| Title: | Aarts and Poos Stock Assessment Model that Estimates Bycatch |
|---|---|
| Description: | FLR version of Aarts and Poos stock assessment model. |
| Authors: | Iago Mosqueira [aut, cre] |
| Maintainer: | Iago Mosqueira <[email protected]> |
| License: | EUPL |
| Version: | 0.3.4.9001 |
| Built: | 2024-11-22 06:09:07 UTC |
| Source: | https://github.com/flr/AAP |
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%USER% %EMAIL%, duplicate ampersand
Maintainer: %USER% %EMAIL%, duplicate ampersand
See vignette("%FLPKG%", package = "%FLPKG%") for an
overview of the package.
## Not run: FLPKG()## Not run: FLPKG()
The output of aaphcxval consist of a list with two elements, named 'stocks'
and 'indices'. The first is an object of class FLStocks, each a peel from
the restrospective run. The second element is a list of FLIndices object.
The first FLIndices object, named 'data', is a copy of the input 'indices'
argument, with the additioned catch.n slot, if originally missing. The next
element, named as the final year of the data set, contains the naive prediction
of the input FLIndices, while the remaining elements are the result of a
hindcast prediction of the relevant indices, those within the year range of
as set ny nyears.
aaphcxval(stock, indices, control, nyears = 5, nsq = 3, pin = NULL)aaphcxval(stock, indices, control, nyears = 5, nsq = 3, pin = NULL)
stock |
Input FLStock object. |
indices |
Input FLIndices object. |
nyears |
Number if years for retrospective, defaults to 5. |
nsq |
Number of years for average biology and selectivity, defaults to 3. |
pin |
dsata.frame of parameter estimates to use as starting values. |
A list containing elements 'stocks', of class FLStocks, and 'indices', a list of FLIndices objects. See details for the structure of this list.
data(sol4) sxval <- aaphcxval(sol4 + fit, indices, control=control(fit), pin=stdfile(fit)) plotXval(sxval$indices) plot(window(sxval$stocks, start=2005), metrics=list(SSB=ssb, F=fbar, Recruits=rec))data(sol4) sxval <- aaphcxval(sol4 + fit, indices, control=control(fit), pin=stdfile(fit)) plotXval(sxval$indices) plot(window(sxval$stocks, start=2005), metrics=list(SSB=ssb, F=fbar, Recruits=rec))
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An object of class CLASS with
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You can inspect the class validity function by using
getValidity(getClassDef('FLCatch'))
All slots in the class have accessor and replacement methods defined that allow retrieving and substituting individual slots.
The values passed for replacement need to be of the class of that slot. A numeric vector can also be used when replacing FLQuant slots, and the vector will be used to substitute the values in the slot, but not its other attributes.
A construction method exists for this class that can take named arguments for
any of its slots. All slots are then created to match the requirements of the
class validity. If an unnamed FLQuant object is provided, this is used
for sizing but not stored in any slot.
Methods exist for various calculations based on values stored in the class:
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The FLR Team
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makeDAT( stock, numYr, qplat_Fmatrix, qplat_surveys, S_age_knots, F_age_knots, F_time_knots, W_time_knots, numAges, pGrp, indMPs, selSpline, X, WSpline, tquants )makeDAT( stock, numYr, qplat_Fmatrix, qplat_surveys, S_age_knots, F_age_knots, F_time_knots, W_time_knots, numAges, pGrp, indMPs, selSpline, X, WSpline, tquants )
PARAM |
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The FLR Team
data(sol4)data(sol4)