aaphcxval: Compute a retrospective hindcast cross-validation of AAP...

In iagomosqueira/AAP: Aarts and Poos Stock Assessment Model that Estimates Bycatch

Compute a retrospective hindcast cross-validation of AAP indices

Description

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.

Usage

aaphcxval(stock, indices, control, nyears = 5, nsq = 3, pin = NULL)

Arguments

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.

Value

A list containing elements 'stocks', of class FLStocks, and 'indices', a list of FLIndices objects. See details for the structure of this list.

Examples

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))

iagomosqueira/AAP documentation built on Oct. 3, 2023, 6:59 a.m.