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DiseasyModel
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| # diseasy 0.0.0.9000 | ||
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| * Added a `NEWS.md` file to track changes to the package. | ||
| ## Features: | ||
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| * `DiseasyModel`: A base class for the model templates (#36). | ||
| * R6 class that defines the interface for the models and empower the flexible configuration of models from the | ||
| functional modules. | ||
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| ## Documentation: | ||
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| * The functions are fully documented. | ||
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| * Vignettes for the use of the package is included. | ||
| - `vignette("diseasy")` | ||
| - `vignette("creating-a-model")` |
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| #' @title Base module for diseasy model templates | ||
| #' | ||
| #' @description | ||
| #' The `DiseasyModel` module implements common functionality that all models have available beyond that provided by | ||
| #' `DiseasyBaseModule`. | ||
| #' Most notably, the model module facilitates: | ||
| #' * Module interfaces: | ||
| #' The module contains the functional modules via its active bindings: | ||
| #' * `$activity`: `DiseasyActivity` | ||
| #' * `$observables`: `DiseasyObservables` | ||
| #' * `$season`: `DiseasySeason` | ||
| #' | ||
| #' Configured instances of these modules can be provided during initialisation. | ||
| #' Alternatively, default instances of these modules can optionally be created. | ||
| #' | ||
| #' * Model interface: | ||
| #' The module defines the functions `$get_results()`, `$get_training_data()` and the `$parameters` binding. | ||
| #' These functions define the "API" of the models and ensure the models can take part in the ensemble. | ||
| #' @examples | ||
| #' # Normally, one would not want to create this module directly, but it is possible. | ||
| #' Model_module <- DiseasyModel$new() | ||
| #' | ||
| #' rm(Model_module) | ||
| #' @return | ||
| #' A new instance of the `DiseasyModel` [R6][R6::R6Class] class. | ||
| #' @export | ||
| #' @seealso [lgr][lgr::lgr] | ||
| DiseasyModel <- R6::R6Class( # nolint: object_name_linter | ||
| classname = "DiseasyModel", | ||
| inherit = DiseasyBaseModule, | ||
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| public = list( | ||
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| #' @description | ||
| #' Creates a new instance of the `DiseasyModel` [R6][R6::R6Class] class. | ||
| #' This module is typically not constructed directly but rather through `DiseasyModel*` classes. | ||
| #' @param activity,observables,season (`boolean` or `R6::R6Class instance`)\cr | ||
| #' If a boolean is given, it dictates whether to load a new instance module of this class. | ||
| #' | ||
| #' If an instance of the module is provided instead, a copy of this instance is added to the `DiseasyModel` | ||
| #' instance. This copy is a "clone" of the instance at the time it is added and any subsequent changes to the | ||
| #' instance will not reflect in the copy that is added to `DiseasyModel`. | ||
| #' @param label (`character`)\cr | ||
| #' A human readable label for the model instance. | ||
| #' @param ... | ||
| #' Parameters sent to `DiseasyBaseModule` [R6][R6::R6Class] constructor | ||
| #' @details | ||
| #' The `DiseasyModel` is the main template that the individual models should inherit from since this defines the | ||
| #' set of methods the later framework expects from each model. In addition, it provides the main interface with | ||
| #' the other modules of the framework. | ||
| #' @return | ||
| #' A new instance of the `DiseasyModel` [R6][R6::R6Class] class. | ||
| initialize = function(activity = FALSE, | ||
| observables = FALSE, | ||
| season = FALSE, | ||
| label = NULL, | ||
| ...) { | ||
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| coll <- checkmate::makeAssertCollection() | ||
| checkmate::assert(checkmate::check_logical(activity, null.ok = TRUE), | ||
| checkmate::check_class(activity, "DiseasyActivity", null.ok = TRUE), | ||
| add = coll) | ||
| checkmate::assert(checkmate::check_logical(observables, null.ok = TRUE), | ||
| checkmate::check_class(observables, "DiseasyObservables", null.ok = TRUE), | ||
| add = coll) | ||
| checkmate::assert(checkmate::check_logical(season, null.ok = TRUE), | ||
| checkmate::check_class(season, "DiseasySeason", null.ok = TRUE), | ||
| add = coll) | ||
| checkmate::assert_character(label, len = 1, any.missing = FALSE, null.ok = TRUE, add = coll) | ||
| checkmate::reportAssertions(coll) | ||
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| # Pass further arguments to the DiseasyBaseModule initializer | ||
| super$initialize(...) | ||
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| # Then try to set the modules | ||
| if (isTRUE(observables)) { | ||
| self$load_module(DiseasyObservables$new()) | ||
| } else if (inherits(observables, "DiseasyObservables")) { | ||
| self$load_module(observables) | ||
| } | ||
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| if (isTRUE(activity)) { | ||
| self$load_module(DiseasyActivity$new()) | ||
| } else if (inherits(activity, "DiseasyActivity")) { | ||
| self$load_module(activity) | ||
| } | ||
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| if (isTRUE(season)) { | ||
| self$load_module(DiseasySeason$new()) | ||
| } else if (inherits(season, "DiseasySeason")) { | ||
