Get ERVISS non-sentinel tests/detections data

Retrieves and filters non-sentinel virological testing data (tests and detections) 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_nonsentinel_tests(
  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: "detections", "tests", or both. Use "" (default) to include all indicators.

age

Character vector of age groups to filter (e.g., "total"). 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 non-sentinel tests data with columns: survtype, countryname, date, pathogen, pathogentype, pathogensubtype, indicator, age, value.

Examples

# \donttest{
# Get non-sentinel detections for Influenza in France
data <- get_nonsentinel_tests(
  date_min = as.Date("2024-01-01"),
  date_max = as.Date("2024-12-31"),
  pathogen = "Influenza",
  indicator = "detections",
  countries = "France"
)

# Get all non-sentinel test data
data <- get_nonsentinel_tests(
  date_min = as.Date("2024-01-01"),
  date_max = as.Date("2024-12-31")
)
# }