[FLR-list] Adding a segregAR1 in FLSR

[Iago MOSQUEIRA (JRC)]

Hi,

I will do it, but do you have an exam[ple with the nsher or other
dataset I could use to build up a test?

Thanks,


Iago

On 10/14/2013 02:08 PM, Mark Payne wrote:
> Brilliant. Cheers. Here it is: does anyone want to add it to SRmodels.r?
> 
> Mark
> 
> #SegregAR1
> segregAR1 <- function(){
>     logl <- function(a, b, rho, rec, ssb){
>        loglAR1(log(rec), FLQuant(log(ifelse(c(ssb)<=b,a*c(ssb),a*b)),dimnames=dimnames(ssb)),rho=rho)}
> 
>     model <- rec ~ FLQuant(ifelse(c(ssb)<=b,a*c(ssb),a*b),dimnames=dimnames(ssb))
> 
>     initial <- structure(function(rec, ssb){
>       return(FLPar(a=median(c(rec/ssb),na.rm=TRUE), b=median(c(ssb),na.rm=TRUE),rho=0))},
>       lower=c( 0, 0,-1),
>       upper=c(Inf, Inf,1))
> 
> return(list(logl=logl, model=model, initial=initial))
> } # }}}
> 
> 
> 
> 
> ________________________________
> Fra: flr-list-bounces at r-forge.wu-wien.ac.at [flr-list-bounces at r-forge.wu-wien.ac.at] på vegne af Laurie [lauriekell at gmail.com]
> Sendt: 14. oktober 2013 13:44
> Til: flr-list at r-forge.wu-wien.ac.at
> Emne: Re: [FLR-list] Adding a segregAR1 in FLSR
> 
> You need to add the initial params and bounds also.
> 
> bevholtAR1 <- function()
>   {
>   ## log likelihood, assuming normal log.
>   logl <- function(a, b, rho, rec, ssb)
>       loglAR1(log(rec), log(a*ssb/(b+ssb)), rho=rho)
> 
>   ## initial parameter values
>   initial <- structure(function(rec, ssb) {
>       a <- max(quantile(c(rec), 0.75, na.rm = TRUE))
>     b <- max(quantile(c(rec)/c(ssb), 0.9, na.rm = TRUE))
>     return(FLPar(a = a, b = a/b, rho=0))
>     },
> 
>   ## bounds
>   lower=c(rep(10e-8, 2), -1),
>     upper=c(rep(Inf, 2), 1))
> 
>   ## model to be fitted
>   model  <- rec~a*ssb/(b+ssb)
> 
>     return(list(logl=logl, model=model, initial=initial))
> } # }}}
> 
> 
> i.e.
>      initial <- structure(function(rec, ssb){
>       return(FLPar(a=median(c(rec/ssb),na.rm=TRUE), b=median(c(ssb),na.rm=TRUE),rho=0.0))},
>       lower=c( 0, 0,-1),
>       upper=c(Inf,Inf,1))
> 
> 
> On 14/10/13 08:49, Mark Payne wrote:
> Hi,
> 
> I'm trying to define a segregAR1 FLSR model, as it seems to be missing from the SRmodels available in FLCore. I have modified the segreg model as follows, based on the bevholtAR1 and rickerAR1 models:
> 
> #SegregAR1
> segregAR1 <- function(){
>     logl <- function(a, b, rho, rec, ssb){
>        loglAR1(log(rec), FLQuant(log(ifelse(c(ssb)<=b,a*c(ssb),a*b)),dimnames=dimnames(ssb)),rho=rho)}
> 
>     model <- rec ~ FLQuant(ifelse(c(ssb)<=b,a*c(ssb),a*b),dimnames=dimnames(ssb))
> 
>     initial <- structure(function(rec, ssb){
>       return(FLPar(a=median(c(rec/ssb),na.rm=TRUE), b=median(c(ssb),na.rm=TRUE)))},
>       lower=rep( 0, 0),
>       upper=rep(Inf, 2))
> 
> return(list(logl=logl, model=model, initial=initial))
> } # }}}
> 
> 
> Basically, I've justed added a rho parameter to the likelihood which should, as I understand it, be sufficient to give me what I want. However, it doesn't seem to work when I go to fit it:
>> model(base.dat) <- "segregAR1"
>> res <- fmle(base.dat)
>   Nelder-Mead direct search function minimizer
> Error in .local(obs, hat, ...) :
>   argument "rho" is missing, with no default
>>
> 
> Any ideas what I've done wrong?
> 
> Mark
> 
> 
> 
> 
> 
> 
> 
> ________________________________
> Fra: flr-list-bounces at r-forge.wu-wien.ac.at<mailto:flr-list-bounces at r-forge.wu-wien.ac.at> [flr-list-bounces at r-forge.wu-wien.ac.at<mailto:flr-list-bounces at r-forge.wu-wien.ac.at>] på vegne af Luis Ridao [luridao at gmail.com<mailto:luridao at gmail.com>]
> Sendt: 4. oktober 2013 16:08
> Til: flr-list at flr-project.org<mailto:flr-list at flr-project.org>
> Emne: [FLR-list] FLBRP<2 sorce code
> 
> FLR help,
> 
> trying to get the source code for FLBRP version<2 (e.g. FLBRP_1.4-1)
> but can't find it anywhere.
> 
> anyone with an older source code version of the package around?
> 
> best,
> Luis
> 
> 
> 
> 
> 
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> 
> 
> 
> 
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-- 
Dr Iago Mosqueira

European Commission – Joint Research Center
Institute for the Protection and Security of the Citizen (IPSC)
Maritime Affairs Unit FISHREG – Scientific Support to Fisheries
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iago.mosqueira at jrc.ec.europa.eu

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