Retrieves and filters sentinel surveillance data (positivity, detections, tests) from the ERVISS (European Respiratory Virus Surveillance Summary) for a specified date range, pathogen(s), indicator(s), and country(ies).
Usage
get_sentineltests_positivity(
csv_file = NULL,
date_min,
date_max,
pathogen = "",
indicator = "",
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.
- 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 data with columns: date, value, pathogen, countryname, indicator, and other ERVISS fields.
Examples
# \donttest{
# Get latest SARS-CoV-2 positivity data for France
data <- get_sentineltests_positivity(
date_min = as.Date("2024-01-01"),
date_max = as.Date("2024-12-31"),
pathogen = "SARS-CoV-2",
countries = "France"
)
# Get detections and tests
data <- get_sentineltests_positivity(
date_min = as.Date("2024-01-01"),
date_max = as.Date("2024-12-31"),
pathogen = "Influenza",
indicator = c("detections", "tests")
)
# Get historical data from a specific snapshot
data <- get_sentineltests_positivity(
date_min = as.Date("2023-01-01"),
date_max = as.Date("2023-12-31"),
use_snapshot = TRUE,
snapshot_date = as.Date("2024-02-23")
)
# }