README.md
In jimtyhurst/covid19: COVID-19 Exploratory Data Analysis

covid19

This covid19 package provides an R API for accessing:

COVID-19 time series of cases and deaths by state, published by the NY Times.
COVID-19 time series of cases and deaths by country, published by the European Centre for Disease Prevention and Control (ECDC).
COVID-19 time series of cases and deaths by country, published by Johns Hopkins University Center for Systems Science and Engineering (JHU CSSE). They have separate files for confirmed cases and deaths.

Vignettes demonstrate how to use this API by providing simple visualizations of the data.

Installation
Example for NY Times data
Example for ECDC data
Examples for JHU CSSE data
License
Resources

Install the development version of covid19 from GitHub with:

remotes::install_github("jimtyhurst/covid19")

There are no plans to created a released version on CRAN or any other repository of published packages.

read_state_cases_nytimes():

Reads a NY Times dataset of COVID-19 cases and deaths by state.

library(covid19)
df <- covid19::read_state_cases_nytimes()

# Number of rows depends on the day that the data is downloaded,
# because the dataset is updated daily.
dim(df)
# [1] 1437    5
[1] "date"   "state"  "fips"   "cases"  "deaths"

read_cases_ecdc():

Reads a European Centre for Disease Prevention and Control (ECDC) dataset of COVID-19 cases and deaths.
Adds a date column of class Date, derived from the original dateRep column, which is a string.

library(covid19)
df <- covid19::read_cases_ecdc()

# Number of rows depends on the day that the data is downloaded,
# because the dataset is updated daily.
dim(df)
# [1] 7515   11
colnames(df)
 [1] "dateRep"                 "day"                     "month"                  
 [4] "year"                    "cases"                   "deaths"                 
 [7] "countriesAndTerritories" "geoId"                   "countryterritoryCode"   
[10] "popData2018"             "date"

read_confirmed_cases_jhu_csse():

Reads a JHU CSSE data file of confirmed COVID-19 cases by country.
Reformats the data as a tidy dataset.
Reformats the column names to snake case.

library(covid19)
confirmed_cases <- covid19::read_confirmed_cases_jhu_csse()

# Number of rows depends on the day that the data is downloaded,
# because the dataset is updated daily.
dim(confirmed_cases)
# [1] 17204     6
colnames(confirmed_cases)
# [1] "country_region"   "province_state"   "lat"             
# [4] "long"             "date"             "cumulative_total"

read_deaths_jhu_csse():

Reads a JHU CSSE data file of COVID-19 deaths by country.
Reformats the data as a tidy dataset.
Reformats the column names to snake case.

library(covid19)
deaths <- covid19::read_deaths_jhu_csse()

# Number of rows depends on the day that the data is downloaded,
# because the dataset is updated daily.
dim(deaths)
# [1] 17204     6
colnames(deaths)
# [1] "country_region"   "province_state"   "lat"             
# [4] "long"             "date"             "cumulative_total"

Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at

http://www.apache.org/licenses/LICENSE-2.0

Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.

World Health Organization (WHO): Coronavirus disease 2019
United States Centers for Disease Control and Prevention (CDC): Coronavirus (COVID-19)
European Centre for Disease Prevention and Control (ECDC): COVID-19
Johns Hopkins University Center for Systems Science and Engineering:
- Coronavirus COVID-19 Global Cases
- Mapping 2019-nCoV