Base module for the ODE class of models

The DiseasyModelOde module implements common structure and functionality to regression class of models beyond the model structure provided by ?DiseasyModel.

Most notably, the model module implements the $get_results() method. This implementation requires the subclass to implement the $rhs() and $initialise_state_vector() methods.

Value

A new instance of the DiseasyModelOde R6 class.

See also

DiseasyObservables

Super classes

diseasy::DiseasyBaseModule -> diseasy::DiseasyModel -> DiseasyModelOde

Methods

Public methods

• DiseasyModelOde$new()

• DiseasyModelOde$get_results()

• DiseasyModelOde$initialise_state_vector()

• DiseasyModelOde$plot()

• DiseasyModelOde$clone()

Inherited methods

• diseasy::DiseasyBaseModule$load_module()
• diseasy::DiseasyBaseModule$set_moduleowner()
• diseasy::DiseasyModel$get_data()

---

Method new()

Merge the user provided mappings with the default mappings during initialisation.

Usage

DiseasyModelOde$new(parameters = NULL, ...)

Arguments

parameters

(list())
List of parameters given to the model.

...

Parameters sent to DiseasyModel R6 constructor.

---

Method get_results()

The primary method used to request model results of a given observable at a given stratification

Usage

DiseasyModelOde$get_results(
  observable,
  prediction_length,
  quantiles = NULL,
  stratification = NULL
)

Arguments

observable

(character)
The observable to provide data or prediction for.

prediction_length

(numeric)
The number of days to predict. The prediction start is defined by last_queryable_date of the ?DiseasyObservables R6 class.

quantiles

(list(numeric))
If given, results are returned at the quantiles given.

stratification

(list(quosures) or NULL)
Use rlang::quos(...) to specify stratification. If given, expressions in stratification evaluated to give the stratification level.

Returns

A tibble tibble::tibble with predictions at the level specified by stratification level. In addition to stratification columns, the output has the columns:

- date (Date) specifying the date of the prediction.
- realisation_id (character) giving a unique id for each realization in the ensemble.
- weight (numeric) giving the weight of the realization in the ensemble.

---

Method initialise_state_vector()

Infer the state_vector from incidence data

Usage

DiseasyModelOde$initialise_state_vector(incidence_data)

Arguments

incidence_data

incidence_data (data.frame)
Incidence observations as a data.frame with columns - date: The date of the observations - age_group: The age group of the incidence observation (following diseasystore::age_labels() format) - variant: The variant of the incidence observation. - incidence: The incidence in the age group at the given date

---

Method plot()

Plot the predictions from the current model.

Usage

DiseasyModelOde$plot(observable, prediction_length, stratification = NULL)

Arguments

observable

(character)
The observable to provide data or prediction for.

prediction_length

(numeric)
The number of days to predict. The prediction start is defined by last_queryable_date of the ?DiseasyObservables R6 class.

stratification

(list(quosures) or NULL)
Use rlang::quos(...) to specify stratification. If given, expressions in stratification evaluated to give the stratification level.

---

Method clone()

The objects of this class are cloneable with this method.

Usage

DiseasyModelOde$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.

Examples

  # This module should not be constructed directly but should instead be used to
  # inherit from when creating a new model class.