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diseasystore 0.3.0

Breaking change

• Additional arguments (...) are now passed to the ?FeatureHandler$compute() and ?FeatureHandler$get() functions in ?FeatureHandler (#162). Furthermore, a reference to the diseasystore is now passed to ?FeatureHandler$compute() as ds to give the ?FeatureHandler access to other features via ?DiseasystoreBase$get_feature().

New Features

• New age helpers add_years() and age_on_date() has been added to help compute features for individual data (#125).

• Added the fields ?DiseasystoreBase$available_observables and ?DiseasystoreBase$available_features for easier overview (#139).

• The data availability period for each diseasystore is now exposed via the ?DiseasystoreBase$min_start_date and ?DiseasystoreBase$max_end_date fields (#138).

• diseasystores can now have variable backend support (#175). In case a backend is insufficient to support the computations, the backend can be blocked for the diseasystore. test_diseasystore() now have a skip_backend argument to skip tests for the disallowed backends.

• Added the ?DiseasystoreSimulist which implements a synthetic, individual-level, data set generated with simulist.

Minor Improvements and Fixes

• A bug was fixed where data was duplicated when features were not divided into separate tables (#192).

• Two bugs were fixed in ?DiseasystoreBase$determine_new_ranges() where existing tables were not detected:

  • On backends that use “catalog” to structure table (DuckDB and SQL Server) (also requires {SCDB} > v0.4) (#158).
  • Due to slice_ts not being correctly matched with existing data on some backends (#172).

• Long stratification expression are now properly parsed in ?DiseasystoreBase$key_join_features() (#161).

• When creating your own diseasystore it is now easier to inherit from the base module (#189).

• When creating your own diseasystore it is now easier to inherit from the base module (#189).

• Warnings about existing stratifications now only appear if the requested stratification contains a named expression matching an existing stratification. Simply requesting the stratification from the feature store will no longer produce a warning (#192).

Testing

• test_diseasystore() now also checks the ?FeatureHandler return data directly:
  • Checks that data is only within the study period (#154).
  • Checks that valid_from and valid_until has class Date (#154).
  • Checks that the valid_from and valid_until columns are chronologically ordered (#176).

Documentation

• An example has been added for building a diseasystore with individual level data (#162). See vignette("extending-diseasystore-example").

• Added benchmarking vignette vignette("benchmarks") (#144).

Minor Improvements and Fixes

• diseasyoption() can now be called without the option argument to return all diseasy/diseasystore options (#159).

  In addition, a new namespace argument can restrict the option look-up to a specific package (e.g. diseasystore).

diseasystore 0.2.2

Minor Improvements and Fixes:

• The %.% operator is made more flexible to function as a drop-in replacement for $ (#145).

diseasystore 0.2.1

• Support for {SCDB} v0.3 is removed.

diseasystore 0.2.0

New Features

• ?DiseasystoreEcdcRespiratoryViruses: A feature store that uses the ECDC Respiratory viruses weekly repository (#124).

• With the release of {SCDB} v0.4, we now support more database backends:

  • SQLite with attached schemas (#121).

  • Microsoft SQL Server (#128).

  • PostgreSQL (#128).

  • DuckDB (#127).

• test_diseasystore() is added to provide a standardised method for testing new diseasystores (#123).

Minor Improvements and Fixes

• diseasyoption() now allows a default option to be set with the .default argument (#122).

diseasystore 0.1.1

Fixes

• Improved the stability of internal functions.

• Adapted to release of {SCDB} v0.3.

Documentation

• Improved documentation of functions.

Testing

• Improved test stability when internet is unavailable.

• Reduced the data footprint during tests.

diseasystore 0.1

Features

• ?DiseasystoreBase: A base class for the diseasystores.

  • R6 class that defines the interface for the diseasystores.

• ?DiseasystoreGoogleCovid19: A feature store that uses the Google COVID-19 Open Data repository.

  • R6 class that builds on the base class to provide interface to the Google COVID-19 data.

• ?FeatureHandler: A simple class to handle individual feature computations.

  • Defines the interface for each individual feature in the diseasystores.

• Aggregators: A set of aggregators for the ?FeatureHandler to use.

• drop_diseasystore(): A function to remove data from a feature store.

• Added a informative operator to access data %.%.

  • Gives error instead of NULL if element does not exist.

• age_labels(): A function to generate human-readable and sortable age groupings.

Testing

• Most package functions are tested here.

Documentation

• The functions are fully documented.

• Vignettes for the use of the package is included.

  • vignette("quick-start")
  • vignette("extending-diseasystore")

• Vignette for the Google COVID-19 data is included.

  • vignette("diseasystore-google-covid-19")

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
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