a4aInternal: Stock assessment model advanced method

In flr/FLa4a: A Simple and Robust Statistical Catch at Age Model

Stock assessment model advanced method

Description

The advanced user interface to the a4a fitting routine.

Usage

a4aInternal(
  stock,
  indices,
  fmodel = defaultFmod(stock),
  qmodel = defaultQmod(indices),
  srmodel = defaultSRmod(stock),
  n1model = defaultN1mod(stock),
  vmodel = defaultVmod(stock, indices),
  covar = missing,
  wkdir = missing,
  verbose = FALSE,
  fit = "assessment",
  center = TRUE,
  mcmc = missing
)

Arguments

stock	an FLStock object containing catch and stock information
indices	an FLIndices object containing survey indices
fmodel	a formula object depicting the model for log fishing mortality at age
qmodel	a list of formula objects depicting the models for log survey catchability at age
srmodel	a formula object depicting the model for log recruitment
n1model	a formula object depicting the model for the first year of catch data
vmodel	a list of formula objects depicting the models for log survey and log fishing mortality variance
covar	a list with covariates
wkdir	used to set a working directory for the admb optimiser. If wkdir is set all admb files are saved to this folder otherwise they are deleted.
verbose	if true admb fitting information is printed to the screen
fit	character with type of fit: 'MP' or 'assessment'; the former doesn't require the hessian to be computed, while the latter does.
center	logical specifying whether data is centered before estimating or not
mcmc	SCAMCMC specifying parameters for the ADMB MCMC run, check ADMB manual for detailed description

Value

an a4aFit object if fit is "MP" or an a4aFitSA if fit is "assessment"

flr/FLa4a documentation built on Dec. 21, 2024, 9:28 p.m.