Package: covidregionaldata 0.9.3

Sam Abbott

covidregionaldata: Subnational Data for COVID-19 Epidemiology

An interface to subnational and national level COVID-19 data sourced from both official sources, such as Public Health England in the UK, and from other COVID-19 data collections, including the World Health Organisation (WHO), European Centre for Disease Prevention and Control (ECDC), John Hopkins University (JHU), Google Open Data and others. Designed to streamline COVID-19 data extraction, cleaning, and processing from a range of data sources in an open and transparent way. This allows users to inspect and scrutinise the data, and tools used to process it, at every step. For all countries supported, data includes a daily time-series of cases. Wherever available data is also provided for deaths, hospitalisations, and tests. National level data are also supported using a range of sources.

Authors:Joseph Palmer [aut], Katharine Sherratt [aut], Richard Martin-Nielsen [aut], Jonnie Bevan [aut], Hamish Gibbs [aut], Hugo Gruson [aut], Sophie Meakin [ctb], Joel Hellewell [ctb], Patrick Barks [ctb], Paul Campbell [ctb], Flavio Finger [ctb], Richard Boyes [ctb], Vang Le [ctb], Sebastian Funk [aut], Sam Abbott [aut, cre]

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covidregionaldata.pdf |covidregionaldata.html✨
covidregionaldata/json (API)
NEWS

# Install 'covidregionaldata' in R:
install.packages('covidregionaldata', repos = c('https://epiforecasts.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/epiforecasts/covidregionaldata/issues

Datasets:
  • JHU_codes - Region Codes for JHU Dataset. Taken from the region codes provided as part of the WHO dataset.
  • all_country_data - Table of available datasets along with level and other information. Rendered from the individual R6 class objects included in this package.
  • colombia_codes - Region Codes for Colombia Dataset.
  • france_codes - Region Codes for France Dataset.
  • lithuania_codes - Region Codes for Lithuania Dataset.
  • mexico_codes - Region Codes for Mexico Dataset.
  • uk_codes - Region Codes for UK Dataset.
  • vietnam_codes - Region Codes for Vietnam Dataset.

On CRAN:

covid-19dataopen-sciencer6regional-data

5.67 score 37 stars 121 scripts 128 downloads 43 exports 46 dependencies

Last updated 3 years agofrom:43f573ef5c (on 0.9.3). Checks:ERROR: 1 WARNING: 6. Indexed: yes.

TargetResultDate
Doc / VignettesFAILOct 31 2024
R-4.5-winWARNINGOct 31 2024
R-4.5-linuxWARNINGOct 31 2024
R-4.4-winWARNINGOct 31 2024
R-4.4-macWARNINGOct 31 2024
R-4.3-winWARNINGOct 31 2024
R-4.3-macWARNINGOct 31 2024

Exports:%>%BelgiumBrazilCanadaColombiaCountryDataClassCovid19DataHubCubaDataClassECDCEstoniaexpect_clean_colsexpect_columns_contain_dataexpect_processed_colsFranceGermanyget_available_datasetsget_national_dataget_regional_dataGoogleIndiainitialise_dataclassItalyJHUJRCLithuaniamake_github_workflowmake_new_data_sourceMexicoNetherlandsreset_cacheSouthAfricastart_using_memoisestop_using_memoiseSwitzerlandtest_cleaningtest_downloadtest_download_JSONtest_processingtest_returnUKUSAWHO

Dependencies:askpassbitbit64cachemcellrangerclicountrycodecpp11crayoncurldplyrfansifastmapgenericsgluehmshttrjsonlitelifecyclelubridatemagrittrmemoisemimeopensslpillarpkgconfigprettyunitsprogresspurrrR6readxlrematchrlangstringistringrsystibbletidyrtidyselecttimechangetzdbutf8vctrsvroomwithrxml2

