[FLR-list] Initialising an FLSR

[Iago Mosqueira]

On 10/18/2013 03:17 PM, Mark Payne wrote:
> Glad to hear it! I guess it serves me right for using the bleeding edge!

It has its pros and cons, of course

We always welcome volunteers for helping with documentation...


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 [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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