Introduction to the covid19italy Datasets

The covid19italy R package provides a tidy format dataset of the 2019 Novel Coronavirus COVID-19 (2019-nCoV) pandemic outbreak in Italy. The package includes the following three datasets:

The data was pull from Italy Department of Civil Protection

Installation

You can install the released version of covid19italy from CRAN with:

install.packages("covid19italy")

Or, install the most recent version from GitHub with:

# install.packages("devtools")
devtools::install_github("RamiKrispin/covid19Italy")

Data refresh

The covid19italy package dev version is been updated on a daily bases. The update_data function enables a simple refresh of the installed package datasets with the most updated version on Github:

library(covid19italy)

update_data()

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

Italy summary

The italy_total dataset provides an overall summary of the cases in Italy since the beginning of the covid19 outbreak since February 24, 2020. The dataset contains the following fields:

library(covid19italy)

data(italy_total)

str(italy_total)
#> Classes 'tbl_df', 'tbl' and 'data.frame':    520 obs. of  19 variables:
#>  $ date                             : Date, format: "2020-02-24" "2020-02-25" ...
#>  $ hospitalized_with_symptoms       : num  101 114 128 248 345 ...
#>  $ intensive_care                   : num  26 35 36 56 64 105 140 166 229 295 ...
#>  $ total_hospitalized               : num  127 150 164 304 409 ...
#>  $ home_confinement                 : num  94 162 221 284 412 ...
#>  $ cumulative_positive_cases        : num  221 311 385 588 821 ...
#>  $ daily_positive_cases             : num  0 90 74 203 233 228 528 258 428 443 ...
#>  $ recovered                        : num  1 1 3 45 46 50 83 149 160 276 ...
#>  $ death                            : num  7 10 12 17 21 29 34 52 79 107 ...
#>  $ positive_clinical_activity       : num  NA NA NA NA NA NA NA NA NA NA ...
#>  $ positive_surveys_tests           : num  NA NA NA NA NA NA NA NA NA NA ...
#>  $ cumulative_cases                 : num  229 322 400 650 888 ...
#>  $ total_tests                      : num  4324 8623 9587 12014 15695 ...
#>  $ total_people_tested              : num  NA NA NA NA NA NA NA NA NA NA ...
#>  $ new_intensive_care               : num  NA NA NA NA NA NA NA NA NA NA ...
#>  $ total_positive_molecular_test    : num  NA NA NA NA NA NA NA NA NA NA ...
#>  $ total_positive_rapid_antigen_test: num  NA NA NA NA NA NA NA NA NA NA ...
#>  $ molecular_test                   : num  NA NA NA NA NA NA NA NA NA NA ...
#>  $ rapid_antigen_test               : num  NA NA NA NA NA NA NA NA NA NA ...

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

Italy region level

The italy_region dataset provides an overall summary of the cases in Italy’s regions. The dataset contains the following fields:

data(italy_region)

str(italy_region)
#> 'data.frame':    10920 obs. of  26 variables:
#>  $ date                      : Date, format: "2020-02-24" "2020-02-24" ...
#>  $ region_code               : chr  "13" "17" "18" "15" ...
#>  $ region_name               : chr  "Abruzzo" "Basilicata" "Calabria" "Campania" ...
#>  $ lat                       : num  42.4 40.6 38.9 40.8 44.5 ...
#>  $ long                      : num  13.4 15.8 16.6 14.3 11.3 ...
#>  $ hospitalized_with_symptoms: num  0 0 0 0 10 0 1 0 76 0 ...
#>  $ intensive_care            : num  0 0 0 0 2 0 1 0 19 0 ...
#>  $ total_hospitalized        : num  0 0 0 0 12 0 2 0 95 0 ...
#>  $ home_confinement          : num  0 0 0 0 6 0 0 0 71 0 ...
#>  $ cumulative_positive_cases : num  0 0 0 0 18 0 2 0 166 0 ...
#>  $ daily_positive_cases      : num  0 0 0 0 0 0 0 0 0 0 ...
#>  $ recovered                 : num  0 0 0 0 0 0 1 0 0 0 ...
#>  $ death                     : num  0 0 0 0 0 0 0 0 6 0 ...
#>  $ positive_clinical_activity: chr  "" "" "" "" ...
#>  $ positive_surveys_tests    : chr  "" "" "" "" ...
#>  $ cumulative_cases          : num  0 0 0 0 18 0 3 0 172 0 ...
#>  $ total_tests               : num  5 0 1 10 148 ...
#>  $ total_people_tested       : chr  "" "" "" "" ...
#>  $ new_intensive_care        : chr  "" "" "" "" ...
#>  $ total_positive_tests      : chr  "" "" "" "" ...
#>  $ total_fast_tests          : chr  "" "" "" "" ...
#>  $ daily_positive_tests      : chr  "" "" "" "" ...
#>  $ daily_fast_tests          : chr  "" "" "" "" ...
#>  $ nuts_code_1               : chr  "" "" "" "" ...
#>  $ nuts_code_2               : chr  "" "" "" "" ...
#>  $ region_spatial            : chr  "Abruzzo" "Basilicata" "Calabria" "Campania" ...

