Subset of JHU daily COVID-19 cases from counties in Massachusetts and Vermont
Source:R/reexports.R
covid_incidence_county_subset.RdThis data source of confirmed COVID-19 cases and deaths is based on reports made available by the Center for Systems Science and Engineering at Johns Hopkins University. This example data is a snapshot as of March 20, 2024, and ranges from March 1, 2020 to December 31, 2021. It is limited to counties from Massachusetts and Vermont.
It is used in the epiprocess aggregation vignette.
Format
An object of class epi_df (inherits from tbl_df, tbl, data.frame) with 16212 rows and 5 columns.
Source
This object contains a modified part of the COVID-19 Data Repository by the Center for Systems Science and Engineering (CSSE) at Johns Hopkins University as republished in the COVIDcast Epidata API. This data set is licensed under the terms of the Creative Commons Attribution 4.0 International license by the Johns Hopkins University on behalf of its Center for Systems Science in Engineering. Copyright Johns Hopkins University 2020.
Modifications:
From the COVIDcast Epidata API: These signals are taken directly from the JHU CSSE COVID-19 GitHub repository without changes. The 7-day average signals are computed by Delphi by as moving averages of the preceding 7 days, so the signal for June 7 is the average of the underlying data for June 1 through 7, inclusive.
Furthermore, the data has been limited to a very small number of rows, formatted into an
epi_df, and the signal names slightly altered.
Data dictionary
The data has columns:
- geo_value
the geographic value associated with each row of measurements.
- time_value
the time value associated with each row of measurements.
- cases
Number of new confirmed COVID-19 cases, daily
- county_name
the name of the county
- state_name
the full name of the state
Examples
# Since this is a re-exported dataset, it cannot be loaded using
# the `data()` function. `data()` looks for a file of the same name
# in the `data/` directory, which doesn't exist in this package.
# works
epiprocess::covid_incidence_county_subset
#> An `epi_df` object, 16,212 x 5 with metadata:
#> * geo_type = county
#> * time_type = day
#> * as_of = 2024-03-20
#>
#> # A tibble: 16,212 × 5
#> geo_value time_value cases county_name state_name
#> * <chr> <date> <dbl> <chr> <chr>
#> 1 25001 2020-06-01 4 Barnstable County Massachusetts
#> 2 25003 2020-06-01 0 Berkshire County Massachusetts
#> 3 25005 2020-06-01 78 Bristol County Massachusetts
#> 4 25007 2020-06-01 0 Dukes County Massachusetts
#> 5 25009 2020-06-01 92 Essex County Massachusetts
#> 6 25011 2020-06-01 0 Franklin County Massachusetts
#> 7 25013 2020-06-01 35 Hampden County Massachusetts
#> 8 25015 2020-06-01 4 Hampshire County Massachusetts
#> 9 25017 2020-06-01 98 Middlesex County Massachusetts
#> 10 25019 2020-06-01 0 Nantucket County Massachusetts
#> # ℹ 16,202 more rows
# works
library(epiprocess)
covid_incidence_county_subset
#> An `epi_df` object, 16,212 x 5 with metadata:
#> * geo_type = county
#> * time_type = day
#> * as_of = 2024-03-20
#>
#> # A tibble: 16,212 × 5
#> geo_value time_value cases county_name state_name
#> * <chr> <date> <dbl> <chr> <chr>
#> 1 25001 2020-06-01 4 Barnstable County Massachusetts
#> 2 25003 2020-06-01 0 Berkshire County Massachusetts
#> 3 25005 2020-06-01 78 Bristol County Massachusetts
#> 4 25007 2020-06-01 0 Dukes County Massachusetts
#> 5 25009 2020-06-01 92 Essex County Massachusetts
#> 6 25011 2020-06-01 0 Franklin County Massachusetts
#> 7 25013 2020-06-01 35 Hampden County Massachusetts
#> 8 25015 2020-06-01 4 Hampshire County Massachusetts
#> 9 25017 2020-06-01 98 Middlesex County Massachusetts
#> 10 25019 2020-06-01 0 Nantucket County Massachusetts
#> # ℹ 16,202 more rows
# fails
if (FALSE) { # \dontrun{
data(covid_incidence_county_subset, package = "epiprocess")
} # }