[FLR-list] Adding a segregAR1 in FLSR

[Iago MOSQUEIRA (JRC)]

Hi,

With much delay, but added today to FLCore in github


Iago

On 10/14/2013 02:21 PM, Iago MOSQUEIRA (JRC) wrote:
> 
> 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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