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Diseasy' observables handler

Source: R/DiseasyObservables.R
DiseasyObservables.Rd

The DiseasyObservables module is responsible for interfacing with the available diseasystores and provide disease data to the models. The module primarily acts as a convenience wrapper around the diseasystores. The observables and stratifications will therefore depend on the data made available by the diseasystores.

See vignette("diseasy-observables")

Value

A new instance of the DiseasyBaseModule R6 class.

See also

diseasystore::diseasystore

SCDB::get_table

SCDB::get_table

Super class

diseasy::DiseasyBaseModule -> DiseasyObservables

Active bindings

diseasystore

(character)
The set diseasystore to get DiseasyObservables for. Read-only.

start_date

(Date)
Study period start. Read only.

end_date

(Date)
Study period end. Read only.

last_queryable_date

(Date)
The latest date that can be queried. Read-only.

ds

(Diseasystore*)
The currently loaded diseasystore which provides the features. Read-only.

available_observables

(character)
The currently available observables in the loaded diseasystore. Read-only.

available_stratifications

(character)
The currently available stratifications in the loaded diseasystore. Read-only.

synthetic_observables

(character)
The synthetic features defined in the module. Read-only.

slice_ts

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

conn

(DBIConnection or function)
A database connection or function that opens a database connection. Read only.

Methods

Public methods

Inherited methods

Method new()

Creates a new instance of the DiseasyObservables R6 class.

Usage

DiseasyObservables$new(
  diseasystore = NULL,
  start_date = NULL,
  end_date = NULL,
  last_queryable_date = NULL,
  conn = diseasyoption("conn", class = "DiseasyObservables"),
  slice_ts = NULL,
  ...
)

Arguments

diseasystore

(character or diseasystore)
Either the name of or an instance of the feature store to get data from.

start_date

(Date)
Study period start. Used as default values for $get_observation().

end_date

(Date)
Study period end. Used as default values for $get_observation().

last_queryable_date

(Date)
Enforce a limit on data that can be pulled (not after this date).

conn

(DBIConnection or function)
A database connection or function that opens a database connection.

slice_ts

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

...

Parameters sent to DiseasyBaseModule R6 constructor.

Returns

A new instance of the DiseasyObservables R6 class.

Method set_diseasystore()

Set the case definition to get DiseasyObservables for.

Usage

DiseasyObservables$set_diseasystore(diseasystore, verbose = NULL)

Arguments

diseasystore

(character)
Text label of the disease to get DiseasyObservables for.
Must match case definition implemented in diseasystore package.

verbose

(logical)
Should the diseasystore use verbose outputs?

Method set_last_queryable_date()

Enforce a limit on data that can be pulled.

Usage

DiseasyObservables$set_last_queryable_date(last_queryable_date)

Arguments

last_queryable_date

(Date)
DiseasyObservables module will not return data after this date.

Method set_study_period()

Set the (default) time period to get observations from.

Usage

DiseasyObservables$set_study_period(start_date, end_date)

Arguments

start_date

(Date)
Study period start.

end_date

(Date)
Study period end.

Method set_slice_ts()

Set the slice_ts to get data for

Usage

DiseasyObservables$set_slice_ts(slice_ts)

Arguments

slice_ts

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

Method define_synthetic_observable()

Adds a synthetic feature computed from existing features.

Usage

DiseasyObservables$define_synthetic_observable(name, mapping)

Arguments

name

(character)
The name of the new feature.

mapping

(function)
The mapping to compute the new feature from existing features. Existing features should be included as formal arguments to the function.

Method get_observation()

Retrieve an "observable" in the data set corresponding to the set diseasystore.
By default, the internal values for start_date and end_date are used to return data, but these can be overwritten.
The results are cached for faster retrieval at subsequent calls.

Usage

DiseasyObservables$get_observation(
  observable,
  stratification = NULL,
  start_date = self %.% start_date,
  end_date = self %.% end_date,
  respect_last_queryable_date = TRUE
)

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.

respect_last_queryable_date

(logical)
Should the module be able to return data past $last_queryable_date?

Returns

If the observable is found, the function returns the corresponding data at the stratification level.
Otherwise, the function fails and lists the available DiseasyObservables from the diseasystore.

Method stratification_names()

Get the names of the stratifications.

Usage

DiseasyObservables$stratification_names(stratification)

Arguments

stratification

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

Returns

The names of the stratifications.

Method describe()

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

Usage

DiseasyObservables$describe()

Method clone()

The objects of this class are cloneable with this method.

Usage

DiseasyObservables$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.

Examples

  # Create observables module using the Simulist data
  obs <- DiseasyObservables$new(
    diseasystore = "Simulist",
    conn = DBI::dbConnect(duckdb::duckdb())
  )

  # See available observables
  print(obs$available_observables)
#> [1] "n_positive"  "n_admission" "n_hospital" 
  print(obs$available_stratifications)
#> [1] "birth" "age"   "sex"  

  # Get data for one observable
  obs$get_observation(
    "n_hospital",
    start_date = as.Date("2020-03-01"),
    end_date = as.Date("2020-03-05")
  )
#> # A tibble: 5 × 2
#>   date       n_hospital
#>   <date>          <dbl>
#> 1 2020-03-01        317
#> 2 2020-03-02        306
#> 3 2020-03-03        298
#> 4 2020-03-04        290
#> 5 2020-03-05        275

  rm(obs)