Stock assessment model advanced method

The advanced user interface to the a4a fitting routine.

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"