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<div style="direction: ltr;font-family: Tahoma;color: #000000;font-size: 10pt;">Brilliant. Cheers. Here it is: does anyone want to add it to SRmodels.r?<br>
<br>
Mark<br>
<br>
#SegregAR1<br>
segregAR1 <- function(){<br>
logl <- function(a, b, rho, rec, ssb){<br>
loglAR1(log(rec), FLQuant(log(ifelse(c(ssb)<=b,a*c(ssb),a*b)),dimnames=dimnames(ssb)),rho=rho)}<br>
<br>
model <- rec ~ FLQuant(ifelse(c(ssb)<=b,a*c(ssb),a*b),dimnames=dimnames(ssb))<br>
<br>
initial <- structure(function(rec, ssb){<br>
return(FLPar(a=median(c(rec/ssb),na.rm=TRUE), b=median(c(ssb),na.rm=TRUE),rho=0))},<br>
lower=c( 0, 0,-1),<br>
upper=c(Inf, Inf,1))<br>
<br>
return(list(logl=logl, model=model, initial=initial))<br>
} # }}}<br>
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<div style="direction: ltr;" id="divRpF677520"><font face="Tahoma" size="2" color="#000000"><b>Fra:</b> flr-list-bounces@r-forge.wu-wien.ac.at [flr-list-bounces@r-forge.wu-wien.ac.at] på vegne af Laurie [lauriekell@gmail.com]<br>
<b>Sendt:</b> 14. oktober 2013 13:44<br>
<b>Til:</b> flr-list@r-forge.wu-wien.ac.at<br>
<b>Emne:</b> Re: [FLR-list] Adding a segregAR1 in FLSR<br>
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<div class="moz-cite-prefix">You need to add the initial params and bounds also.<br>
<br>
bevholtAR1 <- function()<br>
{<br>
## log likelihood, assuming normal log.<br>
logl <- function(a, b, rho, rec, ssb)<br>
loglAR1(log(rec), log(a*ssb/(b+ssb)), rho=rho)<br>
<br>
## initial parameter values<br>
initial <- structure(function(rec, ssb) {<br>
a <- max(quantile(c(rec), 0.75, na.rm = TRUE))<br>
b <- max(quantile(c(rec)/c(ssb), 0.9, na.rm = TRUE))<br>
return(FLPar(a = a, b = a/b, rho=0))<br>
},<br>
<br>
## bounds<br>
lower=c(rep(10e-8, 2), -1),<br>
upper=c(rep(Inf, 2), 1))<br>
<br>
## model to be fitted<br>
model <- rec~a*ssb/(b+ssb)<br>
<br>
return(list(logl=logl, model=model, initial=initial))<br>
} # }}}<br>
<br>
<br>
i.e. <br>
initial <- structure(function(rec, ssb){<br>
return(FLPar(a=median(c(rec/ssb),na.rm=TRUE), b=median(c(ssb),na.rm=TRUE),rho=0.0))},<br>
lower=c( 0, 0,-1),<br>
upper=c(Inf,Inf,1))<br>
<br>
<br>
On 14/10/13 08:49, Mark Payne wrote:<br>
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<div style="direction:ltr; font-family:Tahoma; color:#000000; font-size:10pt">Hi,<br>
<br>
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:<br>
<br>
#SegregAR1<br>
segregAR1 <- function(){<br>
logl <- function(a, b, rho, rec, ssb){<br>
loglAR1(log(rec), FLQuant(log(ifelse(c(ssb)<=b,a*c(ssb),a*b)),dimnames=dimnames(ssb)),rho=rho)}<br>
<br>
model <- rec ~ FLQuant(ifelse(c(ssb)<=b,a*c(ssb),a*b),dimnames=dimnames(ssb))<br>
<br>
initial <- structure(function(rec, ssb){<br>
return(FLPar(a=median(c(rec/ssb),na.rm=TRUE), b=median(c(ssb),na.rm=TRUE)))},<br>
lower=rep( 0, 0),<br>
upper=rep(Inf, 2))<br>
<br>
return(list(logl=logl, model=model, initial=initial))<br>
} # }}}<br>
<br>
<br>
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:<br>
> model(base.dat) <- "segregAR1"<br>
> res <- fmle(base.dat)<br>
Nelder-Mead direct search function minimizer<br>
Error in .local(obs, hat, ...) : <br>
argument "rho" is missing, with no default<br>
> <br>
<br>
Any ideas what I've done wrong?<br>
<br>
Mark<br>
<br>
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<div class="line" id="LC76"><span class="c1"><br>
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<div id="divRpF64123" style="direction:ltr"><font face="Tahoma" size="2" color="#000000"><b>Fra:</b>
<a class="moz-txt-link-abbreviated" href="mailto:flr-list-bounces@r-forge.wu-wien.ac.at" target="_blank">
flr-list-bounces@r-forge.wu-wien.ac.at</a> [<a class="moz-txt-link-abbreviated" href="mailto:flr-list-bounces@r-forge.wu-wien.ac.at" target="_blank">flr-list-bounces@r-forge.wu-wien.ac.at</a>] på vegne af Luis Ridao [<a class="moz-txt-link-abbreviated" href="mailto:luridao@gmail.com" target="_blank">luridao@gmail.com</a>]<br>
<b>Sendt:</b> 4. oktober 2013 16:08<br>
<b>Til:</b> <a class="moz-txt-link-abbreviated" href="mailto:flr-list@flr-project.org" target="_blank">
flr-list@flr-project.org</a><br>
<b>Emne:</b> [FLR-list] FLBRP<2 sorce code<br>
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<div>FLR help,<br>
<br>
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trying to get the source code for FLBRP version<2 (e.g. FLBRP_1.4-1)<br>
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but can't find it anywhere.<br>
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anyone with an older source code version of the package around?<br>
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best,<br>
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Luis<br clear="all">
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