Fit MSA model

Wrapper function that calls RTMB to create the model and perform the numerical optimization

Usage

fit_MSA(
  MSAdata,
  parameters,
  map = list(),
  random = NULL,
  run_model = TRUE,
  do_sd = TRUE,
  report = TRUE,
  silent = FALSE,
  control = list(iter.max = 2e+05, eval.max = 4e+05),
  ...
)

Arguments

MSAdata: Data object. Class MSAdata, validated by check_data()
parameters: List of parameters, e.g., returned by make_parameters() and validated by check_parameters().
map: List of parameters indicated whether they are fixed and how they are shared, e.g., returned by make_parameters(). See RTMB::MakeADFun().
random: Character vector indicating the parameters that are random effects, e.g., returned by make_parameters().
run_model: Logical, whether to fit the model through stats::nlminb().
do_sd: Logical, whether to calculate the standard errors with RTMB::sdreport().
report: Logical, whether to return the report list with obj$report(obj$env$last.par.best).
silent: Logical, whether to report progress to console. Not passed to TMB::MakeADFun(). Recommend to set to TRUE to speed up run time, e.g., when running simulations, multiple fits, etc.
control: Passed to stats::nlminb()
...: Other arguments to RTMB::MakeADFun().

Value

A MSAassess object.

Usage

Arguments

Value

See also