[FLR-list] ssb(stock)
Luis Ridao
luridao at gmail.com
Thu Apr 26 10:19:22 CEST 2018
thanks Iago
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 Thu, Apr 26, 2018 at 9:06 AM, Iago Mosqueira <iago at mosqueira.eu> wrote:
> harvest.spwn and m.spwn are set to NA
>
> m.spwn(stock) <- 0.5
> harvest.spwn(stock) <- 0.5
>
> ssb(stock)
>
> Change 0.5 with the right value, proportion of the year (m.spwn) and
> fishing season (harvest.swpn) when spawning takes place.
>
> There is a new method for FLStock, verify(), that will output a table with
> the results of some basic checks
>
> > verify(stock)
> name items passes fails NAs valid
> 1 anyna 17 12 5 0 FALSE
> 2 catch.wt 741 NA NA 4 NA
> 3 landings.wt 741 728 13 0 FALSE
> 4 discards.wt 741 0 741 0 FALSE
> 5 stock.wt 741 728 13 0 FALSE
> 6 mat 741 741 0 0 TRUE
> 7 harvest.spwn 741 NA NA 741 NA
> 8 m.spwn 741 NA NA 741 NA
> 9 harvest 741 741 0 0 TRUE
> 10 cohorts 352 351 1 0 FALSE
> rule
> 1 !anyna
> 2 catch.wt > 0
> 3 landings.wt > 0
> 4 discards.wt > 0
> 5 stock.wt > 0
> 6 mat <= 1 & mat >= 0
> 7 harvest.spwn <= 1 & harvest.spwn >= 0
> 8 m.spwn <= 1 & m.spwn >= 0
> 9 harvest >= 0
> 10 ccohorts(stock.n)
>
> This is telling you that, for example,
>
> - 1. 5 slots have NAs
> - 2. 4 elements in cactch.wt are NA
>
> > sum(is.na(catch.wt(stock)))
> [1] 4
>
> Some of those NAs might be correct, but it warns you about them.
>
> You should also look at the units of each slot
>
> summary(stock)
>
> and change to valid values, so you get the correct units in ssb().
>
> - Change "tonnes" to "t"
> - Change "thousands" to "1000" or "1e3"
> - Set mat, harvest.spwn and m.spwn to "" (empty, as they are proprotions)
>
>
> Cheers,
>
>
> Iago
>
>
> ---- On Thu, 26 Apr 2018 09:48:07 +0200 *Luis Ridao Cruz <Luisr at hav.fo
> <Luisr at hav.fo>>* wrote ----
>
> see attached
>
> Luis
>
> >>> <Iago.MOSQUEIRA at ec.europa.eu> 19/04/2018 16:30 >>>
> Can you send me the FLStock by email, please?
>
>
> 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
> ________________________________
> From: flr-list-bounces at lists.r-forge.r-project.org
> [flr-list-bounces at lists.r-forge.r-project.org] on behalf of Luis
> Ridao [luridao at gmail.com]
> Sent: 19 April 2018 17:29
> To: flr-list at flr-project.org
> Subject: Re: [FLR-list] ssb(stock)
>
>
> both
>
>
>
>
> *-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-
> * 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<mailto:luisr at hav.fo>
> * luridao at gmail.com<mailto:luridao at gmail.com>
> *-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-
>
>
> On Thu, Apr 19, 2018 at 4:22 PM,
> <Iago.MOSQUEIRA at ec.europa.eu<mailto:Iago.MOSQUEIRA at ec.europa.eu>>
> wrote:
> NAs in the values or NA the units?
>
>
> 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<mailto:iago.mosqueira at ec.europa.eu>
> ________________________________
> From:
> flr-list-bounces at lists.r-forge.r-project.org<mailto:flr
> -list-bounces at lists.r-forge.r-project.org>
> [flr-list-bounces at lists.r-forge.r-project.org<mailto:flr
> -list-bounces at lists.r-forge.r-project.org>]
> on behalf of Luis Ridao [luridao at gmail.com<mailto:luridao at gmail.com>]
> Sent: 19 April 2018 17:10
> To: flr-list at flr-project.org<mailto:flr-list at flr-project.org>
> Subject: [FLR-list] ssb(stock)
>
>
> hi all,
>
> for one reason or another the ssb function on my stock returns NAs
>
> these are the units of my stock:
>
>
> > units(stock)
> $catch
> [1] "tonnes"
>
> $catch.n
> [1] "thousands"
>
> $catch.wt
> [1] "kg"
>
> $discards
> [1] "tonnes"
>
> $discards.n
> [1] "thousands"
>
> $discards.wt
> [1] "kg"
>
> $landings
> [1] "tonnes"
>
> $landings.n
> [1] "thousands"
>
> $landings.wt
> [1] "kg"
>
> $stock
> [1] "tonnes"
>
> $stock.n
> [1] "thousands"
>
> $stock.wt
> [1] "kg"
>
> $m
> [1] "m"
>
> $mat
> [1] "NA"
>
> $harvest
> [1] "f"
>
> $harvest.spwn
> [1] "NA"
>
> $m.spwn
> [1] "NA"
>
> thanks in advance,
> Luis
>
>
>
>
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