Fit TMB model using nlminb

Runs optimization on the TMB model using stats::nlminb. If specified, takes additional Newton steps and calculates standard deviations. Internal function called by fit_wham.

fit_tmb(
  model,
  n.newton = 3,
  do.sdrep = TRUE,
  do.check = FALSE,
  save.sdrep = FALSE,
  use.optim = FALSE,
  opt.control = NULL
)

Arguments

model: Output from TMB::MakeADFun.
n.newton: Integer, number of additional Newton steps after optimization. Default = 3.
do.sdrep: T/F, calculate standard deviations of model parameters? See TMB::sdreport. Default = TRUE.
do.check: T/F, check if model parameters are identifiable? Runs internal check_estimability, originally provided by the TMBhelper package. Default = TRUE.
save.sdrep: T/F, save the full TMB::sdreport object? If FALSE, only save summary.sdreport) to reduce model object file size. Default = FALSE.
use.optim: T/F, use stats::optim instead of stats::nlminb? Default = FALSE.
opt.control: list of control parameters to pass to optimizer. For nlminb default = list(iter.max = 1000, eval.max = 1000). For optim default = list(maxit=1000).

Value

model, appends the following:

model$opt: Output from stats::nlminb
model$date: System date
model$dir: Current working directory
model$rep: model$report(model$env$last.par.best)
model$TMB_version: Version of TMB installed
model$parList: List of parameters, model$env$parList(x = model$opt$par, par = model$env$last.par.best)
model$final_gradient: Final gradient, model$gr(model$opt$par)
model$sdrep: Estimated standard deviations for model parameters, TMB::sdreport or summary.sdreport)

Arguments

Value

See also