fishmethods (version 1.12-1)

ep_growth: Fitting the von Bertalanffy growth model to length-stratified age samples

Description

Estimation of von Bertanffy growth parameters based on length-stratified age samples (Perrault et al., 2020)

Usage

ep_growth(len=NULL,age=NULL,Nh=NULL,nh=NULL,starts=list(Linf=60,
k=0.1,a0=-0.01,CV=0.5), 
bin_size=2,nlminb.control=list(eval.max=5000, 
iter.max=5000,trace=10),
tmb.control=list(maxit=5000,trace=FALSE),plot=TRUE)

Value

List containing list elements of the model convergence, parameter estimates and predicted values.

Arguments

len

vector of lengths.

age

the vector of ages associated with the length vector.

Nh

the total sample size per bin. Includes the unaged fish.

nh

the total aged sample size per bin.

starts

the starting values for L-infinity, K, a0 and CV. Required.

bin_size

the bin size (e.g., 2 for 2-cm) of the length stratification.

nlminb.control

controls for the nlminb function. See function nlminb for more information.

tmb.control

controls for the TMB function. See package TMB for more information.

plot

plot observed and model predicted lengths at age. Default is TRUE.

Author

Andrea Perrault, Marine Institute of Memorial University of Newfoundland

Details

The von Bertalanffy growth model Lage=Linf*(1-exp(-K*(age-a0)) is fitted to length-at-age data collected via length-stratified sampling following the EP method of Perreault et al. (2020). A plot of model fit is generated unless plot=FALSE.

References

Perrault, A. M. J., N. Zhang and Noel G. Cadigan. 2020. Estimation of growth parameters based on length-stratified age samples. Canadian Journal of Fisheries and Aquatic Sciences 77: 439-450.

Examples

 if (FALSE) {
	data(ep.data)
	ep_growth(len=ep.data$length, age=ep.data$age, Nh=ep.data$Nh, nh=ep.data$nh,
        starts=list(Linf=60,
        k=0.1, CV=0.5 ,a0=-0.01), bin_size=2,
          nlminb.control=list(eval.max=5000, iter.max=5000, trace=10), 
          tmb.control=list(maxit=5000, trace=F),plot=TRUE)
 }