[FLR-list] ssb(stock)

Thu Apr 26 10:06:48 CEST 2018

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> 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 

_______________________________________________ 

flr-list mailing list 

flr-list at flr-project.org<mailto:flr-list at flr-project.org> 

https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/flr-list 

_______________________________________________ 

flr-list mailing list 

flr-list at flr-project.org 

https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/flr-list 

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.r-forge.r-project.org/pipermail/flr-list/attachments/20180426/5a2704f5/attachment-0001.html>