Get ERVISS SARI tests/detections/positivity data

Retrieves and filters SARI (Severe Acute Respiratory Infection) virological data (tests, detections, positivity) from the ERVISS (European Respiratory Virus Surveillance Summary) for a specified date range, pathogen(s), indicator(s), age group(s), and country(ies).

Usage

get_sari_positivity(
  csv_file = NULL,
  date_min,
  date_max,
  pathogen = "",
  indicator = "",
  age = "",
  countries = "",
  use_snapshot = FALSE,
  snapshot_date = NULL
)

Arguments

csv_file

Path to a local CSV file or URL containing the ERVISS data. If NULL (default), data is fetched from the official ERVISS repository.

date_min

Start date of the period (Date object)

date_max

End date of the period (Date object)

pathogen

Character vector of pathogen names to filter. Use "" (default) to include all pathogens.

indicator

Character vector of indicators to filter: "positivity", "detections", "tests", or any combination. Use "" (default) to include all indicators.

age

Character vector of age groups to filter (e.g., "total", "0-4", "5-14", "15-64", "65+"). Use "" (default) to include all age groups.

countries

Character vector of country names to filter. Use "" (default) to include all countries.

use_snapshot

Logical. If TRUE, fetches a historical snapshot; if FALSE (default), fetches the latest data. Ignored if csv_file is provided.

snapshot_date

Date of the snapshot to retrieve. Required if use_snapshot = TRUE and csv_file is NULL.

Value

A data.table containing the filtered SARI data with columns: survtype, countryname, date, pathogen, pathogentype, pathogensubtype, indicator, age, value.

Examples

# \donttest{
# Get SARI positivity data for Influenza in France
data <- get_sari_positivity(
  date_min = as.Date("2024-01-01"),
  date_max = as.Date("2024-12-31"),
  pathogen = "Influenza",
  indicator = "positivity",
  countries = "France"
)
#> ℹ No data found for the given filters. Try adjusting date range, countries, pathogen, or indicator.

# Get all SARI indicators for SARS-CoV-2
data <- get_sari_positivity(
  date_min = as.Date("2024-01-01"),
  date_max = as.Date("2024-12-31"),
  pathogen = "SARS-CoV-2"
)
# }