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Fit a FIMS model (BETA)

Source: R/fimsfit.R
fit_fims.Rd

Fit a FIMS model (BETA)

Usage

fit_fims(
  input,
  get_sd = TRUE,
  save_sd = TRUE,
  number_of_loops = 3,
  optimize = TRUE,
  number_of_newton_steps = 0,
  control = list(eval.max = 10000, iter.max = 10000, trace = 0),
  filename = NULL,
  getReportCovariance = FALSE
)

Arguments

input

Input list as returned by initialize_fims().

get_sd

A boolean specifying if the TMB::sdreport() should be calculated?

save_sd

A logical, with the default TRUE, indicating whether the sdreport is returned in the output. If FALSE, the slot for the report will be empty.

number_of_loops

A positive integer specifying the number of iterations of the optimizer that will be performed to improve the gradient. The default is three, leading to four total optimization steps.

optimize

Optimize (TRUE, default) or (FALSE) build and return a list containing the obj and report slot.

number_of_newton_steps

The number of Newton steps using the inverse Hessian to do after optimization. Not yet implemented.

control

A list of optimizer settings passed to stats::nlminb(). The the default is a list of length three with eval.max = 1000, iter.max = 10000, and trace = 0.

filename

Character string giving a file name to save the fitted object as an RDS object. Defaults to 'fit.RDS', and a value of NULL indicates not to save it. If specified, it must end in .RDS. The file is written to folder given by input[["path"]]. Not yet implemented.

getReportCovariance

A logical passed to TMB::sdreport(), with the default FALSE. Standard errors of all parameters and derived quantities are calculated either way. If TRUE, the full covariance matrix of the derived quantities is also calculated and stored as cov in the sdreport; it grows with the square of the number of derived quantities and can use several GB of memory. If FALSE, cov is NA.

Value

An object of class FIMSFit is returned, where the structure is the same regardless if optimize = TRUE or not. Uncertainty information is only included in the estimates slot if get_sd = TRUE.

Details

This function is a beta version still and subject to change without warning.

See also