[FLR-list] Qs about FLStock objects

[Marc Taylor]

Thank you Iago. 'simplify' is exactly what I was looking for. Yes, I am 
using F values (not hr).

I was indeed plotting the stock object with lattice-based plot before 
(which seemed to sum the Fs for a single yearly F value). The ggplotFL 
version looks much nicer, although I'm getting some strange plots when 
applying it to the non-simplified version (with season dimension). I 
will also look further into this - as it may have to do with some NAs 
(or an occasional Inf)...

I'll let you know how things go and try and organize my questions.

Cheers, Marc


Dr. Marc Taylor
Marine Lebende Resourcen / Marine Living Resources
Thünen-Institut für Seefischerei / Thünen Institute of Sea Fisheries
Herwigstraße 31
27572 Bremerhaven, Germany

Tel:  +49 471 94460-252
Mail: marc.taylor at thuenen.de
Web:  www.thuenen.de

On 31-Aug-18 10:13 AM, Iago Mosquera wrote:
>
> Hi,
>
> Q1: Yes. For an FLStock there is a simplify() method, which you can 
> call with
>
> simplify(stock, dims="season")
>
> and will take abundances in season 1 to represent the whole year, add 
> up catches, and calculate a weighted mean across wts. It will then 
> calculate harvest from survivors.
>
> Have a go and let me know, it might need a bit more testing.
>
> Q2: Are you using F or HR? If F, then usually values are for the time 
> period specified, be it a month or a year: the value that would get 
> you survivors at the end of the period from numbers at the start using 
> N /exp(-1/(F + M)).
>
> The FLStock plot in ggplotFL deals with seasonal objects, are you 
> using the lattice-based one in FLCore?
>
> I am dealing at the moment with seasonal FLStock objects, and even 
> running seasonal forecasts wth FLasher. Happy to see if it all works 
> for you.
>
> Cheers,
>
>
> Iago
>
> On Aug 31 2018, at 8:07 am, Marc Taylor <marc.taylor at thuenen.de> wrote:
>
>
>     I am using an FLStock object to record information from a simulation
>     model that is run at monthly time increments; i.e. the @season
>     dimension
>     equals 12.
>
>     Q1. Is there a function in FLCore that can compute the yearly values
>     (i.e. collapse the season dimension)? I would write one for my
>     purposes
>     if this doesn't exist, but I wanted to ask first. As far as I know,
>     there are only the compute functions for specific slots (e.g.
>     computeCatch), but not ones that operate on the whole object at once.
>
>     Q2. How would you recommend that I record mortality at the season
>     (i.e.
>     monthly) level: I started off at having their units be "per year"
>     rates,
>     but the default plot(stock) appears to sum the mortality values
>     for the
>     yearly time series, rather than to average them, which would suggest
>     keeping them in "per season" units. This also seems to be consistent
>     with the output of SMS (one sums the seasonal values to arrive at the
>     yearly ones).
>
>     Hope these questions are clear for you!
>
>     Cheers, Marc
>
>     --
>     Dr. Marc Taylor
>     Marine Lebende Resourcen / Marine Living Resources
>     Thünen-Institut für Seefischerei / Thünen Institute of Sea Fisheries
>     Herwigstraße 31
>     27572 Bremerhaven, Germany
>
>     Tel: +49 471 94460-252
>     Mail: marc.taylor at thuenen.de
>     Web: www.thuenen.de
>
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