call(rgenoud, as.function(fn1), new.env(), as.integer(nvars),
as.integer(pop.size), as.integer(max.generations),
as.integer(wait.generations),
as.integer(nStartingValues), as.real(starting.values), as.vector(P),
as.matrix(Domains), as.integer(max), as.integer(gradient.check),
as.integer(boundary.enforcement), as.double(solution.tolerance),
as.integer(BFGS), as.integer(data.type.int),
as.integer(provide.seeds),
as.integer(unif.seed), as.integer(int.seed),
as.integer(print.level),
as.integer(share.type), as.integer(instance.number),
as.integer(MemoryMatrix),
as.integer(debug), as.character(output.path),
as.integer(output.type),
as.character(project.path), as.integer(hard.generation.limit),
as.function(genoud.optim.wrapper101), as.integer(lexical),
as.function(fnLexicalSort), as.function(fnMemoryMatrixEvaluate),
as.integer(UserGradient), as.function(gr1func), as.real(P9mix),
as.integer(BFGSburnin), as.integer(transform), PACKAGE = rgenoud)
3: genoud(Qmin, nvars = 2, starting.values = InitVal, max.generations = 10,
wait.generations = 3, n = n, yper = yper, pertype = pertype) at
wFGN.R#75
Wonsang You
Leibniz Institute for Neurobiology
--
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[R] How to fix error in the package 'rgenoud'
Dear R user fellows, I would like to ask you about the package 'rgenoud' which is a genetic optimization tool. I ran the function 'genoud' with two variables to be minimized by the following command. result-genoud(fn,nvars=2,starting.values=c(0.5,0), pop.size=1000, max.generations=10, wait.generations=3) Then, I had the following error message. Error in solve.default(Djl) : system is computationally singular: reciprocal condition number = 0 Can anyone give me some tip on how to fix the problem? Thank you for your great help in advance. Best Regards, Wonsang You - -- Wonsang You Special Lab Non-Invasive Brain Imaging Leibniz Institute for Neurobiology http://www.ifn-magdeburg.de -- View this message in context: http://r.789695.n4.nabble.com/How-to-fix-error-in-the-package-rgenoud-tp2993489p2993489.html Sent from the R help mailing list archive at Nabble.com. [[alternative HTML version deleted]] __ 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.
Re: [R] How to fix error in the package 'rgenoud'
I have to make correction in my error message which I introduced in my
original message. Sorry for my mistake.
Finally, I had the following error message after running the function '
genoud'.
Error in optim(foo.vals, fn = fn1, gr = gr1, method = optim.method, control
= control) :
non-finite finite-difference value [1]
When I execute 'traceback()' to trace where the error occured, I got the
following results. Unfortunately, I could not figure out what was the
problem from the above information.
6: optim(foo.vals, fn = fn1, gr = gr1, method = optim.method, control =
control)
5: function (foo.vals)
{
ret - optim(foo.vals, fn = fn1, gr = gr1, method = optim.method,
control = control)
return(c(ret$value, ret$par))
}(c(0.220878697173384, -13.3643173824871))
4: .Call(rgenoud, as.function(fn1), new.env(), as.integer(nvars),
as.integer(pop.size), as.integer(max.generations),
as.integer(wait.generations),
as.integer(nStartingValues), as.real(starting.values), as.vector(P),
as.matrix(Domains), as.integer(max), as.integer(gradient.check),
as.integer(boundary.enforcement), as.double(solution.tolerance),
as.integer(BFGS), as.integer(data.type.int),
as.integer(provide.seeds),
as.integer(unif.seed), as.integer(int.seed),
as.integer(print.level),
as.integer(share.type), as.integer(instance.number),
as.integer(MemoryMatrix),
as.integer(debug), as.character(output.path),
as.integer(output.type),
as.character(project.path), as.integer(hard.generation.limit),
as.function(genoud.optim.wrapper101), as.integer(lexical),
as.function(fnLexicalSort), as.function(fnMemoryMatrixEvaluate),
as.integer(UserGradient), as.function(gr1func), as.real(P9mix),
as.integer(BFGSburnin), as.integer(transform), PACKAGE = rgenoud)
3: genoud(Qmin, nvars = 2, starting.values = InitVal, max.generations = 10,
wait.generations = 3, n = n, yper = yper, pertype = pertype) at
wFGN.R#75
On 13 October 2010 13:03, Wonsang You y...@ifn-magdeburg.de wrote:
Dear R user fellows,
I would like to ask you about the package 'rgenoud' which is a genetic
optimization tool.
I ran the function 'genoud' with two variables to be minimized by the
following command.
result-genoud(fn,nvars=2,starting.values=c(0.5,0),
pop.size=1000, max.generations=10, wait.generations=3)
Then, I had the following error message.
Error in solve.default(Djl) :
system is computationally singular: reciprocal condition number = 0
Can anyone give me some tip on how to fix the problem? Thank you for your
great help in advance.
Best Regards,
Wonsang You
-
Wonsang You
Leibniz Institute for Neurobiology
--
View this message in context:
http://r.789695.n4.nabble.com/Re-How-to-fix-error-in-the-package-rgenoud-tp2993614p2993614.html
Sent from the R help mailing list archive at Nabble.com.
[[alternative HTML version deleted]]
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] How to fix error in the package 'rgenoud'
I have to make correction in my error message which I introduced in my
original message. Sorry for my mistake.
Finally, I had the following error message after running the function
'genoud'.
Error in optim(foo.vals, fn = fn1, gr = gr1, method = optim.method, control
= control) :
non-finite finite-difference value [1]
When I execute 'traceback()' to trace where the error occured, I got the
following results. Unfortunately, I could not figure out what was the
problem from the above information.
6: optim(foo.vals, fn = fn1, gr = gr1, method = optim.method, control =
control)
5: function (foo.vals)
{
ret - optim(foo.vals, fn = fn1, gr = gr1, method = optim.method,
control = control)
return(c(ret$value, ret$par))
}(c(0.220878697173384, -13.3643173824871))
4: .Call(rgenoud, as.function(fn1), new.env(), as.integer(nvars),
as.integer(pop.size), as.integer(max.generations),
as.integer(wait.generations),
as.integer(nStartingValues), as.real(starting.values), as.vector(P),
as.matrix(Domains), as.integer(max), as.integer(gradient.check),
as.integer(boundary.enforcement), as.double(solution.tolerance),
as.integer(BFGS), as.integer(data.type.int),
as.integer(provide.seeds),
as.integer(unif.seed), as.integer(int.seed), as.integer(print.level),
as.integer(share.type), as.integer(instance.number),
as.integer(MemoryMatrix),
as.integer(debug), as.character(output.path),
as.integer(output.type),
as.character(project.path), as.integer(hard.generation.limit),
as.function(genoud.optim.wrapper101), as.integer(lexical),
as.function(fnLexicalSort), as.function(fnMemoryMatrixEvaluate),
as.integer(UserGradient), as.function(gr1func), as.real(P9mix),
as.integer(BFGSburnin), as.integer(transform), PACKAGE = rgenoud)
3: genoud(Qmin, nvars = 2, starting.values = InitVal, max.generations = 10,
wait.generations = 3, n = n, yper = yper, pertype = pertype) at
wFGN.R#75
-
Wonsang You
Leibniz Institute for Neurobiology
--
View this message in context:
http://r.789695.n4.nabble.com/How-to-fix-error-in-the-package-rgenoud-tp2993489p2993619.html
Sent from the R help mailing list archive at Nabble.com.
__
R-help@r-project.org mailing list
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
