covid_us: CDC COVID-19 Case Surveillance Public Use Data (2020-2021)

A compact aggregation of the U.S. CDC's individual-level COVID-19 case surveillance database, prepared to illustrate batch reporting. Each row is a unique (event date, report date) pair with the number of cases n.

Usage

data(covid_us)

Format

A data frame with three variables:

cdc_case_earliest_dt: Date. The event date – the earlier of the clinical date and the date received by CDC.
cdc_report_dt: Date. The report date – when the case was first reported to CDC.
n: integer. Number of cases with this (event date, report date) pair.

Source

Centers for Disease Control and Prevention (CDC), COVID-19 Response. COVID-19 Case Surveillance Public Use Data (version date: June 21, 2024). https://data.cdc.gov/Case-Surveillance/COVID-19-Case-Surveillance-Public-Use-Data/vbim-akqf/about_data. COVID-19 case surveillance data are collected by jurisdictions and reported voluntarily to CDC.

Details

In the nowcasting context the event date is cdc_case_earliest_dt (the earlier of the clinical/specimen date and the date the case was received by CDC) and the report date is cdc_report_dt (the date the case was first reported to CDC). The delay between them is enormous and heavily right-skewed: cases were reported to CDC not smoothly but in large backlog dumps – a textbook batch-reporting pattern that batch_test() and transport_discriminant() recover.

Cases are kept when both their event date and their report date fall between 2020-01-01 and 2021-12-31 – a self-consistent "as of the end of 2021" snapshot, so the epidemic and its reporting are seen over the same two years. The handful of rows whose report date precedes their event date (data-entry errors) were dropped. See data-raw/covid_us.R for the exact duckdb aggregation of the 14 GB source file.

Examples

data(covid_us)
tn <- tbl_now(
  covid_us,
  event_date  = cdc_case_earliest_dt,
  report_date = cdc_report_dt,
  case_count  = n,
  data_type   = "count-incidence",
  verbose     = FALSE
)
tn
#> # A tibble:  173,190 × 6
#> # Data type: "count-incidence"
#> # Frequency: Event: `days` | Report: `days`
#>    cdc_case_earliest_dt cdc_report_dt       n .event_num .report_num .delay
#>    <date>               <date>          <int>      <dbl>       <dbl>  <dbl>
#>    [event_date]         [report_date] [cases]      [...]       [...]  [...]
#>  1 2020-01-01           2020-01-01         29          0           0      0
#>  2 2020-01-01           2020-04-03          1          0          93     93
#>  3 2020-01-01           2020-04-07          1          0          97     97
#>  4 2020-01-01           2020-04-14          4          0         104    104
#>  5 2020-01-01           2020-04-15          2          0         105    105
#>  6 2020-01-01           2020-04-17          4          0         107    107
#>  7 2020-01-01           2020-04-18          4          0         108    108
#>  8 2020-01-01           2020-04-19          1          0         109    109
#>  9 2020-01-01           2020-04-21          2          0         111    111
#> 10 2020-01-01           2020-04-22          1          0         112    112
#> # ────────────────────────────────────────────────────────────────────────────────
#> # Now: 2021-12-31 | Event date: "cdc_case_earliest_dt" | Report date:
#> # "cdc_report_dt"
#> # ────────────────────────────────────────────────────────────────────────────────
#> # ℹ 173,180 more rows