Readme and manuals

Help Manual

Help pageTopics
Add extra columns filled with NA values to a dataset.add_extra_na_cols
Table of available datasets along with level and other information. Rendered from the individual R6 class objects included in this package.all_country_data
Belgium Class for downloading, cleaning and processing notification dataBelgium
Brazil Class for downloading, cleaning and processing notification dataBrazil
Cumulative counts from daily counts or daily counts from cumulative, dependent on which columns already existcalculate_columns_from_existing_data
Canada Class containing origin specific attributes and methodsCanada
Checks a given level is supportedcheck_level
Colombia Class for downloading, cleaning and processing notification dataColombia
Region Codes for Colombia Dataset.colombia_codes
Completes cumulative columns if rows were added with NAs.complete_cumulative_columns
R6 Class containing national level methodsCountryDataClass
R6 Class containing specific attributes and methods for Covid19 Data HubCovid19DataHub
Custom CSV reading functioncsv_reader
Cuba Class for downloading, cleaning and processing notification dataCuba
R6 Class containing non-dataset specific methodsDataClass
Download Excel Documentsdownload_excel
R6 Class containing specific attributes and methods for the European Centre for Disease Prevention and Control datasetECDC
Estonia Class for downloading, cleaning and processing notification dataEstonia
Test clean columns contain the correct data and typesexpect_clean_cols
Test that cleaned columns contain data/expect_columns_contain_data
Test that processed columns contain the correct data and typesexpect_processed_cols
Add rows of NAs for dates where a region does not have any datafill_empty_dates_with_na
France Class containing origin specific attributes and methodsFrance
Region Codes for France Dataset.france_codes
Germany Class for downloading, cleaning and processing notification dataGermany
Get supported data setsget_available_datasets
Get national-level data for countries globally from a range of sourcesget_national_data
Get regional-level dataget_regional_data
Glue the spatial level into a variable nameglue_level
R6 Class containing specific attributes and methods for Google dataGoogle
India Class for downloading, cleaning and processing notification dataIndia
Initialise a child class of DataClass if it existsinitialise_dataclass
Italy Class for downloading, cleaning and processing notification dataItaly
R6 Class containing specific attributes and methods for John Hopkins University dataJHU
Region Codes for JHU Dataset. Taken from the region codes provided as part of the WHO dataset.JHU_codes
R6 Class containing specific attributes and methods for European Commission's Joint Research Centre dataJRC
Custom JSON reading functionjson_reader
Lithuania Class for downloading, cleaning and processing notification dataLithuania
Region Codes for Lithuania Dataset.lithuania_codes
Create github action for a given sourcemake_github_workflow
Create new country class for a given sourcemake_new_data_source
Wrapper for messagemessage_verbose
Meixco Class for downloading, cleaning and processing notification dataMexico
Region Codes for Mexico Dataset.mexico_codes
Netherlands Class for downloading, cleaning and processing notification dataNetherlands
Internal Shared Regional Dataset Processingprocess_internal
Control Grouping Variables used in process_internalregion_dispatch
Reset Cache and Update all Local Datareset_cache
Control data returnreturn_data
Default processing steps to runrun_default_processing_fns
Optional processing steps to runrun_optional_processing_fns
Set negative data to 0set_negative_values_to_zero
SouthAfrica Class for downloading, cleaning and processing notification dataSouthAfrica
Add useMemoise to optionsstart_using_memoise
Stop using useMemoisestop_using_memoise
Switzerland Class for downloading, cleaning and processing notification dataSwitzerland
Test clean method works correctlytest_cleaning
Test download method works correctlytest_download
Test download method for JSON files works correctlytest_download_JSON
Test process method works correctlytest_processing
Test return method works correctlytest_return
Get totals data given the time series data.totalise_data
United Kingdom Class for downloading, cleaning and processing notification data.UK
Region Codes for UK Dataset.uk_codes
USA Class for downloading, cleaning and processing notification dataUSA
Region Codes for Vietnam Dataset.vietnam_codes
R6 Class containing specific attributes and methods for World Health Organisation dataWHO