Thierry Warin, PhD: [API] covid19Italy

Thierry Warin

doi:10.6084/m9.figshare.11763759.v2

Database description

The coronavirus package provides a tidy format dataset of the 2019 Novel Coronavirus COVID-19 (2019-nCoV) epidemic. The raw data pulled from the Johns Hopkins University Center for Systems Science and Engineering (JHU CCSE) Coronavirus repository.

A csv format of the package dataset available here.

A summary dashboard is available here.

Functions

The covid19italy package dev version is updated on a daily bases. The function below allows you to download the data.

update_data()

Each of these functions are detailed in this course and some examples are provided.

update_data()

The update_data function enables a simple refresh of the installed package datasets with the most updated version on Github:

library(covid19italy)

update_data()

Updates are available on the covid19italy Dev version, do you want to update? n/Y

Note: must restart the R session to have the updates available.

Usage

data(italy_total)

head(italy_total)

        date hospitalized_with_symptoms intensive_care
1 2020-02-24                        101             26
2 2020-02-25                        114             35
3 2020-02-26                        128             36
4 2020-02-27                        248             56
5 2020-02-28                        345             64
6 2020-02-29                        401            105
  total_hospitalized home_confinement cumulative_positive_cases
1                127               94                       221
2                150              162                       311
3                164              221                       385
4                304              284                       588
5                409              412                       821
6                506              543                      1049
  daily_positive_cases recovered death positive_clinical_activity
1                    0         1     7                         NA
2                   90         1    10                         NA
3                   74         3    12                         NA
4                  203        45    17                         NA
5                  233        46    21                         NA
6                  228        50    29                         NA
  positive_surveys_tests cumulative_cases total_tests
1                     NA              229        4324
2                     NA              322        8623
3                     NA              400        9587
4                     NA              650       12014
5                     NA              888       15695
6                     NA             1128       18661
  total_people_tested
1                  NA
2                  NA
3                  NA
4                  NA
5                  NA
6                  NA

Plotting the active cases distribution

library(plotly)

plot_ly(data = italy_total,
        x = ~ date,
        y = ~home_confinement, 
        name = 'Home Confinement', 
        fillcolor = '#FDBBBC',
        type = 'scatter',
        mode = 'none', 
        stackgroup = 'one') %>%
  add_trace( y = ~ hospitalized_with_symptoms, 
             name = "Hospitalized with Symptoms",
             fillcolor = '#E41317') %>%
  add_trace(y = ~intensive_care, 
                name = 'Intensive Care', 
                fillcolor = '#9E0003') %>%
  layout(title = "Italy - Distribution of Active Covid19 Cases",
         legend = list(x = 0.1, y = 0.9),
         yaxis = list(title = "Number of Cases"),
         xaxis = list(title = "Source: Italy Department of Civil Protection"))

Check here to see more graphics examples of the data retrived from the covid19italy package.

tl;dr

library(covid19italy)

update_data()

data(italy_total)

head(italy_total)

library(plotly)

plot_ly(data = italy_total,
        x = ~ date,
        y = ~home_confinement, 
        name = 'Home Confinement', 
        fillcolor = '#FDBBBC',
        type = 'scatter',
        mode = 'none', 
        stackgroup = 'one') %>%
  add_trace( y = ~ hospitalized_with_symptoms, 
             name = "Hospitalized with Symptoms",
             fillcolor = '#E41317') %>%
  add_trace(y = ~intensive_care, 
                name = 'Intensive Care', 
                fillcolor = '#9E0003') %>%
  layout(title = "Italy - Distribution of Active Covid19 Cases",
         legend = list(x = 0.1, y = 0.9),
         yaxis = list(title = "Number of Cases"),
         xaxis = list(title = "Source: Italy Department of Civil Protection"))

Code learned this week

Command	Detail
update_data()	Get data for of all Corona Virus cases in Italy

References

This course uses the covid19Italy package, created by Rami Krispin.

[API] covid19Italy