calcIndices: Function to estimate fitted indices

In flr/bbm: FLR Implementation of a Two-Stage Stock Assessment Model

Function to estimate fitted indices

Description

This function estimates fitted indices, given information on growth, periods duration, catches and estimated parameters.

Usage

calcIndices(g, findicesB, findicesP, catch, inits)

Arguments

g	A vector with information on instantaneous rate of biomass decrease, g = M - G, for recruits (rec) and adults (adult).
findicesB	A vector with fraction of the year corresponding to each of the indicesB.
findicesP	A vector with fraction of the year corresponding to each of the indicesP.
catch	An FLQuant with catch information (for recruits and adults).
inits	An FLPar with parameter values for the parameters required by the bbm function.

Value

A list with information on estimated indices (FLQuants). The list has 2 elements: indicesB (for indices in biomass) and indicesP (for proportions of recruits in biomass).

Methods

Methods exist for various calculations based on the output class (FLPar). For details: ?FLPar.

Author(s)

Leire Ibaibarriaga & Sonia Sanchez.

See Also

FLPar, bbmFLPar, bbmControl

Examples

# Load data
data(ane)

args(calcIndices)

indices <- calcIndices( g=control.ane@g, 
                        findicesB=unlist(lapply( indicesB.ane, function(x) mean(range(x)[c('startf','endf')]))),
                        findicesP=unlist(lapply( indicesP.ane, function(x) mean(range(x)[c('startf','endf')]))),
                        catch=catch.ane, inits=inits.ane )

class(indices)
slotNames(indices)

flr/bbm documentation built on Sept. 6, 2022, 8:56 p.m.