[R] sampling and nls formula

[Marco Geraci]

Hi

--- Susan  Imholt <smimholt at excite.com> wrote:

> 
> Hello,
> 
> I am trying to bootstrap a function that extracts
> the log-likelihood value and the nls coefficients
> from an nls object.  I want to sample my dataset
> (pdd) with replacement and for each sampled dataset,
> I want to run nls and output the nls coefficients
> and the log-likelihood value.
> 
> Code:
> x<-c(1,2,3,4,5,6,7,8,9,10)
> y<-c(10,11,12,15,19,23,26,28,28,30)
> pdd<-data.frame(x,y)
> 
> i<-sample(10, replace=TRUE)

i don't think you need a starting sample of the
'index'. You can omit 
> i<-sample(10, replace=TRUE)

 
> pdd.lik.coef<-function(data,i){
>      d<-data[i,]
>      pdd.nls<-nls(d$y~(a*(d$x)^2)/(b+(d$x)^2),
> data=pdd, start = list(a = 30, b = 36), trace=FALSE)

there's a programming error here
The argument 'data' of 'nls' must match the one that
you pass through 'pdd.lik.coef' or the one that you
redefine ('d'). Also, when a function like 'nls' has
the argument 'data' you don't need to use '$' in the
formula (providing that 'data' contains the variables
named in the formula). 

>     pdd.logLik<-logLik(pdd.nls)
>     coeff <- coef(pdd.nls)
>     lik.coef <- c(pdd.logLik, coeff)
>}

to gain some speed you might want to avoid assigning
the result to 'lik.coef', 'coeff', and 'lik.coef'.

Summarizing, the following code should work. 'should'
means that might not work. I tried with few boot
samples, and it did work. When I tried with R=1000,
the program stopped because 'nls' didn't like a
particular sample of the data and it reached maxit=50
(default). I added a 'control=list(maxiter=100)' to
'nls' to your code. I suggest you to 
work on that.

code:

x<-c(1,2,3,4,5,6,7,8,9,10)
y<-c(10,11,12,15,19,23,26,28,28,30)
pdd<-data.frame(x,y)

pdd.lik.coef<-function(data,i){
     d<-data[i,]
     pdd.nls<-nls(y~(a*x^2)/(b+x^2), data=d, start =
list(a = 30, b = 36), trace=FALSE,
control=list(maxiter=100))
     c(logLik(pdd.nls), coef(pdd.nls))
}

pdd.boot<-boot(data=pdd, statistic=pdd.lik.coef,
R=1000)
pdd.boot$t

hope this helps

Marco

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