Daily case counts of COVID-19 from Colombia's national epidemiological
surveillance system (INS), aggregated by notification date, diagnosis date,
and sex. Each row is a unique combination of these three variables together
with the number of cases n.
Format
A data frame with 35,501 rows and 4 variables:
- notification_date
Date. The event date – when the case was notified / symptom onset was recorded.- diagnosis_date
Date. The report date – when the laboratory diagnosis was registered in the national system.- sex
character. Biological sex of the case:"Female"or"Male".- n
integer. Number of cases with this (notification_date, diagnosis_date, sex) combination.
Source
Instituto Nacional de Salud (INS), Colombia. Data accessed via the SIVIGILA open-data platform and pre-processed for the diseasenowcasting benchmarking study.
Details
In the nowcasting context the event date is notification_date (when the
case symptom onset was recorded in the system) and the report date is
diagnosis_date (when the laboratory result was entered). The delay between
the two reflects the time from symptom onset to laboratory confirmation and
data entry – the quantity the nowcasting model estimates and corrects for.
The dataset covers the full first three years of the Colombian epidemic (2020-03-02 to 2023-03-03) and was used in the NobBS comparison study to benchmark the diseasenowcasting / diseasenowcast2 engine.
Examples
# Build a stratified tbl_now (event = notification, report = diagnosis,
# strata = sex). Pipe through temporal effects for day-of-week covariates.
if (requireNamespace("tbl.now", quietly = TRUE)) {
tn <- tbl.now::tbl_now(
covid_colombia,
event_date = notification_date,
report_date = diagnosis_date,
strata = sex,
case_count = n,
data_type = "count-incidence",
verbose = FALSE
)
print(tn)
}
#> # A tibble: 35,501 × 7
#> # Data type: "count-incidence"
#> # Frequency: Event: `days` | Report: `days`
#> notification_date diagnosis_date sex n .event_num .report_num .delay
#> <date> <date> <chr> <int> <dbl> <dbl> <dbl>
#> [event_date] [report_date] [strata] [cas… [...] [...] [...]
#> 1 2020-03-02 2020-03-06 Female 1 0 4 4
#> 2 2020-03-03 2020-03-14 Female 1 1 12 11
#> 3 2020-03-06 2020-03-09 Male 1 4 7 3
#> 4 2020-03-07 2020-03-09 Female 1 5 7 2
#> 5 2020-03-08 2020-03-11 Female 2 6 9 3
#> 6 2020-03-09 2020-03-11 Female 1 7 9 2
#> 7 2020-03-09 2020-03-11 Male 2 7 9 2
#> 8 2020-03-10 2020-03-11 Female 1 8 9 1
#> 9 2020-03-10 2020-03-12 Female 2 8 10 2
#> 10 2020-03-10 2020-03-13 Male 1 8 11 3
#> # ────────────────────────────────────────────────────────────────────────────────
#> # Now: 2023-05-26 | Event date: "notification_date" | Report date:
#> # "diagnosis_date"
#> # Strata: "sex"
#> # ────────────────────────────────────────────────────────────────────────────────
#> # ℹ 35,491 more rows