This is largely a patch release dealing with processing issues introduced by the recent release of tidyr 1.2.0
. In addition support for data from Estonia and Vietnam has been added. See the full release notes for details. Thanks to @RichardMN, @biocyberman, @Bisaloo, @sbfnk, and @kathsherratt for contributing to this release.
?Estonia
for details.?Vietnam
for details. Note that this class is only available if installing the vietnam
branch from GitHub due to API instability issues. fill_empty_dates_with_na()
caused by changes made in version 1.2.0
of tidyr
. stringr
(#448 by @RichardMN).RSocrata
be a suggested package (#433 by @RichardMN).get_interventions_data()
has been depreciated and removed.get_info_covidregionaldata()
has been depreciated and removed.country
argument to get_national_data()
has been depreciated and removed. It's functionality can be replicated using the countries
argument.get_linelist()
has been updated to fail on use vs warn on use and will be removed from future versions of the package. This release adds support for the Covid19 Data Hub which includes Google and Apple mobility data amongst a large range of other data sets, data from the European Commission's Joint Research Centre which is at both the regional and national level, and individual sources for regional data from several countries. Package updates have been made in line with a software review at the Journal of Open Source Software. Finally, this release exposes more of the testing infrastructure to users and adds a package hexsticker.
Thanks to @joseph-palmer, @RichardMN, and @kathsherratt for contributions towards this release.
common_data_urls
or level_data_urls
to be present. The previous default which forced the presence of common_data_urls
meant that several classes had to define an empty field (by @joseph-palmer).DataClass
. test_regional-datasets
now calls the test function for all classes at each level. Data set specific tests (such as for NHS regions in the UK) are included as a specific_tests
function within the country class, which is called by the parent (DataClass) test
after performing standard checks. This allows all the code about a country to be defined in its own class. In addition, users can run tests interactively by calling the test method (e.g. $test()
) (by @joseph-palmer)make_new_data_source()
with the country / source name to add and it will set up the basic structure for you. There is also now a github check to make sure all new sources have a workflow set up (by @joseph-palmer).source_
fields to all data sets to help users properly attribute their data sources (by @RichardMN).Lithuania()
data set would ignore optional class specific arguments has been fixed (by @RichardMN).JHU()
source had multiple region codes for each country has been fixed, giving just one region code per country (by @joseph-palmer).This release adds support for data sets from John Hopkins University and the Google open data project. Both of these sources aggregate a range of data at national and subnational levels. It also contains a range of small fixes and improvements to documentation. Finally, this release adds optional data processing which will be extended in future releases (contributions warmly welcomed).
Thanks to @joseph-palmer, @RichardMN, and @kathsherratt for contributions towards this release.
available_regions
method for all classes that shows level 1 regions with data available for the region of interest. This is of particular use when combined with the JHU or Google datasets where processing a large number of regions that are not required can take some time.get_national_data()
. This may also now be used to access lower level data from these sources but it may be better to instead use the classes directly or via initialise_dataclass()
.UK()
has been improved to include both the dynamic data previously supported and the archive document now produced (by @kathsherratt).UK()
class have been expanded to better showcase the package functionality.get_regional_data()
, get_national_data()
, and get_available_datasets()
has been expanded with a focus on increasing the visibility of the underlying package structure.initialise_dataclass()
, DataClass()
, and CountryDataClass()
has been expanded and improved.pkgdown
documentation to organise packages into appropriate subcategories.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.
step = TRUE
argument in get_regional_data()
.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()
.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
.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.get_info_covidregionaldata()
.vroom
for faster csv
downloads.get_linelist
: argument clean
changed to clean_dates
to reflect slight change in use case.Fixed inconsistent reference dates for variables in UK data. cases_new and cases_total now by "Specimen date" (date of test), while deaths_new and deaths_total are by "Date of death", for all regions and nations.
Additional delays added to get_linelist
when clean_dates = TRUE
.
covidregionaldata
cache of the public linelist as a fall back option if the source is not available.memoise
functionality to automatically cache in the current directory all remote resources.NEWS.md
file to track changes to the package.get_linelist
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