[R] optim "a log-likelihood function"

Zhen Pang nusbj at hotmail.com
Thu Sep 30 03:00:48 CEST 2004

>From: Sundar Dorai-Raj <sundar.dorai-raj at pdf.com>
>Reply-To: sundar.dorai-raj at pdf.com
>To: Christian Schulz <ozric at web.de>
>CC: r-help at stat.math.ethz.ch
>Subject: Re: [R] optim "a log-likelihood function"
>Date: Wed, 29 Sep 2004 10:41:45 -0700
>Christian Schulz wrote:
>>i know that i have to use optim, but i'm confused how its
>>possible  maximize  the sum over all l[i] and get the optimized
>>max(LL), r  and alpha?
>>LL <- function(trans,time){
>>    for(i in 1:length(trans){
>>      l[i] <- log(lgamma(r+trans[i] - 
>>    }
>>i'm confused how i have to set r and alpha and i found no related help in 
>>...in Excel it works with solver but only for ~65.000 rows :-)
>>#This notation is 1 for trans  and 1  for time instead the Startvalues for 
>>r and alpha?
>I'm not sure what the above statement means, so I may have misinterpretted 
>what you are trying to accomplish.
>>many thanks  for an easy example or hint regards,christian
>Did you look at the first example in ?optim? There also numerous errors in 
>LL: missing parans, time is not used, t is undefined in the function.
>LL <- function(x, trans, time) {
>   r <- x[1]
>   alpha <- x[2]
>   ...
>   sum(l)
>optim(c(1, 1), LL, control = list(fnscale = -1),
>       trans = trans, time = time)
>Some style issues:
>1. Break up lines that run too long, especially if you expect others to 
>read your code.
>2. You don't need an explicit "return" at the end of a function.
>3. You should remove the "for" loop in LL and vectorise "l", which should 
>be easy.

I also use optim, however, for my case, can you show some light on avoiding 
the loop?

There are around 200 sets of (i,j,k) where i<=j<=k. 3 situations exist 
whether "=" hold, I list one for example,


then sum all the log(ss) is my log-liklihood function.

One loop from 1 to 200 is inevitable. I have tried to use vector, however, I 
only can simply to this situation.  Thanks.



>Hope this is helpful,
>R-help at stat.math.ethz.ch mailing list
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