├── .Rbuildignore ├── .covrignore ├── .devcontainer ├── Dockerfile ├── devcontainer.json └── library-scripts │ └── common-debian.sh ├── .github ├── .gitignore └── workflows │ ├── Belgium.yaml │ ├── Brazil.yaml │ ├── Canada.yaml │ ├── Colombia.yaml │ ├── Covid19DataHub.yaml │ ├── Cuba.yaml │ ├── ECDC.yaml │ ├── Estonia.yaml │ ├── France.yaml │ ├── Germany.yaml │ ├── Google.yaml │ ├── India.yaml │ ├── Italy.yaml │ ├── JHU.yaml │ ├── JRC.yaml │ ├── Lithuania.yaml │ ├── Mexico.yaml │ ├── Netherlands.yaml │ ├── R-CMD-check.yaml │ ├── SouthAfrica.yaml │ ├── Switzerland.yaml │ ├── UK.yaml │ ├── USA.yaml │ ├── WHO.yaml │ ├── build-image.yaml │ ├── greetings.yml │ ├── lint.yaml │ ├── pkgdown.yaml │ ├── pr-checklist.yaml │ ├── source_actions_exist.yaml │ ├── stale.yml │ ├── test-coverage.yaml │ └── test-regional-datasets.yml ├── .gitignore ├── .lintr ├── .pre-commit-config.yaml ├── CODE_OF_CONDUCT.md ├── CRAN-SUBMISSION ├── DESCRIPTION ├── LICENSE ├── LICENSE.md ├── NAMESPACE ├── NEWS.md ├── R ├── Belgium.R ├── Brazil.R ├── Canada.R ├── Colombia.R ├── Covid19DataHub.R ├── Cuba.R ├── ECDC.R ├── Estonia.R ├── France.R ├── Germany.R ├── Google.R ├── India.R ├── Italy.R ├── JHU.R ├── JRC.R ├── Lithuania.R ├── Mexico.R ├── Netherlands.R ├── SouthAfrica.R ├── Switzerland.R ├── UK.R ├── USA.R ├── WHO.R ├── datasets.R ├── get_available_datasets.R ├── get_linelist.R ├── get_national_data.R ├── get_regional_data.R ├── processing.R ├── shared-methods.R ├── test-DataClass.R └── utils.R ├── README.Rmd ├── README.md ├── _pkgdown.yml ├── codecov.yml ├── covidregionaldata.Rproj ├── cran-comments.md ├── data-raw ├── colombia_codes.R ├── france_codes.R ├── jhu_codes.R ├── lithuania_codes.R ├── lithuania_codes.csv ├── mexico_codes.R ├── mexico_codes.csv ├── render_available_datasets.R ├── uk_codes.R └── vietnam_codes.R ├── data ├── JHU_codes.rda ├── all_country_data.rda ├── colombia_codes.rda ├── france_codes.rda ├── lithuania_codes.rda ├── mexico_codes.rda ├── uk_codes.rda └── vietnam_codes.rda ├── inst ├── CITATION ├── CountryTemplate.R ├── WORDLIST ├── examples │ └── overview.R ├── github_workflow_template.yaml ├── make_hexsticker.R ├── paper │ ├── paper.bib │ └── paper.md └── test-github_workflow_present.R ├── man ├── Belgium.Rd ├── Brazil.Rd ├── Canada.Rd ├── Colombia.Rd ├── CountryDataClass.Rd ├── Covid19DataHub.Rd ├── Cuba.Rd ├── DataClass.Rd ├── ECDC.Rd ├── Estonia.Rd ├── France.Rd ├── Germany.Rd ├── Google.Rd ├── India.Rd ├── Italy.Rd ├── JHU.Rd ├── JHU_codes.Rd ├── JRC.Rd ├── Lithuania.Rd ├── Mexico.Rd ├── Netherlands.Rd ├── SouthAfrica.Rd ├── Switzerland.Rd ├── UK.Rd ├── USA.Rd ├── WHO.Rd ├── add_extra_na_cols.Rd ├── all_country_data.Rd ├── calculate_columns_from_existing_data.Rd ├── check_level.Rd ├── colombia_codes.Rd ├── complete_cumulative_columns.Rd ├── csv_reader.Rd ├── download_excel.Rd ├── expect_clean_cols.Rd ├── expect_columns_contain_data.Rd ├── expect_processed_cols.Rd ├── figures │ ├── README-g7_plot-1.png │ ├── README-supported_region_plot-1.png │ ├── README-uk_plot-1.png │ ├── README-utla_plot-1.png │ ├── lifecycle-archived.svg │ ├── lifecycle-defunct.svg │ ├── lifecycle-deprecated.svg │ ├── lifecycle-experimental.svg │ ├── lifecycle-maturing.svg │ ├── lifecycle-questioning.svg │ ├── lifecycle-stable.svg │ ├── lifecycle-superseded.svg │ └── logo.png ├── fill_empty_dates_with_na.Rd ├── france_codes.Rd ├── get_available_datasets.Rd ├── get_linelist.Rd ├── get_national_data.Rd ├── get_regional_data.Rd ├── glue_level.Rd ├── initialise_dataclass.Rd ├── json_reader.Rd ├── lithuania_codes.Rd ├── make_github_workflow.Rd ├── make_new_data_source.Rd ├── message_verbose.Rd ├── mexico_codes.Rd ├── process_internal.Rd ├── reexports.Rd ├── region_dispatch.Rd ├── reset_cache.Rd ├── return_data.Rd ├── roxygen │ └── meta.R ├── run_default_processing_fns.Rd ├── run_optional_processing_fns.Rd ├── set_negative_values_to_zero.Rd ├── start_using_memoise.Rd ├── stop_using_memoise.Rd ├── test_cleaning.Rd ├── test_download.Rd ├── test_download_JSON.Rd ├── test_processing.Rd ├── test_return.Rd ├── totalise_data.Rd ├── uk_codes.Rd └── vietnam_codes.Rd ├── tests ├── spelling.R ├── testthat.R └── testthat │ ├── custom_data │ ├── Belgium_level_1.rds │ ├── Belgium_level_2.rds │ ├── Brazil_level_1.rds │ ├── Brazil_level_2.rds │ ├── Canada_level_1.rds │ ├── Colombia_level_1.rds │ ├── Colombia_level_2.rds │ ├── Covid19DataHub_level_1.rds │ ├── Covid19DataHub_level_2.rds │ ├── Covid19DataHub_level_3.rds │ ├── Cuba_level_1.rds │ ├── ECDC_level_1.rds │ ├── Estonia_level_1.rds │ ├── France_level_1.rds │ ├── France_level_2.rds │ ├── Germany_level_1.rds │ ├── Germany_level_2.rds │ ├── Google_level_1.rds │ ├── Google_level_2.rds │ ├── Google_level_3.rds │ ├── India_level_1.rds │ ├── Italy_level_1.rds │ ├── JHU_level_1.rds │ ├── JHU_level_2.rds │ ├── JRC_level_1.rds │ ├── JRC_level_2.rds │ ├── Lithuania_level_1.rds │ ├── Lithuania_level_2.rds │ ├── Mexico_level_1.rds │ ├── Mexico_level_2.rds │ ├── Netherlands_level_1.rds │ ├── Netherlands_level_2.rds │ ├── SouthAfrica_level_1.rds │ ├── Switzerland_level_1.rds │ ├── UK_level_1.rds │ ├── UK_level_1_nhs.rds │ ├── UK_level_2.rds │ ├── USA_level_1.rds │ ├── USA_level_2.rds │ ├── Vietnam_level_1.rds │ ├── WHO_level_1.rds │ ├── ecdc.csv │ ├── ecdc.rds │ ├── generate_data.R │ ├── mexico_level_1_snap.rds │ ├── mexico_level_2_snap.rds │ ├── mtcars.csv │ ├── mtcars.json │ └── who.rds │ ├── custom_tests │ ├── expect_colname.R │ ├── mock_data.R │ └── test-regional-dataset.R │ ├── functions │ ├── dummy_class.R │ └── test_initialise.R │ ├── test-CountryDataClass.R │ ├── test-DataClass.R │ ├── test-check_country_class.R │ ├── test-csv_reader.R │ ├── test-get_available_datasets.R │ ├── test-get_national_data.R │ ├── test-get_regional_data.R │ ├── test-initialise_dataclass.R │ ├── test-json_reader.R │ ├── test-message_verbose.R │ ├── test-processing.R │ ├── test-region_dispatch.R │ └── test-regional-datasets.R └── vignettes ├── .gitignore ├── 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