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epiforecasts/covidregionaldata: 0.9.0 CRAN release

Sam Abbott; Joe Palmer; Kath Sherratt; Jonnie-Bevan; Richard Martin-Nielsen; hamishgibbs; Flavio Finger; Hugo Gruson; Sebastian Funk; Joel Hellewell; Paul Campbell; Richard Boyes; Patrick Barks; Maria; Haze Lee; joeHickson; Sophie Meakin

In this release covidregionaldata has been substantially retooled to be more robust, and to handle data in a more transparent way. Adding new data sets and functionality has also been made more streamlined. As this update is a substantial package refactor some breaking changes may be been inadvertently introduced. If requiring the old behaviour please install covidregionaldata@0.8.3 from GitHub.

Thanks to @joseph-palmer, @RichardMN, and @kathsherratt for major contributions to this release. Thanks to @RichardMN for volunteering his time.

New features
  • Track data processing from raw to clean using the step = TRUE argument in get_regional_data().
  • Filter datasets for regions and countries of interest.
  • Access the underlying methods for data sets and all steps in the data processing pipeline.
Documentation
  • All vignettes have been updated for readability.
  • A quickstart has been added to the package README.
Technical improvements
  • get_regional_data() and get_national_data() now use R6 method dispatch. This is an internal change and so should have minimal user impact for users of the get_ functions. However, all datasets are now available to be used as R6 methods (see get_available_datasets) which may allow for more modular use cases. These classes can also be initialised using initialise_dataclass() which is used internally by both get_regional_data() and get_national_data().
  • Unit testing has been separated from data downloading which is now tested individually by data set. This allows for contributors to more easily assess the impact of their additions and also allows us to publish data status updates for each data sets (see the README: https://github.com/epiforecasts/covidregionaldata#readme).
Deprecated functions
  • get_available_datasets() replaces get_info_covidregionaldata() to view available data. get_info_covidregionaldata() is deprecated.
  • get_interventions_data() is deprecated. These data no longer update as of December 2020. Check for alternatives at https://supertracker.spi.ox.ac.uk/policy-trackers/
  • get_linelist is deprecated. Linelist stopped updating June 2020. Up to date linelist data are now behind a login: access at https://global.health/. We are working on a solution for accessing with covidregionaldata.
Data changes since 0.8.3
  • Colombia now has capitalized region names.
  • Germany level 2 region codes have been removed (previously was all NAs).
  • India uses NA for unknown region codes, a change from IN-UN previously.
  • Italy column region is now regioni.
  • Mexico codes 'inegi_code' has been changed to 'inegi'.
  • UK Level 1 'ons_region_code' is now 'region_code'.
  • UK level 2 "ltla_code" is now "local_authority_code".
  • get_available_datasets() now return an origin column rather than a country column and a type column rather than a get_data_function to better reflect the types of data supported.

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