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Optimized Model Specification

Source: R/mp_tmb_calibrator.R
mp_optimized_spec.Rd

Create a new model specification using parameter values that have been optimized.

Usage

mp_optimized_spec(model, spec_structure = c("original", "modified"))

Arguments

model

A model object that can be optimized/calibrated. Currently, only models produced by mp_tmb_calibrator are valid.

spec_structure

A character string identifying the structure of the returned model specification. Use "original" for the specification originally passed to the mp_tmb_calibrator function, and "modified" for the one that was used to fit to data. See the details below for more information on these modifications.

Value

A copy of the model specification used to produce the calibrator model, with calibrated default values.

Details

The following is a list of additional model specification structure that was or could have been added to the "modified" specification by mp_tmb_calibrator for the purposes of fitting to data.

  • Observed data in a format that can be compared with simulated data.

  • Expressions preparing simulated data so that they can be compared with the observed data.

  • Distributional parameters for likelihood and prior components of the objective function (e.g., a dispersion parameter for a negatively binomial likelihood component, or a prior standard deviation for a transmission rate parameter).

  • Data, parameters, and expressions for modelling time-variation of parameters (e.g., basis functions and weights for a spline determining the time-variation of transmission rate).