# Subnational Data for COVID-19 Epidemiology

## Documentation for package ‘covidregionaldata’ version 0.9.3

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

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