[FLR-list] Release of FLCore 2.6.6

Mon Mar 5 13:49:19 CET 2018

thanks Iago and Ernesto for your prompt responses

i will start by incorporating the data into FLR and see how far i get

best,
Luis

*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-
*   Luis Ridao Cruz
*   Faroe Marine Research Institute
*   Nóatún 1, P.O. Box 3051
*   FO-110 Tórshavn
*   Faroe Islands
*   Tel    : (+298) 353900
*   Fax: : (+298) 353901
*   e-mail: luisr at hav.fo
*              luridao at gmail.com
*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-

On Mon, Mar 5, 2018 at 12:00 PM, <Ernesto.JARDIM at ec.europa.eu> wrote:

> BTW that code is not in any package yet. If you'd like to try it please
> mail me and I'll make it available.
>
> Best
>
> EJ
>
>
> On 05/03/2018 12:00, JARDIM Ernesto (JRC-ISPRA) wrote:
> > 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
>
> _______________________________________________
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