head(italy_region)
#>         date region_code           region_name      lat     long
#> 1 2020-02-24          13               Abruzzo 42.35122 13.39844
#> 2 2020-02-24          17            Basilicata 40.63947 15.80515
#> 3 2020-02-24          18              Calabria 38.90598 16.59440
#> 4 2020-02-24          15              Campania 40.83957 14.25085
#> 5 2020-02-24          08        Emilia-Romagna 44.49437 11.34172
#> 6 2020-02-24          06 Friuli Venezia Giulia 45.64944 13.76814
#>   hospitalized_with_symptoms intensive_care total_hospitalized home_confinement
#> 1                          0              0                  0                0
#> 2                          0              0                  0                0
#> 3                          0              0                  0                0
#> 4                          0              0                  0                0
#> 5                         10              2                 12                6
#> 6                          0              0                  0                0
#>   cumulative_positive_cases daily_positive_cases recovered death
#> 1                         0                    0         0     0
#> 2                         0                    0         0     0
#> 3                         0                    0         0     0
#> 4                         0                    0         0     0
#> 5                        18                    0         0     0
#> 6                         0                    0         0     0
#>   positive_clinical_activity positive_surveys_tests cumulative_cases
#> 1                                                                  0
#> 2                                                                  0
#> 3                                                                  0
#> 4                                                                  0
#> 5                                                                 18
#> 6                                                                  0
#>   total_tests total_people_tested new_intensive_care total_positive_tests
#> 1           5                                                            
#> 2           0                                                            
#> 3           1                                                            
#> 4          10                                                            
#> 5         148                                                            
#> 6          58                                                            
#>   total_fast_tests daily_positive_tests daily_fast_tests nuts_code_1
#> 1                                                                   
#> 2                                                                   
#> 3                                                                   
#> 4                                                                   
#> 5                                                                   
#> 6                                                                   
#>   nuts_code_2        region_spatial
#> 1                           Abruzzo
#> 2                        Basilicata
#> 3                          Calabria
#> 4                          Campania
#> 5                    Emilia-Romagna
#> 6             Friuli-Venezia Giulia

Italy province level

The italy_region dataset provides an overall summary of the cases in Italy’s regions. The dataset contains the following fields:

data(italy_province)

str(italy_province)
#> Classes 'tbl_df', 'tbl' and 'data.frame':    74918 obs. of  14 variables:
#>  $ date            : Date, format: "2020-02-24" "2020-02-24" ...
#>  $ region_name     : chr  "Abruzzo" "Abruzzo" "Abruzzo" "Abruzzo" ...
#>  $ region_code     : chr  "13" "13" "13" "13" ...
#>  $ province_name   : chr  "L'Aquila" "Teramo" "Pescara" "Chieti" ...
#>  $ province_spatial: chr  "L'Aquila" "Teramo" "Pescara" "Chieti" ...
#>  $ province_abb    : chr  "AQ" "TE" "PE" "CH" ...
#>  $ province_code   : chr  "066" "067" "068" "069" ...
#>  $ lat             : num  42.4 42.7 42.5 42.4 NA ...
#>  $ long            : num  13.4 13.7 14.2 14.2 NA ...
#>  $ new_cases       : num  0 0 0 0 0 0 0 0 0 0 ...
#>  $ total_cases     : num  0 0 0 0 0 0 0 0 0 0 ...
#>  $ nuts_code_1     : chr  "" "" "" "" ...
#>  $ nuts_code_2     : chr  "" "" "" "" ...
#>  $ nuts_code_3     : chr  "" "" "" "" ...

head(italy_province)
#>         date region_name region_code                        province_name
#> 1 2020-02-24     Abruzzo          13                             L'Aquila
#> 2 2020-02-24     Abruzzo          13                               Teramo
#> 3 2020-02-24     Abruzzo          13                              Pescara
#> 4 2020-02-24     Abruzzo          13                               Chieti
#> 5 2020-02-24     Abruzzo          13 In fase di definizione/aggiornamento
#> 6 2020-02-24  Basilicata          17                              Potenza
#>                       province_spatial province_abb province_code      lat
#> 1                             L'Aquila           AQ           066 42.35122
#> 2                               Teramo           TE           067 42.65892
#> 3                              Pescara           PE           068 42.46458
#> 4                               Chieti           CH           069 42.35103
#> 5 In fase di definizione/aggiornamento                        979       NA
#> 6                              Potenza           PZ           076 40.63947
#>       long new_cases total_cases nuts_code_1 nuts_code_2 nuts_code_3
#> 1 13.39844         0           0                                    
#> 2 13.70440         0           0                                    
#> 3 14.21365         0           0                                    
#> 4 14.16755         0           0                                    
#> 5       NA         0           0                                    
#> 6 15.80515         0           0