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Diseasy' season handler

Source: R/DiseasySeason.R
DiseasySeason.Rd

The DiseasySeason module is responsible for implementing various models for the seasonal dependency of the diseases. The module implements a number season models with different functional forms. Models for season are either extracted from the module through get_* functions or the module is configured to use these models internally through use_* functions whereafter the model can be accessed through $model_t() and $model_date(). Each season model has varying number of parameters. See documentation for each for details.

See the vignette("diseasy-season") for examples of use.

Value

A new instance of the DiseasySeason R6 class.

See also

DiseasyObservables

Super class

diseasy::DiseasyBaseModule -> DiseasySeason

Active bindings

reference_date

(Date)
The reference date of the season models. Read-only.

model_t

(function)
The model currently being used in the module (days past reference date). Read-only.

model_date

(function)
The model currently being used in the module (date of interest). Read-only.

available_season_models

(character)
The list of available season models

observables

(diseasy::DiseasyObservables)
The local copy of an DiseasyObservables module. Read-only.

Methods

Public methods

Inherited methods

Method new()

Creates a new instance of the DiseasySeason R6 class.

Usage

DiseasySeason$new(reference_date = NULL, observables = NULL, ...)

Arguments

reference_date

(Date)
Date the season modifier is computed relatively to.

observables

(R6::R6Class instance)
A instance of DiseasyObservables are needed for some season models.

...

parameters sent to DiseasyBaseModule R6 constructor.

Method set_reference_date()

Sets the reference_date for the DiseasySeason module.

Usage

DiseasySeason$set_reference_date(reference_date)

Arguments

reference_date

(Date)
Date the season modifier is computed relatively to.

Method set_scale()

Sets the scale for the active season model.

Usage

DiseasySeason$set_scale(scale)

Arguments

scale

(numeric)
Sets the scale of the season model. The scale is the percent wise difference between most active and least active period. Read only.

Method get_season_model()

Retrieves the specified season model.

Usage

DiseasySeason$get_season_model(model_name, dots = NULL)

Arguments

model_name

(character)
Name of the season_model to use (calls the equivalent $get_<model_name>()).

dots

(list)
Named list of arguments that will be passed at dot-ellipsis to the season model.

Method use_season_model()

Sets the DiseasySeason module to use the specified season model.

Usage

DiseasySeason$use_season_model(model_name, dots = NULL)

Arguments

model_name

(character)
Name of the season_model to use (calls the equivalent $use_<model_name>()).

dots

(list)
Named list of arguments that will be passed at dot-ellipsis to the season model.

Method get_constant_season()

Retrieves the season model with a constant value (1).

Usage

DiseasySeason$get_constant_season()

Method use_constant_season()

Sets the season module to use a constant value (1).

Usage

DiseasySeason$use_constant_season()

Method get_cosine_season()

Retrieves the season model with a cosine relationship.

Usage

DiseasySeason$get_cosine_season(peak = 20.09946, scale = 0.5726693)

Arguments

peak

(numeric)
Sets the period of maximal activity (days past new-year). By default, risk of infection is antiphase with the DMI climate normal of the maximum daily temperature.

scale

(numeric)
Sets the scale of the season model. The scale is the percent wise difference between most active and least active period.

Method use_cosine_season()

Sets the DiseasySeason module to use a cosine model for season.

Usage

DiseasySeason$use_cosine_season(peak = 20.09946, scale = 0.5726693)

Arguments

peak

(numeric)
Sets the period of maximal activity (days past new-year). By default, risk of infection is antiphase with the DMI climate normal of the maximum daily temperature.

scale

(numeric)
Sets the scale of the season model. The scale is the percent wise difference between most active and least active period.

Method get_covid_season_v1()

Retrieves the first version of the COVID-19 season model.

Usage

DiseasySeason$get_covid_season_v1(scale = 0.4825524)

Arguments

scale

(numeric)
Sets the scale of the season model. The scale is the percent wise difference between most active and least active period.

Method use_covid_season_v1()

Sets the DiseasySeason module to use the first version of the covid 19 season model

Usage

DiseasySeason$use_covid_season_v1(scale = 0.4825524)

Arguments

scale

(numeric)
Sets the scale of the season model. The scale is the percent wise difference between most active and least active period.

Method get_covid_season_v2()

Retrieves the second version of the COVID-19 season model.

Usage

DiseasySeason$get_covid_season_v2(scale = 0.5042782)

Arguments

scale

(numeric)
Sets the scale of the season model. The scale is the percent wise difference between most active and least active period.

Method use_covid_season_v2()

Sets the DiseasySeason module to use the second version of the COVID-19 season model

Usage

DiseasySeason$use_covid_season_v2(scale = 0.5042782)

Arguments

scale

(numeric)
Sets the scale of the season model. The scale is the percent wise difference between most active and least active period.

Method describe()

Prints a human readable report of the internal state of the module.

Usage

DiseasySeason$describe()

Method clone()

The objects of this class are cloneable with this method.

Usage

DiseasySeason$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.

Examples

  # Season module with an constant season
  s1 <- DiseasySeason$new()

  t <- 0:365
  plot(t, purrr::map_dbl(t, s1$model_t), ylab = "Effect")


  # Season module with an cosine season
  s2 <- DiseasySeason$new(reference_date = Sys.Date())
  s2$use_cosine_season()
  plot(t, purrr::map_dbl(t, s2$model_t), ylab = "Effect")


  rm(s1, s2)