Calibrator: An R6 class to calibrate a model to data

In junlingm/REpiSim: Mathematical Epidemiological Model Simulations in R

An R6 class to calibrate a model to data

Description

An R6 class to calibrate a model to data

An R6 class to calibrate a model to data

Details

Like a simulator, to calibrate the model to a dataset, a calibrator expects the known and unknown initial conditions and the parameter values, and the data to calibrate to. In addition, it also expects a mapping from model solutions to observation variables.

Public fields

the

names of all parameters

Active bindings

the

names of all parameters

Methods

Public methods

• Calibrator$new()

• Calibrator$calibrate()

• Calibrator$clone()

---

Method new()

initializer

Usage

Calibrator$new(
  model,
  time,
  data,
  ...,
  cumulative = FALSE,
  mapping = character()
)

Arguments

model

the model to calibrate

time

either a numeric vector containing the times (including the initial time) of the ODE solution that corresponds to the data, or a character value giving the name of the column in data that corresponds to time.

data

a data.frame object containign the data for the calibration

...

each argument is a formula defining the maps between the data columns and the model variables. Please see the details section.

Details

A mapping is a named argument, where name is the data colummn name, and value corresponds to the model variables (or an expression to calculate from the model variables.) Calibrate the model to data

---

Method calibrate()

Usage

Calibrator$calibrate(initial.values, parms, ...)

Arguments

initial.values

the initial values for the model. The parameters that need to be estimate should be NA, those that do not need to be estimated must contain a finite value.

parms

the parameter values of the model. The parameters that need to be estimate should be NA, those that do not need to be estimated must contain a finite value.

...

extra arguments to be passed to calibrators

---

Method clone()

The objects of this class are cloneable with this method.

Usage

Calibrator$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.

junlingm/REpiSim documentation built on Nov. 28, 2023, 2:35 a.m.