Package overview

Installing and loading the package

The package can either be installed from CRAN, from our r-universe repository, or from GitHub. See the README for details. Once installed load the package using the following,

library(covidregionaldata)

Worldwide data

Accessing national data

Both the World Health Organisation (WHO) and European Centre for Disease Control (ECDC) provide worldwide national data. Access national level data for any country using:

get_national_data()

This returns daily new and cumulative (total) cases, and where available, deaths, hospitalisations, and tests. For a complete list of variables returned, see section 5, “Data glossary” below. See the documentation (?get_national_data) for details of optional arguments.

Data is returned with no gaps in the structure of the data by country over time, and NAs fill in where data are not available.

Sub-national time-series data

Accessing sub-national data

Access sub-national level data for a specific country over time using get_regional_data(). Use get_available_datasets() to explore the currently supported sub-national datasets and select the data set of interest using the country (selects the country of interest), and level (selects the spatial scale of the data) arguments of get_regional_data.

This function returns daily new and cumulative (total) cases, and where available, deaths, hospitalisations, and tests. For a complete list of variables returned, see section 5, “Data glossary” below. See the documentation (?get_regional_data) for details of optional arguments.

As for national level data any gaps in reported data are filled with NAs.

For example, data for France Level 1 regions over time can be accessed using:

get_regional_data(country = "france")

This data then has the following format:

date region iso_3166_2 cases_new cases_total deaths_new deaths_total recovered_new recovered_total hosp_new hosp_total tested_new tested_total insee_code
2022-02-03 Pays-de-la-Loire FR-PDL 15203 5017117 NA NA NA NA NA NA 42615 55188170 52
2022-02-03 Pays-de-la-Loire FR-PDL 15203 5032320 NA NA NA NA NA NA 42615 55230785 52
2022-02-03 Saint-Barthelemy FR-PM 1 114 NA NA NA NA NA NA 15 3466 05
2022-02-03 La Réunion FR-RE 116 258638 NA NA NA NA NA NA 602 2508043 04
2022-02-03 Mayotte FR-YT 18 34783 NA NA NA NA NA NA 818 343329 06

Alternatively, the same data can be accessed using the underlying class as follows (the France object now contains data at each processing step and the methods used at each step),

france <- France$new(get = TRUE)
france$return()

Level 1 and Level 2 regions

All countries included in the package (see below,“Coverage”) have data for regions at the admin-1 level, the largest administrative unit of the country (e.g. state in the USA). Some countries also have data for smaller areas at the admin-2 level (e.g. county in the USA).

Data for Level 2 units can be returned by using the level = "2" argument. The dataset will still show the corresponding Level 1 region.

An example of a country with Level 2 units is France, where Level 2 units are French departments:

get_regional_data(country = "france", level = "2")

This data again has the following format:

date region iso_3166_2 department ons_region_code cases_new cases_total deaths_new deaths_total recovered_new recovered_total hosp_new hosp_total tested_new tested_total insee_code
2022-02-06 La Réunion FR-RE La Réunion FR-974 NA 258638 5 574 NA NA 7 5611 NA 2508043 04
2022-02-06 Saint-Pierre et Miquelon FR-MF Saint-Pierre et Miquelon FR-975 NA 114 NA 0 NA NA NA 0 NA 3466 NA
2022-02-06 Mayotte FR-YT Mayotte FR-976 NA 34783 0 159 NA NA 0 2019 NA 343329 06
2022-02-06 Saint-Barthelemy FR-PM Saint-Barthelemy FR-977 NA 3649 NA 0 NA NA NA 0 NA 79700 NA
2022-02-06 Saint-Martin FR-BL Saint-Martin FR-978 NA 9684 0 1 NA NA 0 0 NA 111888 07

Totals

For totalled data up to the most recent date available, use the totals argument.

get_regional_data("france", totals = TRUE)

This data now has no date variable and reflects the latest total:

region iso_3166_2 cases_total deaths_total recovered_total hosp_total tested_total
Guyane (française) FR-GF 75282 0 0 0 601294
Mayotte FR-YT 34783 0 0 0 343329
Saint-Pierre et Miquelon FR-MF 9684 0 0 0 111888
Saint-Martin FR-BL 3649 0 0 0 79700
Saint-Barthelemy FR-PM 114 0 0 0 3466

Data glossary

Subnational data

The data columns that will be returned by get_regional_data() are listed below.

To standardise across countries and regions, the columns returned for each country will always be the same. If the corresponding data was missing from the original source then that data field is filled with NA values (or 0 if accessing totals data).

Note that Date is not included if the totals argument is set to TRUE. Level 2 region/level 2 region code are not included if the level = "1".

National data

In addition to the above, the following columns are included when using get_national_data().