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diseasystore base handler

Source: R/DiseasystoreBase.R
DiseasystoreBase.Rd

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

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)