Re: [R] loop in optim

[EdBo]

Hi Josh,

1) I got hold of the library(optimx) but surprising I seem to be
failing to use it.

On the previous code, that was working, I replaced the optim function with:

out[i, ] <- optimx(llik, par = start.par, method = "Nelder-Mead",
control=list(maximize=TRUE))[[1]] but it is giving me an error
message.

Error in out[i, ] <- optimx(llik, par = start.par, method = "Nelder-Mead",  :
  incorrect number of subscripts on matrix


The full code is as follows:

afull=read.table("D:/a.txt",header=T)
afull
library(optimx)
#likilihood function

llik = function(x)
   {
    al_j=x[1]; au_j=x[2]; sigma_j=x[3];  b_j=x[4]
    sum(na.rm=T,
        ifelse(a$R_j< 0, log(1/(2*pi*(sigma_j^2)))-
                           (1/(2*(sigma_j^2))*(a$R_j+al_j-b_j*a$R_m))^2,
         ifelse(a$R_j>0 , log(1/(2*pi*(sigma_j^2)))-
                           (1/(2*(sigma_j^2))*(a$R_j+au_j-b_j*a$R_m))^2,
                                log(ifelse (( pnorm (au_j, mean=b_j * a$R_m, 
sd= sqrt(sigma_j^2))-
                           pnorm(al_j, mean=b_j * a$R_m, sd=sqrt
(sigma_j^2) )) > 0,
                                        (pnorm (au_j,mean=b_j * a$R_m, sd= 
sqrt(sigma_j^2))-
                           pnorm(al_j, mean=b_j * a$R_m, sd= sqrt(sigma_j^2) )),
                                        1)) ))
      )
   }
start.par = c(-0.01,0.01,0.1,1)

#looping now

out <- matrix(NA, nrow = 4, ncol = 4,

dimnames = list(paste("Qtr:", 1:4, sep = ''),

c("al_j", "au_j", "sigma_j", "b_j")))


## Estimate parameters based on rows 0-20, 21-40, 41-60 of a
for (i in 1:4) {
                index_start=20*(i-1)+1
                index_end= 20*i
                a=afull[index_start:index_end,]
                out[i, ] <- optimx(llik, par = start.par, method = 
"Nelder-Mead",
control=list(maximize=TRUE))[[1]]
                }

## Yields
out


2) Is it possible to control estimates of sigma_j so that they are
never negative?

3) I had not thought of using previous estimates as starting values of
the next loop because I did not know I could do that but I think it
will help quicken the maximisation.

Edward
UCT


On 7 July 2011 13:40, John C Nash [via R]
<ml-node+3651249-776550566-247...@n4.nabble.com> wrote:
> 2 comments below.
>
> On 07/07/2011 06:00 AM, [hidden email] wrote:
>> Date: Wed, 6 Jul 2011 20:39:19 -0700 (PDT)
>> From: EdBo <[hidden email]>
>> To: [hidden email]
>> Subject: Re: [R] loop in optim
>> Message-ID: <[hidden email]>
>> Content-Type: text/plain; charset=us-ascii
>>
>> I have one last theoretical question, I did not adjust my code prior so
>> that
>> it maximise the likehood function. I googled that to make optim maximise
>> you
>> multiply fn by -1.
>>
>> In my code, would that be the same as saying "-sum" on the "sum" part of
>> my
>> code (see below)?
>>
>> llik = function(x)
>>    {
>>     al_j=x[1]; au_j=x[2]; sigma_j=x[3];  b_j=x[4]
>>     sum(na.rm=T,
>>
>>         ifelse(a$R_j< 0, log(1 / ( sqrt(2*pi) * sigma_j) )-
>>
> The optimx package has a "maximize" control because we felt that the fnscale
> approach,
> while perfectly correct, is not comfortable for users and is not standard
> across other
> optimization tools. Note that this package is undergoing a fairly extensive
> overhaul at
> the moment (the development version is on R-forge in the project
> 'optimizer') to include
> some safeguards on functions that return NaN etc. as well as a number of
> other changes --
> hopefully improvements.
>
> A second comment on this looping: Why do you not use the parameters from the
> last
> estimation as the starting parameters for the next? Unless you are expecting
> very extreme
> changes over the moving window of data, this should appreciably speed up the
> optimization.
>
> John Nash
>
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