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Class constructors for class FIMSFit and associated child classes

Source: R/fimsfit.R
FIMSFit.Rd

Create an object with the class of FIMSFit after running a FIMS model. This is typically done within fit_fims() but it can be create manually by the user if they have used their own bespoke code to fit a FIMS model.

Usage

FIMSFit(
  input,
  obj,
  opt = list(),
  sdreport = list(),
  timing = c(time_total = as.difftime(0, units = "secs")),
  version = utils::packageVersion("FIMS")
)

Arguments

input

Input list as returned by initialize_fims().

obj

An object returned from TMB::MakeADFun().

opt

An object returned from an optimizer, typically from stats::nlminb(), used to fit a TMB model.

sdreport

An object of the sdreport class as returned from TMB::sdreport().

timing

A vector of at least length one, where all entries are of the timediff class and at least one is named "time_total". This information is available in fit_fims() and added to this argument internally but if you are a power user you can calculate the time it took to run your model by subtracting two Sys.time() objects.

version

The version of FIMS that was used to optimize the model. If fit_fims() was not used to optimize the model, then the default is to use the current version of the package that is loaded.

Value

An object with an S4 class of FIMSFit is returned. The object will have the following slots:

input:

A list containing the model setup in the same form it was passed.

obj:

A list returned from TMB::MakeADFun() in the same form it was passed.

opt:

A list containing the optimized model in the same form it was passed.

max_gradient:

The maximum gradient found when optimizing the model. The default is NA, which means that the model was not optimized.

report:

A list containing the model report from obj[["report"]]().

sdreport:

A object with the sdreport class containing the output from TMB::sdreport(obj).

estimates:

A table of parameter values and their uncertainty.

timing:

The length of time it took to run the model if it was optimized.

version:

The package version of FIMS used to fit the model or at least the version used to create this output, which will not always be the same if you are running this function yourself.