Subnational Data for COVID-19 Epidemiology


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Documentation for package ‘covidregionaldata’ version 0.9.3

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add_extra_na_cols Add extra columns filled with NA values to a 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.
Belgium Belgium Class for downloading, cleaning and processing notification data
Brazil Brazil Class for downloading, cleaning and processing notification data
calculate_columns_from_existing_data Cumulative counts from daily counts or daily counts from cumulative, dependent on which columns already exist
Canada Canada Class containing origin specific attributes and methods
check_level Checks a given level is supported
Colombia Colombia Class for downloading, cleaning and processing notification data
colombia_codes Region Codes for Colombia Dataset.
complete_cumulative_columns Completes cumulative columns if rows were added with NAs.
CountryDataClass R6 Class containing national level methods
Covid19DataHub R6 Class containing specific attributes and methods for Covid19 Data Hub
csv_reader Custom CSV reading function
Cuba Cuba Class for downloading, cleaning and processing notification data
DataClass R6 Class containing non-dataset specific methods
download_excel Download Excel Documents
ECDC R6 Class containing specific attributes and methods for the European Centre for Disease Prevention and Control dataset
Estonia Estonia Class for downloading, cleaning and processing notification data
expect_clean_cols Test clean columns contain the correct data and types
expect_columns_contain_data Test that cleaned columns contain data/
expect_processed_cols Test that processed columns contain the correct data and types
fill_empty_dates_with_na Add rows of NAs for dates where a region does not have any data
France France Class containing origin specific attributes and methods
france_codes Region Codes for France Dataset.
Germany Germany Class for downloading, cleaning and processing notification data
get_available_datasets Get supported data sets
get_national_data Get national-level data for countries globally from a range of sources
get_regional_data Get regional-level data
glue_level Glue the spatial level into a variable name
Google R6 Class containing specific attributes and methods for Google data
India India Class for downloading, cleaning and processing notification data
initialise_dataclass Initialise a child class of DataClass if it exists
Italy Italy Class for downloading, cleaning and processing notification data
JHU R6 Class containing specific attributes and methods for John Hopkins University data
JHU_codes Region Codes for JHU Dataset. Taken from the region codes provided as part of the WHO dataset.
JRC R6 Class containing specific attributes and methods for European Commission's Joint Research Centre data
json_reader Custom JSON reading function
Lithuania Lithuania Class for downloading, cleaning and processing notification data
lithuania_codes Region Codes for Lithuania Dataset.
make_github_workflow Create github action for a given source
make_new_data_source Create new country class for a given source
message_verbose Wrapper for message
Mexico Meixco Class for downloading, cleaning and processing notification data
mexico_codes Region Codes for Mexico Dataset.
Netherlands Netherlands Class for downloading, cleaning and processing notification data
process_internal Internal Shared Regional Dataset Processing
region_dispatch Control Grouping Variables used in process_internal
reset_cache Reset Cache and Update all Local Data
return_data Control data return
run_default_processing_fns Default processing steps to run
run_optional_processing_fns Optional processing steps to run
set_negative_values_to_zero Set negative data to 0
SouthAfrica SouthAfrica Class for downloading, cleaning and processing notification data
start_using_memoise Add useMemoise to options
stop_using_memoise Stop using useMemoise
Switzerland Switzerland Class for downloading, cleaning and processing notification data
test_cleaning Test clean method works correctly
test_download Test download method works correctly
test_download_JSON Test download method for JSON files works correctly
test_processing Test process method works correctly
test_return Test return method works correctly
totalise_data Get totals data given the time series data.
UK United Kingdom Class for downloading, cleaning and processing notification data.
uk_codes Region Codes for UK Dataset.
USA USA Class for downloading, cleaning and processing notification data
vietnam_codes Region Codes for Vietnam Dataset.
WHO R6 Class containing specific attributes and methods for World Health Organisation data