fishmethods (version 1.12-1)

growth_sel: 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))

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).

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).

Author

Amy M. Schueller, National Marine Fisheries Service, Beaufort, NC

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).

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

 if (FALSE) {
  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"))
 }