[FLR-list] Error in a4aout at harvest + m(stock) : non-con

[Ernesto]

Hi,

Sorry for the late reply.

The problem is that your catch data has a large number of ages that 
don't have tunning data. The default model for a4a was not written for 
those cases. Check

a4afit <- sca(gul0001, gul.indices)
wireframe(data~year+age, data=harvest(a4afit))

F in the last ages gets loose and the fit is quite poor.

Once that you want to compare with XSA we can take the same kind of 
approach, which is to force the oldest ages Fs the same. In this case 
the model will fit one coefficient (times the year coefficients) for 
ages older than 18, which mean they are fit together, which I think is 
slightly different from XSA. Note that you have a large +group in some 
years.

This can be done using the "replace" method.

fmod <- ~te(replace(age, age>18, 18), year, k = c(6, 10), bs = "tp")
a4afit <- sca(gul0001, gul.indices, fmodel=fmod)

For comparison
xsafit <- FLXSA(gul0001, gul.indices, FLXSA.control())

wireframe(data~year+age|qname, 
data=as.data.frame(FLQuants(a4a=harvest(a4afit), xsa=xsafit at harvest)))

Now, the one million dollars question is why you want to replicate XSA ;)

Best

EJ

ps: Take a look at the residuals and you'll see that both fits have some 
odd residuals. In a4a you have a couple of simple options to improve 
this fit, like including a year trend in the catchability of the trawl 
cpue, etc.

bubbles(age~year|qname, data=xsafit at index.res)
plot(residuals(a4afit, gul0001, gul.indices))

On 02/18/2015 02:35 PM, Havstovan FAMRI wrote:
> Hi,
>
> Well that solved the problem (trimming the indices object 
> trim(gul.indices[[2]], age 4:12). No errors come up but stock numbers 
> and F's are really spurious
> and nothing in the range of the XSA run. F are given below as a example:
>
> > gulfit at harvest[,ac(2010:2014)]  # a4a output
> An object of class "FLQuant"
> , , unit = unique, season = all, area = unique
>
>     year
> age  2010       2011       2012       2013       2014
>   4  0.00061883 0.00054841 0.00088312 0.00104010 0.00070947
>   5  0.00194001 0.00170594 0.00221326 0.00254813 0.00223464
>   6  0.00515556 0.00454088 0.00496769 0.00561751 0.00602334
>   7  0.01007180 0.00901793 0.00900872 0.01006750 0.01202780
>   8  0.01384780 0.01273870 0.01257350 0.01389800 0.01666770
>   9  0.01448220 0.01365150 0.01385510 0.01499370 0.01669910
>   10 0.01336920 0.01269240 0.01303890 0.01351880 0.01358130
>   11 0.01248430 0.01165750 0.01145380 0.01107690 0.01019620
>   12 0.01247860 0.01127330 0.00997400 0.00880635 0.00769486
>   13 0.01285800 0.01125750 0.00874288 0.00700203 0.00595635
>   14 0.01248820 0.01082000 0.00757566 0.00557152 0.00460538
>   15 0.01064480 0.00939845 0.00633618 0.00439713 0.00344647
>   16 0.00797521 0.00732193 0.00509501 0.00344610 0.00249670
>   17 0.00569563 0.00541743 0.00403299 0.00273092 0.00182383
>   18 0.00435670 0.00416232 0.00326465 0.00224600 0.00142545
>   19 0.00388555 0.00355594 0.00278197 0.00194974 0.00124088
>   20 0.00406418 0.00340829 0.00250123 0.00177887 0.00119688
>   21 0.00465988 0.00349410 0.00231912 0.00166745 0.00122197
>
> units:  f
> > gul_F[,ac(2010:2014)]  # XSA output
>      2010   2011   2012   2013   2014
> 4  0.0047 0.0115 0.0015 0.0066 0.0053
> 5  0.0143 0.0311 0.0100 0.0154 0.0296
> 6  0.0675 0.0787 0.0485 0.0655 0.0872
> 7  0.1257 0.1506 0.0947 0.1182 0.1404
> 8  0.1696 0.2211 0.1632 0.1897 0.2082
> 9  0.2107 0.2428 0.1669 0.2651 0.2607
> 10 0.2624 0.3209 0.2170 0.2783 0.2700
> 11 0.2686 0.3086 0.2396 0.3374 0.2840
> 12 0.3309 0.4213 0.2750 0.3371 0.2146
> 13 0.4980 0.6288 0.4110 0.4805 0.2861
> 14 0.4428 0.5557 0.4666 0.5562 0.3298
> 15 0.4462 0.5266 0.4679 0.6606 0.4605
> 16 0.3444 0.4555 0.4277 0.5946 0.4433
> 17 0.2812 0.3540 0.3561 0.5347 0.3910
> 18 0.2529 0.3157 0.3512 0.4841 0.3601
> 19 0.4566 0.2772 0.1803 0.2773 0.3215
> 20 0.2534 0.3124 0.2804 0.4170 0.4099
> 21 0.2534 0.3124 0.2804 0.4170 0.4099
>
> best,
> Luis
>
>
>
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-- 
Ernesto Jardim<ernesto.jardim at jrc.ec.europa.eu>
Fisheries Scientist
FISHREG – Scientific Support to Fisheries
IPSC Maritime Affairs Unit
EC Joint Research Center
TP 051, Via Enrico Fermi 2749
I-21027 Ispra (VA), Italy
Office : +39 0332 785311
Fax: +39 0332 789658
https://fishreg.jrc.ec.europa.eu/


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