README.md

In RamiKrispin/covid19swiss: The 2019 Novel Coronavirus COVID-19 (2019-nCoV) Cases in Switzerland and Principality of Liechtenstein

covid19swiss

The covid19swiss R package provides a tidy format dataset of the 2019 Novel Coronavirus COVID-19 (2019-nCoV) pandemic outbreak in Switzerland cantons and the Principality of Liechtenstein (FL). The covid19swiss dataset includes the following fields:

• date - the timestamp of the case, a Date object
• location - the Cantons of Switzerland and the Principality of Liechtenstein (FL) abbreviation code
• location_type - description of the location, either Canton of Switzerland or the Principality of echtenstein
• location_code - a canton index code for merging geometry data from the rnaturalearth package, ailable only for Switzerland cantons
• location_code_type - the name of code in the rnaturalearth package for Switzerland map
• data_type - the type of case
• value - the number of cases corresponding to the date and data_type fields

Where the available data_type field includes the following cases:

• total_tested - number of tests performed as of the date
• total_confirmed - number of positive cases as of the date
• new_hosp - new hospitalizations with respect to the previously reported date
• current_hosp - number of hospitalized patients as of the current date
• current_icu - number of hospitalized patients in ICUs as of the current date
• current_vent - number of hospitalized patients requiring ventilation as of the current date
• total_recovered - total number of patients recovered as of the current date
• total_death - total number of death as of the current date

More information can be found the following vignettes:

• Introduction to the covid19swiss Dataset
• Updating the covid19swiss Dataset
• Geospatial Visualization of Switzerland Cantons (non CRAN vignette)

Data source: Specialist Unit for Open Government Data Canton of Zurich, raw data is available on the following repository. Special thanks for all the people that collaborate and contribute to pull the data from multiple sources and make this data available!

Installation

You can install the released version of covid19swiss from CRAN with:

install.packages("covid19swiss")

Or, install the most recent version from GitHub with:

# install.packages("devtools")
devtools::install_github("Covid19R/covid19swiss")

Data refresh

The covid19swiss package dev version is been updated on a daily bases. The update_swiss_data function enables a simple refresh of the installed package datasets with the most updated version on Github:

library(covid19swiss)

update_swiss_data()

More information about updating the data is available on this vignette

Note: must restart the R session after using the update_swiss_data function in order to have the updates available

Usage

data(covid19swiss)

head(covid19swiss)
#>         date location         location_type location_code location_code_type       data_type value
#> 1 2020-02-25       GE Canton of Switzerland         CH.GE         gn_a1_code    total_tested    72
#> 2 2020-02-25       GE Canton of Switzerland         CH.GE         gn_a1_code total_confirmed     0
#> 3 2020-02-25       GE Canton of Switzerland         CH.GE         gn_a1_code        new_hosp    NA
#> 4 2020-02-25       GE Canton of Switzerland         CH.GE         gn_a1_code    current_hosp     0
#> 5 2020-02-25       GE Canton of Switzerland         CH.GE         gn_a1_code     current_icu     0
#> 6 2020-02-25       GE Canton of Switzerland         CH.GE         gn_a1_code    current_vent     0

Wide format

library(tidyr)

covid19swiss_wide <- covid19swiss %>% 
  pivot_wider(names_from = data_type, values_from = value)

head(covid19swiss_wide)
#> # A tibble: 6 x 13
#>   date       location location_type                 location_code location_code_type total_tested total_confirmed new_hosp current_hosp current_icu current_vent total_recovered total_death
#>   <date>     <chr>    <chr>                         <chr>         <chr>                     <int>           <int>    <int>        <int>       <int>        <int>           <int>       <int>
#> 1 2020-02-25 GE       Canton of Switzerland         CH.GE         gn_a1_code                   72               0       NA            0           0            0              NA          NA
#> 2 2020-02-25 TI       Canton of Switzerland         CH.TI         gn_a1_code                   NA               1       NA           NA          NA           NA              NA          NA
#> 3 2020-02-26 GE       Canton of Switzerland         CH.GE         gn_a1_code                  178               1       NA            1           0            0              NA          NA
#> 4 2020-02-26 TI       Canton of Switzerland         CH.TI         gn_a1_code                   NA              NA       NA           NA          NA           NA              NA          NA
#> 5 2020-02-27 BS       Canton of Switzerland         CH.BS         gn_a1_code                   NA               1       NA           NA          NA           NA              NA          NA
#> 6 2020-02-27 FL       Principality of Liechtenstein <NA>          gn_a1_code                    3              NA       NA           NA          NA           NA              NA          NA

Missing values

The data is collected from multiple resources on the canton level, and not necessarily each data resource provides the same field. Therefore, some fields, such as total recovered or total tested may not be available at this point for some cantons and are marked as missing values (i.e., NA).

Contributing

Please submit issues and pull requests with any package improvements!

Please note that the ‘covid19swiss’ project is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.

RamiKrispin/covid19swiss documentation built on May 18, 2020, 11:54 a.m.