growth_sel: Fitting a von Bertalanffy curve to length and age data biased...

In fishmethods: Fishery Science Methods and Models

Fitting a von Bertalanffy curve to length and age data biased by gear selectivity

Description

A von Bertalanffy growth curve is fitted to age and length data corrected for gear selectivity via the method of Schueller et al. (2014).

Usage

growth_sel(age = NULL, size = NULL, weights = NULL, minlimit = NULL, maxlimit = NULL,
 minmax = NULL, switch_varpar = 1, 
 Linf = list(init = 1000, lb = 100, ub = 2000, prior.mean = 1000, prior.var = -0.5,
 prior.pdf = 1), 
 K = list(init = 0.3, lb = 0.1, ub = 0.9, prior.mean = 0.3, prior.var = -0.05,
 prior.pdf = 1), 
 t0 = list(init = -0.5, lb = -2, ub = -1e-04, prior.mean = -0.5, prior.var = -0.5,
 prior.pdf = 1), 
 varpar = list(init = 50, lb = 10, ub = 100, prior.mean = 5, prior.var = -1,
 prior.pdf = 1),
 tmb.control = list(maxit = 5000, trace = F),
 nlminb.control = list(eval.max = 1e+05, iter.max = 1000),
 species_info = list(species = NULL, size_units = NULL))

Arguments

age	a vector of ages.
size	a vector of body sizes associated with the age data.
weights	a vector of observation weights associated with length data and used to produce weighted likelihood. Set to 1 for unweighted likelihood.
minlimit	a single value or vector associated with the length data. If a single value, a vector the length of the age vector is produced.
maxlimit	a single value or vector associated with the length data. If a single value, a vector the length of the age vector is produced.
minmax	a vector of 1 and 2s indicating whether the data row is being applied to the minimum (1) or maximum part (2) of the likelihood. In general, the break between a 1 and 2 would be the age that has the fullest distribution of length (a well sampled age class where no bias correction is expected).
switch_varpar	estimated variance parameter: 1 = standard deviation (sigma), 2 = CV (sigma / mean), 3 = variance to mean ratio (sigma^2/mean)
Linf	list specifying the initial starting value (init) of L-infinity, the parameter's lower (lb) and upper bounds (ul) for box constraints, prior mean (prior.mean), prior variance (prior.variance) and prior distribution (pdf). pdf: 1 = prior not used, 2 = lognormal, 3 = normal, 4 = beta.
K	list specifying same arguments for K as Linf.
t0	list specifying same arguments for t0 as Linf.
varpar	list specifying same arguments for the estimated variance parameter (varpar) as Linf.
tmb.control	controls for the MakeADFun function. See package TMB for more information.
nlminb.control	controls for the nlminb function. See function nlminb for more information.
species_info	list specifying the species analyzed (species) and units of the size measurements (size_units).

Details

The von Bertalanffy growth model Lage=Linf*(1-exp(-K*(age-t0)) is fitted to length-at-age data adjusted for bias related to selectivity of gears used to collect the length and age samples following the method of Schueller et al. (2014).

Value

List containing list elements of the run information (run_info), filtering indicator (message), convergence information (convergence_info), parameter estimates with associated standard errors and boundary values (estimates), likelihood values (likelihood) and predicted values (predicted).

Note

Amy Schueller provided her AD Model Builder code which was translated to TMB code by Gary Nelson.

Author(s)

Amy M. Schueller, National Marine Fisheries Service, Beaufort, NC [e-mail]

References

Schueller, A. M., E. H. Williams and R. T. Cheshire. 2014. A proposed, tested, and applied adjustment to account for bias in growth parameter estimates due to selectivity. Fisheries Research 158: 26-39.

Examples

 ## Not run: 
  data(simulus)
  growth_sel(age=simulus$age,size=simulus$size,weights=simulus$weight,
    minlimit=simulus$minlimit,
    maxlimit=simulus$maxlimit,minmax=simulus$minmax,
    switch_varpar=1,
    Linf=list(init=1000,lb=100,ub=2000,prior.mean=1000,prior.var=-0.5,prior.pdf=1),
    K=list(init=0.3,lb=0.1,ub=0.9,prior.mean=0.3,prior.var=-0.05,prior.pdf=1),
    t0=list(init=-0.5,lb=-4,ub=-0.001,prior.mean=-0.5,prior.var=-0.5,prior.pdf=1),
    varpar=list(init=50.0,lb=10,ub=100,prior.mean=100,prior.var=-1.0,prior.pdf=1),
    tmb.control=list(maxit=5000,trace=F),nlminb.control=list(eval.max=100000,
    iter.max=1000),
    species_info=list(species="gag",size_units="inches"))
 
## End(Not run)

fishmethods documentation built on April 27, 2023, 9:10 a.m.