[FLR-list] Release of FLCore 2.6.6

[Ernesto.JARDIM at ec.europa.eu]

Hi Luis,

The MSE code developed within a4a can take any assessment model, as long
as it can be called from R. You'll need to code your estimation function
to deal with it.

The sca wrapper is

sca.wrapper <- function(stk, idx, ...){

    args <- list(...)
    args$stock <- stk
    args$indices <- idx
    if(is.null(args$fit)) args$fit <- 'MP'
    tracking <- args$tracking
    args$tracking <- NULL
    fit <- do.call('a4aSCA', args)
    stk <- stk + fit
    tracking["convergence",ac(range(stk)["maxyear"]+1)] <-
fit at fitSumm["maxgrad",]
    list(stk = stk, tracking = tracking)
}

Adding a SAM model is just about changing the call to "a4aSCA" by the
call to SAM and fixing the arguments. Convergence flags will need to be
extracted from the right place, here it's in fitSumm.

Best

EJ


On 05/03/2018 11:35, Luis Ridao wrote:
> Dear all,
>
> I'm trying to set up a MSE in which the assessment model is neither 
> FLXSA nor FLa4a.
>
> The SAM model (stockassessment.org implemented in R) is used as the 
> basis of the advice.
>
> Can anyone inform me whether it's possible to incorporate this into the 
> 'mse' package in FLR
> and conduct simulations or another way around it?
>
> thanks in advance,
> Luis
>
>
> On 02/22/2018 02:51 PM, Iago.MOSQUEIRA at ec.europa.eu wrote:
>> Dear all,
>>
>> A new release of FLCore, version 2.6.6, has made it to the FLR repository. Source packages (Linux) as well as binary packages for Windows and Mac OSX El Capitan (10.11.6) are available. Please install using the usual
>>
>> install.packages(repos="http://flr-project.org/R")
>>
>> and test with your code. Please do not hesitate reporting any problem by filling an issue at
>>
>> https://github.com/flr/flcore/issues
>>
>> These are the most notable changes in FLCore 2.6.6:
>>
>> FLCore 2.6.6
>>
>>   NEW FEATURES
>>
>> - window(FLStocks) method to apply same window call across all elements.
>> - combine(FLStocks) method collapses all elements into a single FLStock object.
>>    with as many iters as elements in the list, must all have 1 iter.
>> - combine(FLQuants, FLQuants) merges them one element at a time.
>> - drop(FLQuant) returns the result of a call to base::drop on @.Data.
>> - New verify() method for complex classes evaluates object against a set of
>>    rules. Checks content rather than structure, as validity functions do.
>> - New ruleset method to return standard verify rules per class.
>> - window() and expand() methods for FLPar.
>> - iter() method for FLlst, lapplies it along the list
>>
>>   USER-VISIBLE CHANGES
>>
>> - propagate(FLPar) to return object if iter == iters #45.
>> - Ratios of numbers written in alternative ways now also return an empty character.
>>
>>   BUG FIXES
>>
>> - dimnames<- for FLStock with no ages failed when changing age name #42.
>> - uom can now handle better products with units containing divisions.
>> - coerce(FLBiol, FLBiolcpp) will now extend srparam to have as many years as the
>>    object, to allow params per time period to be passed and used.
>> - coerce(FLBiol, FLBiolcpp) now windows FLPar if year is given.
>> - trim(FLBiol) is able to handle predictModel slots.
>> - [[<- and $<- FLlst now work on extended classes, like predictModel.
>> - predict(predictModel) now handles correctly iters and extra FLPar dimensions.
>>
>>   DEPRECATED & DEFUNCT
>> - catchSel is to be substituted by catch.sel, use the later instead
>> - wt<-(FLStock) is to be deprecated, use the individual accessor methods instead
>>
>>
>> Iago
>>
>> --
>> Dr Iago Mosqueira
>>
>> European Commission
>> DG Joint Research Centre
>> Directorate D - Sustainable Resources
>> Unit D.02 Water and Marine Resources
>>
>> TP 051, Via Enrico Fermi 2749
>> I-21027 Ispra (VA), Italy
>>
>> Phone : +39 0332 785413
>>
>> iago.mosqueira at ec.europa.eu
>> _______________________________________________
>> flr-list mailing list
>> flr-list at flr-project.org
>> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/flr-list


-- 
Ernesto Jardim <ernesto.jardim at ec.europa.eu>
Fisheries Scientist
Joint Research Centre (JRC), Sustainable resources directorate, Water and Marine Resources unit
TP 051, Via Enrico Fermi 2749
I-21027 Ispra (VA), Italy
Office : +39 0332 785311
Fax: +39 0332 789658