| self$load_module(season) | ||
| } | ||
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| # Set the label for the model | ||
| private$label <- label | ||
| }, | ||
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| # Roxygen has only limited support for R6 docs currently, so we need to do some tricks for the documentation | ||
| # of get_results | ||
| #' @description `r rd_get_results_description` | ||
| #' @param observable `r rd_observable()` | ||
| #' @param prediction_length `r rd_prediction_length()` | ||
| #' @param quantiles `r rd_quantiles()` | ||
| #' @param stratification `r rd_stratification()` | ||
| #' @return `r rd_get_results_return` | ||
| #' @seealso `r rd_get_results_seealso` | ||
| get_results = function(observable, prediction_length, quantiles = NULL, stratification = NULL) { | ||
| private$not_implemented_error( | ||
| "`DiseasyModel` should not be used directly. Did you do so by mistake?", | ||
| "Instead, use a model that inherits`DiseasyModel` as it should implement the `$get_results()` method." | ||
| ) | ||
| }, | ||
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| #' @description | ||
| #' A method that returns training data for the models based on the model value of `training_length` and | ||
| #' the `last_queryable_date` of the `DiseasyObservables` module. | ||
| #' @param observable `r rd_observable()` | ||
| #' @param stratification `r rd_stratification()` | ||
| #' @return The output of `DiseasyObservables$get_observation` constrained to the training period. | ||
| get_training_data = function(observable, stratification = NULL) { | ||
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| # Input validation | ||
| coll <- checkmate::makeAssertCollection() | ||
| checkmate::assert_character(observable, add = coll) | ||
| checkmate::assert_number(self %.% parameters %.% training_length, add = coll) | ||
| checkmate::assert_date(self %.% observables %.% last_queryable_date, add = coll) | ||
| checkmate::reportAssertions(coll) | ||
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| # Get the observable at the stratification level | ||
| start_date <- self %.% observables %.% last_queryable_date - | ||
| lubridate::days(self %.% parameters %.% training_length) | ||
| end_date <- self %.% observables %.% last_queryable_date # Only within the training period | ||
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| data <- self %.% observables %.% get_observation(observable, stratification, start_date, end_date) |> | ||
| dplyr::mutate(t = lubridate::interval(max(zoo::as.Date(date)), zoo::as.Date(date)) / lubridate::days(1)) | ||
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| return(data) | ||
| } | ||
| ), | ||
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| # Make active bindings to the private variables | ||
| active = list( | ||
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| #' @field activity (`diseasy::activity`)\cr | ||
| #' The local copy of an activity module. Read-only. | ||
| #' @seealso [diseasy::DiseasyActivity] | ||
| #' @importFrom diseasystore `%.%` | ||
| activity = purrr::partial( | ||
| .f = active_binding, # nolint: indentation_linter | ||
| name = "activity", | ||
| expr = return(private %.% .DiseasyActivity)), | ||
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| #' @field observables (`diseasy::DiseasyObservables`)\cr | ||
| #' The local copy of an DiseasyObservables module. Read-only. | ||
| #' @seealso [diseasy::DiseasyObservables] | ||
| #' @importFrom diseasystore `%.%` | ||
| observables = purrr::partial( | ||
| .f = active_binding, # nolint: indentation_linter | ||
| name = "observables", | ||
| expr = return(private %.% .DiseasyObservables)), | ||
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| #' @field season (`diseasy::season`)\cr | ||
| #' The local copy of an season module. Read-only. | ||
| #' @seealso [diseasy::DiseasySeason] | ||
| #' @importFrom diseasystore `%.%` | ||
| season = purrr::partial( | ||
| .f = active_binding, # nolint: indentation_linter | ||
| name = "season", | ||
| expr = return(private %.% .DiseasySeason)), | ||
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| #' @field parameters (`list()`)\cr | ||
| #' The parameters used in the model. Read-only. | ||
| #' @importFrom diseasystore `%.%` | ||
| parameters = purrr::partial( | ||
| .f = active_binding, # nolint: indentation_linter | ||
| name = "parameters", | ||
| expr = return(private %.% .parameters)) | ||
| ), | ||
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| private = list( | ||
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| .DiseasyActivity = NULL, | ||
| .DiseasyObservables = NULL, | ||
| .DiseasySeason = NULL, | ||
| .parameters = NULL, | ||
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| # @param label (`character`)\cr | ||
| # A human readable label for the model instance. | ||
| label = NULL, | ||
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| model_cannot_predict = function(observable = NULL, stratification = NULL) { | ||
| coll <- checkmate::makeAssertCollection() | ||
| if (!is.null(observable)) { | ||
| coll$push(glue::glue("Model not configured to predict for observable: {observable}")) | ||
| } | ||
| if (!is.null(stratification)) { | ||
| coll$push(glue::glue("Model not configured to predict at stratification: ", | ||
| "{private$stratification_to_string(stratification)}")) | ||
| } | ||
| checkmate::reportAssertions(coll) | ||
| } | ||
| ) | ||
| ) |
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