[FLR-list] Initialising an FLSR

[Mark Payne]

Glad to hear it! I guess it serves me right for using the bleeding edge!

Mark
________________________________________
Fra: flr-list-bounces at r-forge.wu-wien.ac.at [flr-list-bounces at r-forge.wu-wien.ac.at] på vegne af Iago Mosqueira [iago.mosqueira at gmail.com]
Sendt: 18. oktober 2013 15:04
Til: flr-list at flr-project.org
Emne: Re: [FLR-list] Initialising an FLSR

On 10/18/2013 03:02 PM, Mark Payne wrote:
> Ok, so it looks like there's nothing wrong really - the initial guesses are just really good!

That's right, true even more for Ricker

> BTW, what happened to the help files in the most recent version of FLCore?

We are in the process of reviewing them and moving to Roxygen format,
should be done soon, apologies.


Iago


>
> Mark
> ________________________________________
> Fra: flr-list-bounces at r-forge.wu-wien.ac.at [flr-list-bounces at r-forge.wu-wien.ac.at] på vegne af Iago MOSQUEIRA (JRC) [iago.mosqueira-sanchez at jrc.ec.europa.eu]
> Sendt: 18. oktober 2013 14:59
> Til: flr-list at flr-project.org
> Emne: Re: [FLR-list] Initialising an FLSR
>
> On 10/18/2013 02:51 PM, Mark Payne wrote:
>> Hi,
>>
>> Cheers for the reply. I have tried that, but it doesn't actually speed it up! eg
>>
>> #Without initialisation
>> system.time(fmle(nsher))
>>  user  system elapsed
>>   8.444   0.084   8.928
>>
>> #With correct initial guesses
>> system.time(fmle(nsher, start=params(nsher)))
>>   user  system elapsed
>>   8.121   0.060   8.675
>>
>> But there may be something wierd with the dispatching - I get this warning to start with
>>
>>> system.time(fmle(nsher, start=params(nsher)))
>> Note: method with signature ‘FLModel#FLPar’ chosen for function ‘fmle’,
>>  target signature ‘FLSR#FLPar’.
>>  "FLSR#ANY" would also be valid
>>
>> Mark
>
> Hi,
>
> Well, not passing start means you get the initial parameter values from
> a call to the function stored in @initial, which it the case of ricker
> gives results already very close, so the optimizer does equally well.
>
> I do not get any warning using the very latest FLCore on R 3.0, are you
> on the development version from github too?
>
> I run a quick check before replying, to make sure optim was being passed
> the new values, and that seems to be the case.
>
> Some quick timings
>
> # with initial
> system.time(fmle(nsher))
>
>    user  system elapsed
>   2.840   0.004   2.849
>
>
> # with fitted
> system.time(fmle(nsher, start=params(nsher)))
>
>    user  system elapsed
>   2.996   0.000   3.002
>
> # with bad initial values
> params(nsher)[] <- c(1,1)
> system.time(fmle(nsher, start=params(nsher)))
>
>    user  system elapsed
>   7.345   0.016   7.373
>
>
>
>
> Iago
>
>>
>>
>> ________________________________________
>> Fra: flr-list-bounces at r-forge.wu-wien.ac.at [flr-list-bounces at r-forge.wu-wien.ac.at] på vegne af Iago MOSQUEIRA (JRC) [iago.mosqueira-sanchez at jrc.ec.europa.eu]
>> Sendt: 18. oktober 2013 14:43
>> Til: flr-list at flr-project.org
>> Emne: Re: [FLR-list] Initialising an FLSR
>>
>> On 10/18/2013 02:27 PM, Mark Payne wrote:
>>> Hi,
>>>
>>> I have an FLSR object that I have fitted. I now wish to use these parameters as the initial conditions for fitting a second FLSR, based on similar but slightly different data. What's the best way to do this?
>>>
>>> The @initial slot seems to need a function, which I wasn't expecting... Can I feed the FLPar object to fmle for example?
>>>
>>> Cheers,
>>>
>>> Mark
>>
>> Hi,
>>
>> This should do it, use the start argument
>>
>> library(FLCore)
>>
>> data(nsher)
>>
>> params(nsher)
>>
>> out <- fmle(nsher, start=params(nsher))
>>
>>
>>
>> Iago
>>
>>
>> --
>> 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
>> TP 051, Via Enrico Fermi 2749
>> I-21027 Ispra (VA), Italy
>>
>> Office : +39 0332 785413
>> Fax: +39 0332 789658
>>
>> iago.mosqueira at jrc.ec.europa.eu
>>
>> http://fishreg.jrc.ec.europa.eu/home
>>
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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
> TP 051, Via Enrico Fermi 2749
> I-21027 Ispra (VA), Italy
>
> Office : +39 0332 785413
> Fax: +39 0332 789658
>
> iago.mosqueira at jrc.ec.europa.eu
>
> http://fishreg.jrc.ec.europa.eu/home
>
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