DiseasystoreBase: diseasystore base handler

In diseasystore: Feature Stores for the 'diseasy' Framework

diseasystore base handler

Description

This DiseasystoreBase R6 class forms the basis of all feature stores. It defines the primary methods of each feature stores as well as all of the public methods.

Value

A new instance of the DiseasystoreBase R6 class.

Active bindings

ds_map

(⁠named list⁠(character))
A list that maps features known by the feature store to the corresponding feature handlers that compute the features. Read only.

available_features

(character())
A list of available features in the feature store. Read only.

available_observables

(character())
A list of available observables in the feature store. Read only.

available_stratifications

(character())
A list of available stratifications in the feature store. Read only.

observables_regex

(character(1))
A list of available stratifications in the feature store. Read only.

label

(character(1))
A human readable label of the feature store. Read only.

source_conn

(DBIConnection or ⁠file path⁠)
Used to specify where data is located. Read only. Can be DBIConnection or file path depending on the diseasystore.

target_conn

(DBIConnection)
A database connection to store the computed features in. Read only.

target_schema

(character)
The schema to place the feature store in. Read only. If the database backend does not support schema, the tables will be prefixed with ⁠<target_schema>.⁠.

start_date

(Date)
Study period start. Read only.

end_date

(Date)
Study period end. Read only.

min_start_date

(Date)
(Minimum)Study period start. Read only.

max_end_date

(Date)
(Maximum)Study period end. Read only.

slice_ts

(Date or character)
Date or timestamp (parsable by as.POSIXct) to slice the (time-versioned) data on. Read only.

Methods

Public methods

• DiseasystoreBase$new()

• DiseasystoreBase$get_feature()

• DiseasystoreBase$key_join_features()

• DiseasystoreBase$clone()

---

Method new()

Creates a new instance of the DiseasystoreBase R6 class.

Usage

DiseasystoreBase$new(
  start_date = NULL,
  end_date = NULL,
  slice_ts = NULL,
  source_conn = NULL,
  target_conn = NULL,
  target_schema = NULL,
  verbose = diseasyoption("verbose", self)
)

Arguments

start_date

(Date)
Study period start.

end_date

(Date)
Study period end.

slice_ts

(Date or character)
Date or timestamp (parsable by as.POSIXct) to slice the (time-versioned) data on.

source_conn

(DBIConnection or ⁠file path⁠)
Used to specify where data is located. Can be DBIConnection or file path depending on the diseasystore.

target_conn

(DBIConnection)
A database connection to store the computed features in.

target_schema

(character)
The schema to place the feature store in. If the database backend does not support schema, the tables will be prefixed with ⁠<target_schema>.⁠.

verbose

(boolean)
Boolean that controls enables debugging information.

Returns

A new instance of the DiseasystoreBase R6 class.

---

Method get_feature()

Computes, stores, and returns the requested feature for the study period.

Usage

DiseasystoreBase$get_feature(
  feature,
  start_date = self %.% start_date,
  end_date = self %.% end_date,
  slice_ts = self %.% slice_ts
)

Arguments

feature

(character)
The name of a feature defined in the feature store.

start_date

(Date)
Study period start.

end_date

(Date)
Study period end.

slice_ts

(Date or character)
Date or timestamp (parsable by as.POSIXct) to slice the (time-versioned) data on.

Returns

A tbl_dbi with the requested feature for the study period.

---

Method key_join_features()

Joins various features from the feature store assuming a primary feature (observable) that contains keys to witch the secondary features (defined by stratification) are joined.

Usage

DiseasystoreBase$key_join_features(
  observable,
  stratification = NULL,
  start_date = self %.% start_date,
  end_date = self %.% end_date
)

Arguments

observable

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

stratification

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

start_date

(Date)
Study period start.

end_date

(Date)
Study period end.

Returns

A tbl_dbi with the requested joined features for the study period.

---

Method clone()

The objects of this class are cloneable with this method.

Usage

DiseasystoreBase$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.

Examples

  # DiseasystoreBase is mostly used as the basis of other, more specific, classes
  # The DiseasystoreBase can be initialised individually if needed.

  ds <- DiseasystoreBase$new(source_conn = NULL,
                             target_conn = DBI::dbConnect(RSQLite::SQLite()))

  rm(ds)

diseasystore documentation built on April 4, 2025, 5:56 a.m.