Class FLSR

Description

Class for stock-recruitment models, based on FLModel-class. Two extra FLQuant-class slots are used for input data: rec for the recruitment series, and ssb for Spawning Stock Biomass or any other index of reproductive potential.

All the main methods for this class are inherited from FLModel-class, although the plot method is specific to FLSR, and methods exist to access the specific FLQuant slots, rec and ssb.

A series of commonly-used stock-recruitment models are already available, including the correspodning likelihood functions and calculation of initial values. See SRModels for more details and the exact formulation implemented for each of them.

Slots

name

Name of the object. character.

desc

Description of the object. character.

range

Range. numeric.

rec

Recruitment series. FLQuant.

ssb

Index of reproductive potential. FLQuant.

fitted

Estimated values for rec. FLQuant.

residuals

Residuals obtained from the model fit. FLQuant.

covar

Covariates for SR model. FLQuants.

model

Model formula. formula.

grad

Function returning the gradient of the model. function.

logl

Log-likelihood function. function.

initial

Function returning initial parameter values for the optimizer. function.

params

Estimated parameter values. FLPar.

logLik

Value of the log-likelihood. logLik.

vcov

Variance-covariance matrix. array.

details

extra information on the model fit procedure. list.

Extends

FLModel FLComp

Methods

All methods are inherited from FLModel-class, except for

plot(graphics) :

Plot an FLSR object

signature(x=FLSR,y=missing)

Author(s)

The FLR Team

See Also

FLModel, FLComp

Examples

# NS Herring stock-recruitment dataset
data(nsher)

# already fitted with a Ricker SR model
summary(nsher)

plot(nsher)

# change model
model(nsher) <- bevholt()

# fit through MLE
nsher <- fmle(nsher)

plot(nsher)